Query psy8320
Match_columns 119
No_of_seqs 90 out of 106
Neff 3.4
Searched_HMMs 46136
Date Sat Aug 17 00:42:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8320.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8320hhsearch_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-56 5.3E-61 319.8 2.7 100 20-119 1-100 (100)
2 PF10235 Cript: Microtubule-as 100.0 5.7E-48 1.2E-52 273.6 4.0 88 30-119 1-90 (90)
3 PF10217 DUF2039: Uncharacteri 94.9 0.0032 7E-08 45.3 -1.8 41 66-107 49-90 (92)
4 COG5152 Uncharacterized conser 91.3 0.052 1.1E-06 44.9 -0.3 34 75-108 198-240 (259)
5 PF12773 DZR: Double zinc ribb 90.3 0.19 4E-06 30.6 1.6 33 76-109 1-40 (50)
6 KOG3241|consensus 90.1 0.025 5.4E-07 46.1 -3.1 46 65-111 60-106 (227)
7 PRK14559 putative protein seri 81.0 0.9 1.9E-05 41.8 1.7 35 74-109 2-38 (645)
8 PF13248 zf-ribbon_3: zinc-rib 78.0 1.1 2.3E-05 24.8 0.7 22 74-96 3-24 (26)
9 PF13240 zinc_ribbon_2: zinc-r 74.7 1.3 2.8E-05 24.2 0.5 20 75-95 1-20 (23)
10 PF14634 zf-RING_5: zinc-RING 72.9 0.9 2E-05 27.2 -0.4 20 87-106 21-44 (44)
11 TIGR00570 cdk7 CDK-activating 70.9 1.7 3.7E-05 37.1 0.6 36 75-110 5-55 (309)
12 KOG1813|consensus 60.8 4.1 8.8E-05 35.1 1.0 36 75-110 243-287 (313)
13 PF13920 zf-C3HC4_3: Zinc fing 60.6 1.7 3.8E-05 26.3 -0.9 25 87-111 21-50 (50)
14 PRK12496 hypothetical protein; 55.5 5.3 0.00012 30.5 0.7 22 88-109 127-154 (164)
15 smart00504 Ubox Modified RING 55.3 4.7 0.0001 24.6 0.4 23 87-109 20-46 (63)
16 PF10764 Gin: Inhibitor of sig 52.1 7.7 0.00017 24.4 1.0 25 13-37 12-36 (46)
17 PF07191 zinc-ribbons_6: zinc- 51.9 3.7 8E-05 28.4 -0.6 36 75-110 3-42 (70)
18 KOG2272|consensus 47.6 11 0.00024 32.5 1.5 52 55-109 148-206 (332)
19 TIGR00599 rad18 DNA repair pro 47.3 8 0.00017 33.9 0.7 36 74-109 27-71 (397)
20 PF10571 UPF0547: Uncharacteri 45.8 9.8 0.00021 21.4 0.6 22 75-97 2-23 (26)
21 PF06906 DUF1272: Protein of u 45.2 8.6 0.00019 25.8 0.4 36 74-109 6-52 (57)
22 PF03660 PHF5: PHF5-like prote 41.9 6.4 0.00014 29.3 -0.7 27 69-95 51-77 (106)
23 cd00162 RING RING-finger (Real 41.4 11 0.00024 20.5 0.4 21 87-107 19-44 (45)
24 PRK11595 DNA utilization prote 40.9 14 0.00031 28.8 1.1 33 75-107 7-43 (227)
25 smart00132 LIM Zinc-binding do 39.8 22 0.00048 19.1 1.5 9 100-108 29-37 (39)
26 PF14471 DUF4428: Domain of un 39.7 14 0.00031 23.4 0.8 16 100-115 1-16 (51)
27 cd04476 RPA1_DBD_C RPA1_DBD_C: 39.0 12 0.00025 27.6 0.3 22 73-94 34-57 (166)
28 KOG3799|consensus 38.2 15 0.00031 29.1 0.8 36 73-110 65-101 (169)
29 PF01258 zf-dskA_traR: Prokary 36.3 15 0.00033 21.2 0.4 12 99-110 4-15 (36)
30 PF13923 zf-C3HC4_2: Zinc fing 35.8 5.4 0.00012 23.0 -1.5 10 87-96 18-27 (39)
31 PF14446 Prok-RING_1: Prokaryo 35.2 18 0.00038 23.9 0.7 14 96-109 3-16 (54)
32 PF13894 zf-C2H2_4: C2H2-type 34.6 9.8 0.00021 18.6 -0.5 15 100-114 2-16 (24)
33 PLN03208 E3 ubiquitin-protein 34.0 14 0.00031 29.7 0.1 36 75-110 20-80 (193)
34 PF05715 zf-piccolo: Piccolo Z 33.8 16 0.00034 24.9 0.3 10 98-107 30-39 (61)
35 TIGR00375 conserved hypothetic 33.2 19 0.00041 31.3 0.8 38 65-109 230-269 (374)
36 KOG0320|consensus 32.9 11 0.00024 30.4 -0.6 36 74-109 132-178 (187)
37 PRK00420 hypothetical protein; 26.7 30 0.00064 25.6 0.7 22 73-94 23-46 (112)
38 TIGR02420 dksA RNA polymerase- 26.4 27 0.00059 24.7 0.5 11 99-109 81-91 (110)
39 PHA02929 N1R/p28-like protein; 26.3 28 0.0006 28.6 0.6 40 73-112 174-230 (238)
40 COG0266 Nei Formamidopyrimidin 24.7 30 0.00064 29.1 0.5 33 63-95 235-272 (273)
41 smart00746 TRASH metallochaper 24.6 36 0.00077 16.9 0.6 9 101-109 1-9 (39)
42 KOG4458|consensus 24.5 28 0.0006 24.5 0.2 33 63-102 4-36 (78)
43 PF06827 zf-FPG_IleRS: Zinc fi 24.3 20 0.00042 19.9 -0.5 21 75-95 3-28 (30)
44 PRK14810 formamidopyrimidine-D 24.2 33 0.00073 27.8 0.7 30 65-94 236-270 (272)
45 PRK01103 formamidopyrimidine/5 24.2 31 0.00067 27.9 0.5 30 66-95 238-272 (274)
46 PF10367 Vps39_2: Vacuolar sor 24.1 18 0.0004 23.9 -0.7 23 14-36 73-98 (109)
47 PF10621 FpoO: F420H2 dehydrog 24.1 34 0.00073 26.0 0.6 35 68-108 29-70 (119)
48 PHA03096 p28-like protein; Pro 23.4 22 0.00047 29.8 -0.6 25 92-116 135-160 (284)
49 PF11571 Med27: Mediator compl 22.8 45 0.00098 22.9 1.0 23 18-40 53-76 (90)
50 PF09706 Cas_CXXC_CXXC: CRISPR 22.3 46 0.00099 22.1 0.9 11 97-107 4-14 (69)
51 TIGR03826 YvyF flagellar opero 21.9 38 0.00082 25.7 0.5 24 71-96 79-102 (137)
52 PRK05580 primosome assembly pr 21.8 51 0.0011 30.2 1.4 22 88-109 408-432 (679)
53 COG1996 RPC10 DNA-directed RNA 21.7 37 0.00081 21.9 0.4 28 75-109 8-35 (49)
54 KOG1734|consensus 21.5 31 0.00067 30.0 -0.0 16 97-112 223-238 (328)
55 COG1645 Uncharacterized Zn-fin 21.4 38 0.00081 25.9 0.4 24 74-97 29-53 (131)
56 PRK14811 formamidopyrimidine-D 21.1 40 0.00086 27.4 0.6 33 65-97 227-264 (269)
57 PHA02565 49 recombination endo 21.1 44 0.00096 26.3 0.8 14 96-109 18-31 (157)
No 1
>KOG3476|consensus
Probab=100.00 E-value=2.5e-56 Score=319.83 Aligned_cols=100 Identities=68% Similarity=1.234 Sum_probs=97.8
Q ss_pred cchhHHHhhhccccCCCCCCCCCCccccCCCeecccccchhhhhhccCCCcccCccchhhhhhcccCCCccCcccccccc
Q psy8320 20 MVCSKCEKKLGKVITPDNWKSGSRNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKG 99 (119)
Q Consensus 20 MVC~KCEKKL~klatPD~~k~Gs~~~~~~g~rki~eNKlLs~~k~r~~Py~~~~~~C~iCK~~vhq~g~~YCq~CAYkkG 99 (119)
|||+||||||++|++|||||+|+||++++|+|+|+|||.|.+.++||+||+..+.+|+|||+.|||+|+||||.|||+||
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 99999999999999999999999999999999999999888878999999999999999999999999999999999999
Q ss_pred cccccCcccccccccccccC
Q psy8320 100 ICAMCGKKLLDVKNYKQSAA 119 (119)
Q Consensus 100 iCamCGKki~Dt~~ykqS~~ 119 (119)
|||||||+|+||++|+||++
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=5.7e-48 Score=273.56 Aligned_cols=88 Identities=66% Similarity=1.194 Sum_probs=83.9
Q ss_pred ccccCCCCCCCCC--CccccCCCeecccccchhhhhhccCCCcccCccchhhhhhcccCCCccCcccccccccccccCcc
Q psy8320 30 GKVITPDNWKSGS--RNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKGICAMCGKK 107 (119)
Q Consensus 30 ~klatPD~~k~Gs--~~~~~~g~rki~eNKlLs~~k~r~~Py~~~~~~C~iCK~~vhq~g~~YCq~CAYkkGiCamCGKk 107 (119)
++||||||||+|+ +++.++|+|+||||||||+. ++ |||++++++|++||++|||+|+||||.|||++||||||||+
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 99999999999999999873 44 99999999999999999999999999999999999999999
Q ss_pred cccccccccccC
Q psy8320 108 LLDVKNYKQSAA 119 (119)
Q Consensus 108 i~Dt~~ykqS~~ 119 (119)
|+||++|+||+|
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=94.91 E-value=0.0032 Score=45.29 Aligned_cols=41 Identities=37% Similarity=0.808 Sum_probs=33.4
Q ss_pred cCCCcccCccchhhhh-hcccCCCccCcccccccccccccCcc
Q psy8320 66 FNPYTQKFESCKICRQ-KVHQVGSHYCQACAYKKGICAMCGKK 107 (119)
Q Consensus 66 ~~Py~~~~~~C~iCK~-~vhq~g~~YCq~CAYkkGiCamCGKk 107 (119)
|-|..+ .++|-.|.+ .|.+.=|..|+.||-..++||.||++
T Consensus 49 YKpLt~-p~kC~~C~qktVk~AYh~iC~~Ca~~~~vCaKC~k~ 90 (92)
T PF10217_consen 49 YKPLTQ-PKKCNKCQQKTVKHAYHVICDPCAKELKVCAKCGKP 90 (92)
T ss_pred cccCCC-CccccccccchHHHHHHHHHHHHHHhhccCcccCCC
Confidence 334433 469999996 67777788999999999999999986
No 4
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=91.27 E-value=0.052 Score=44.94 Aligned_cols=34 Identities=41% Similarity=1.117 Sum_probs=27.9
Q ss_pred cchhhhhhc-----ccCCCccCcccc---cccc-cccccCccc
Q psy8320 75 SCKICRQKV-----HQVGSHYCQACA---YKKG-ICAMCGKKL 108 (119)
Q Consensus 75 ~C~iCK~~v-----hq~g~~YCq~CA---YkkG-iCamCGKki 108 (119)
.|.|||... ..-||++|..|| |++| .|-.||+..
T Consensus 198 ~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t 240 (259)
T COG5152 198 LCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKAT 240 (259)
T ss_pred eehhchhhccchhhhhcchhHHHHHHHHHhccCCcceecchhh
Confidence 899999753 344999999999 6776 799999864
No 5
>PF12773 DZR: Double zinc ribbon
Probab=90.29 E-value=0.19 Score=30.56 Aligned_cols=33 Identities=24% Similarity=0.673 Sum_probs=19.4
Q ss_pred chhhhhhcccCCCccCcccccccc-------cccccCcccc
Q psy8320 76 CKICRQKVHQVGSHYCQACAYKKG-------ICAMCGKKLL 109 (119)
Q Consensus 76 C~iCK~~vhq~g~~YCq~CAYkkG-------iCamCGKki~ 109 (119)
|..|.+.+.. ++.||..|-..-. +|.-||..+.
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 4455555555 4666666655444 5777776654
No 6
>KOG3241|consensus
Probab=90.09 E-value=0.025 Score=46.06 Aligned_cols=46 Identities=28% Similarity=0.755 Sum_probs=37.2
Q ss_pred ccCCCcccCccchhhhh-hcccCCCccCcccccccccccccCcccccc
Q psy8320 65 RFNPYTQKFESCKICRQ-KVHQVGSHYCQACAYKKGICAMCGKKLLDV 111 (119)
Q Consensus 65 r~~Py~~~~~~C~iCK~-~vhq~g~~YCq~CAYkkGiCamCGKki~Dt 111 (119)
+|-|.+. ..+|..|+. .|.|.-|..|..||-...+||-|+|.+.++
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 3455544 459999987 788888899999999999999999976543
No 7
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=81.03 E-value=0.9 Score=41.77 Aligned_cols=35 Identities=23% Similarity=0.651 Sum_probs=28.1
Q ss_pred ccchhhhhhcccCCCccCccccccc--ccccccCcccc
Q psy8320 74 ESCKICRQKVHQVGSHYCQACAYKK--GICAMCGKKLL 109 (119)
Q Consensus 74 ~~C~iCK~~vhq~g~~YCq~CAYkk--GiCamCGKki~ 109 (119)
..|..|...+.. +++||+.|-.+- ..|+-||..+.
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 378899988876 889999998774 36888888765
No 8
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=78.05 E-value=1.1 Score=24.77 Aligned_cols=22 Identities=18% Similarity=0.694 Sum_probs=16.4
Q ss_pred ccchhhhhhcccCCCccCccccc
Q psy8320 74 ESCKICRQKVHQVGSHYCQACAY 96 (119)
Q Consensus 74 ~~C~iCK~~vhq~g~~YCq~CAY 96 (119)
..|..|...+.. +++||+.|-.
T Consensus 3 ~~Cp~Cg~~~~~-~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDP-DAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCc-ccccChhhCC
Confidence 478899996655 7898887643
No 9
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=74.72 E-value=1.3 Score=24.19 Aligned_cols=20 Identities=20% Similarity=0.866 Sum_probs=14.7
Q ss_pred cchhhhhhcccCCCccCcccc
Q psy8320 75 SCKICRQKVHQVGSHYCQACA 95 (119)
Q Consensus 75 ~C~iCK~~vhq~g~~YCq~CA 95 (119)
.|..|..++.. ++++|+.|-
T Consensus 1 ~Cp~CG~~~~~-~~~fC~~CG 20 (23)
T PF13240_consen 1 YCPNCGAEIED-DAKFCPNCG 20 (23)
T ss_pred CCcccCCCCCC-cCcchhhhC
Confidence 37788888876 778776654
No 10
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=72.88 E-value=0.9 Score=27.16 Aligned_cols=20 Identities=35% Similarity=0.936 Sum_probs=16.7
Q ss_pred CCccCcccccccc----cccccCc
Q psy8320 87 GSHYCQACAYKKG----ICAMCGK 106 (119)
Q Consensus 87 g~~YCq~CAYkkG----iCamCGK 106 (119)
||.+|+.|+.+.- .|..|++
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 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=70.90 E-value=1.7 Score=37.06 Aligned_cols=36 Identities=28% Similarity=0.755 Sum_probs=25.6
Q ss_pred cchhhhhh----------cccCCCccCcccccc-----cccccccCccccc
Q psy8320 75 SCKICRQK----------VHQVGSHYCQACAYK-----KGICAMCGKKLLD 110 (119)
Q Consensus 75 ~C~iCK~~----------vhq~g~~YCq~CAYk-----kGiCamCGKki~D 110 (119)
.|.+|++. |+.=||.+|.+|.-. .+.|+.|++.+..
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 233489999999743 3489999987753
No 12
>KOG1813|consensus
Probab=60.77 E-value=4.1 Score=35.14 Aligned_cols=36 Identities=33% Similarity=0.907 Sum_probs=29.2
Q ss_pred cchhhhhhc-----ccCCCccCcccc---ccc-ccccccCccccc
Q psy8320 75 SCKICRQKV-----HQVGSHYCQACA---YKK-GICAMCGKKLLD 110 (119)
Q Consensus 75 ~C~iCK~~v-----hq~g~~YCq~CA---Ykk-GiCamCGKki~D 110 (119)
+|-||+..- ..-||++|-.|| |++ -.|-.|++++.-
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 777 589999998763
No 13
>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=60.55 E-value=1.7 Score=26.28 Aligned_cols=25 Identities=28% Similarity=0.813 Sum_probs=19.1
Q ss_pred CCc-cCccccccc----ccccccCcccccc
Q psy8320 87 GSH-YCQACAYKK----GICAMCGKKLLDV 111 (119)
Q Consensus 87 g~~-YCq~CAYkk----GiCamCGKki~Dt 111 (119)
||. +|..|+.+- ..|.+|-..|.++
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 8999999988753
No 14
>PRK12496 hypothetical protein; Provisional
Probab=55.46 E-value=5.3 Score=30.49 Aligned_cols=22 Identities=27% Similarity=1.001 Sum_probs=16.7
Q ss_pred CccCcccc--c----ccccccccCcccc
Q psy8320 88 SHYCQACA--Y----KKGICAMCGKKLL 109 (119)
Q Consensus 88 ~~YCq~CA--Y----kkGiCamCGKki~ 109 (119)
.++|++|- | ..+.|..||-++.
T Consensus 127 ~~~C~gC~~~~~~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 127 RKVCKGCKKKYPEDYPDDVCEICGSPVK 154 (164)
T ss_pred eEECCCCCccccCCCCCCcCCCCCChhh
Confidence 35688887 5 4567999998875
No 15
>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=55.25 E-value=4.7 Score=24.64 Aligned_cols=23 Identities=22% Similarity=0.353 Sum_probs=17.8
Q ss_pred CCccCccccc----ccccccccCcccc
Q psy8320 87 GSHYCQACAY----KKGICAMCGKKLL 109 (119)
Q Consensus 87 g~~YCq~CAY----kkGiCamCGKki~ 109 (119)
|+.||..|.. ..+.|.+||+.+.
T Consensus 20 G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 20 GQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred CCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 7788887764 3578999998873
No 16
>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=52.08 E-value=7.7 Score=24.42 Aligned_cols=25 Identities=36% Similarity=0.591 Sum_probs=20.4
Q ss_pred hhhhhhccchhHHHhhhccccCCCC
Q psy8320 13 AEEIYFIMVCSKCEKKLGKVITPDN 37 (119)
Q Consensus 13 ~~~~~~~MVC~KCEKKL~klatPD~ 37 (119)
-+.|.....|..||++|-.+-+-||
T Consensus 12 GI~I~~~fIC~~CE~~iv~~~~~d~ 36 (46)
T PF10764_consen 12 GIHIYGKFICSDCEKEIVNTETDDP 36 (46)
T ss_pred CEEEECeEehHHHHHHhccCCCCCC
Confidence 3456678899999999998877776
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=51.94 E-value=3.7 Score=28.35 Aligned_cols=36 Identities=33% Similarity=0.778 Sum_probs=21.7
Q ss_pred cchhhhhhcccCC-CccCcccc---cccccccccCccccc
Q psy8320 75 SCKICRQKVHQVG-SHYCQACA---YKKGICAMCGKKLLD 110 (119)
Q Consensus 75 ~C~iCK~~vhq~g-~~YCq~CA---YkkGiCamCGKki~D 110 (119)
.|..|.+.+...+ ..+|..|. -+.+.|+-||..+--
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 6888888886555 66788876 356789999887753
No 18
>KOG2272|consensus
Probab=47.58 E-value=11 Score=32.50 Aligned_cols=52 Identities=31% Similarity=0.709 Sum_probs=38.5
Q ss_pred cccchhhhhhccCCCcccCccchhhhhhccc-----CCCccCcccccccc--cccccCcccc
Q psy8320 55 ENKALTASKARFNPYTQKFESCKICRQKVHQ-----VGSHYCQACAYKKG--ICAMCGKKLL 109 (119)
Q Consensus 55 eNKlLs~~k~r~~Py~~~~~~C~iCK~~vhq-----~g~~YCq~CAYkkG--iCamCGKki~ 109 (119)
.|-+|.- |-|||-+|.-+|..|+..+.. .|.-||..|--+-| ||.-|-+.|-
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 668888888899999987753 36789999987665 6766666664
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=47.30 E-value=8 Score=33.92 Aligned_cols=36 Identities=19% Similarity=0.606 Sum_probs=27.4
Q ss_pred ccchhhhhhcccC-----CCccCccccc----ccccccccCcccc
Q psy8320 74 ESCKICRQKVHQV-----GSHYCQACAY----KKGICAMCGKKLL 109 (119)
Q Consensus 74 ~~C~iCK~~vhq~-----g~~YCq~CAY----kkGiCamCGKki~ 109 (119)
-.|.||..-+..+ ||.||..|.. ..+.|..|...+.
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=45.84 E-value=9.8 Score=21.36 Aligned_cols=22 Identities=27% Similarity=0.957 Sum_probs=16.8
Q ss_pred cchhhhhhcccCCCccCcccccc
Q psy8320 75 SCKICRQKVHQVGSHYCQACAYK 97 (119)
Q Consensus 75 ~C~iCK~~vhq~g~~YCq~CAYk 97 (119)
.|..|.+.|.. .++.|..|-|.
T Consensus 2 ~CP~C~~~V~~-~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPE-SAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchh-hcCcCCCCCCC
Confidence 68889998877 57877777663
No 21
>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=45.15 E-value=8.6 Score=25.81 Aligned_cols=36 Identities=28% Similarity=0.854 Sum_probs=26.6
Q ss_pred ccchhhhhhcccCC---------CccCccccccc--ccccccCcccc
Q psy8320 74 ESCKICRQKVHQVG---------SHYCQACAYKK--GICAMCGKKLL 109 (119)
Q Consensus 74 ~~C~iCK~~vhq~g---------~~YCq~CAYkk--GiCamCGKki~ 109 (119)
..|..|.+.+.++. -.||..||-.. |+|.-||=-+.
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 46788888887743 25788888665 99999996543
No 22
>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=41.85 E-value=6.4 Score=29.27 Aligned_cols=27 Identities=22% Similarity=0.532 Sum_probs=15.6
Q ss_pred CcccCccchhhhhhcccCCCccCcccc
Q psy8320 69 YTQKFESCKICRQKVHQVGSHYCQACA 95 (119)
Q Consensus 69 y~~~~~~C~iCK~~vhq~g~~YCq~CA 95 (119)
|+.+..+|.+|........+.||..|-
T Consensus 51 ~G~~~~rCIiCg~~~g~sdAYYC~eC~ 77 (106)
T PF03660_consen 51 FGSLQGRCIICGSGPGVSDAYYCWECV 77 (106)
T ss_dssp TSSTTSB-TTTSSSB--EE-EE-HHHH
T ss_pred CCCcCceEEEecCCCCcccceehhhhH
Confidence 334567999999555444689999983
No 23
>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=41.36 E-value=11 Score=20.47 Aligned_cols=21 Identities=29% Similarity=0.920 Sum_probs=14.4
Q ss_pred CCccCccccc-----ccccccccCcc
Q psy8320 87 GSHYCQACAY-----KKGICAMCGKK 107 (119)
Q Consensus 87 g~~YCq~CAY-----kkGiCamCGKk 107 (119)
||.||..|.. ....|.+|...
T Consensus 19 ~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 19 GHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 6777777764 24568888764
No 24
>PRK11595 DNA utilization protein GntX; Provisional
Probab=40.88 E-value=14 Score=28.78 Aligned_cols=33 Identities=27% Similarity=0.650 Sum_probs=14.2
Q ss_pred cchhhhhhcccCCCccCcccccc----cccccccCcc
Q psy8320 75 SCKICRQKVHQVGSHYCQACAYK----KGICAMCGKK 107 (119)
Q Consensus 75 ~C~iCK~~vhq~g~~YCq~CAYk----kGiCamCGKk 107 (119)
.|-.|...++......|..|.-+ ...|..||+.
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 25
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=39.85 E-value=22 Score=19.09 Aligned_cols=9 Identities=56% Similarity=1.250 Sum_probs=4.9
Q ss_pred cccccCccc
Q psy8320 100 ICAMCGKKL 108 (119)
Q Consensus 100 iCamCGKki 108 (119)
.|+.||+.|
T Consensus 29 ~C~~C~~~L 37 (39)
T smart00132 29 KCSKCGKPL 37 (39)
T ss_pred CCcccCCcC
Confidence 355566554
No 26
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=39.74 E-value=14 Score=23.45 Aligned_cols=16 Identities=50% Similarity=0.939 Sum_probs=11.3
Q ss_pred cccccCcccccccccc
Q psy8320 100 ICAMCGKKLLDVKNYK 115 (119)
Q Consensus 100 iCamCGKki~Dt~~yk 115 (119)
+|+.||+++--.+.++
T Consensus 1 ~C~iCg~kigl~~~~k 16 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFK 16 (51)
T ss_pred CCCcccccccccccee
Confidence 5899999886555433
No 27
>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=39.03 E-value=12 Score=27.58 Aligned_cols=22 Identities=32% Similarity=0.881 Sum_probs=15.3
Q ss_pred CccchhhhhhcccCC--CccCccc
Q psy8320 73 FESCKICRQKVHQVG--SHYCQAC 94 (119)
Q Consensus 73 ~~~C~iCK~~vhq~g--~~YCq~C 94 (119)
-..|..|+.+|.+.+ .-+|..|
T Consensus 34 Y~aC~~C~kkv~~~~~~~~~C~~C 57 (166)
T cd04476 34 YPACPGCNKKVVEEGNGTYRCEKC 57 (166)
T ss_pred EccccccCcccEeCCCCcEECCCC
Confidence 459999999998753 3444443
No 28
>KOG3799|consensus
Probab=38.20 E-value=15 Score=29.12 Aligned_cols=36 Identities=31% Similarity=0.725 Sum_probs=24.5
Q ss_pred Cccchhhhh-hcccCCCccCcccccccccccccCccccc
Q psy8320 73 FESCKICRQ-KVHQVGSHYCQACAYKKGICAMCGKKLLD 110 (119)
Q Consensus 73 ~~~C~iCK~-~vhq~g~~YCq~CAYkkGiCamCGKki~D 110 (119)
-..|-||-. +...--+|-|..|-.+ .||.||=++.-
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 458999954 5555345667666544 79999977653
No 29
>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=36.26 E-value=15 Score=21.21 Aligned_cols=12 Identities=42% Similarity=1.137 Sum_probs=9.1
Q ss_pred ccccccCccccc
Q psy8320 99 GICAMCGKKLLD 110 (119)
Q Consensus 99 GiCamCGKki~D 110 (119)
|+|..||..|.+
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 30
>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=35.79 E-value=5.4 Score=23.02 Aligned_cols=10 Identities=30% Similarity=1.075 Sum_probs=6.7
Q ss_pred CCccCccccc
Q psy8320 87 GSHYCQACAY 96 (119)
Q Consensus 87 g~~YCq~CAY 96 (119)
||.||..|+.
T Consensus 18 GH~fC~~C~~ 27 (39)
T PF13923_consen 18 GHSFCKECIE 27 (39)
T ss_dssp SEEEEHHHHH
T ss_pred CCchhHHHHH
Confidence 6677777764
No 31
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=35.19 E-value=18 Score=23.88 Aligned_cols=14 Identities=43% Similarity=0.990 Sum_probs=10.7
Q ss_pred cccccccccCcccc
Q psy8320 96 YKKGICAMCGKKLL 109 (119)
Q Consensus 96 YkkGiCamCGKki~ 109 (119)
|...+|..||+++.
T Consensus 3 ~~~~~C~~Cg~~~~ 16 (54)
T PF14446_consen 3 YEGCKCPVCGKKFK 16 (54)
T ss_pred ccCccChhhCCccc
Confidence 56678888888875
No 32
>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=34.59 E-value=9.8 Score=18.56 Aligned_cols=15 Identities=27% Similarity=0.742 Sum_probs=8.2
Q ss_pred cccccCccccccccc
Q psy8320 100 ICAMCGKKLLDVKNY 114 (119)
Q Consensus 100 iCamCGKki~Dt~~y 114 (119)
.|.+||+...+-..+
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 477888876654443
No 33
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=34.04 E-value=14 Score=29.66 Aligned_cols=36 Identities=28% Similarity=0.799 Sum_probs=27.0
Q ss_pred cchhhhhhccc-----CCCccCcccccc--------------------cccccccCccccc
Q psy8320 75 SCKICRQKVHQ-----VGSHYCQACAYK--------------------KGICAMCGKKLLD 110 (119)
Q Consensus 75 ~C~iCK~~vhq-----~g~~YCq~CAYk--------------------kGiCamCGKki~D 110 (119)
.|.||...+.. =||.||..|.++ ...|..|...|..
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 68888664432 389999999963 3479999998864
No 34
>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=33.76 E-value=16 Score=24.88 Aligned_cols=10 Identities=30% Similarity=1.059 Sum_probs=6.1
Q ss_pred cccccccCcc
Q psy8320 98 KGICAMCGKK 107 (119)
Q Consensus 98 kGiCamCGKk 107 (119)
.-+|.+||-.
T Consensus 30 ~~VCnlCGFN 39 (61)
T PF05715_consen 30 SQVCNLCGFN 39 (61)
T ss_pred hhhhcccCCC
Confidence 3467777753
No 35
>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=33.19 E-value=19 Score=31.26 Aligned_cols=38 Identities=16% Similarity=0.477 Sum_probs=23.5
Q ss_pred ccCCCc-cc-CccchhhhhhcccCCCccCcccccccccccccCcccc
Q psy8320 65 RFNPYT-QK-FESCKICRQKVHQVGSHYCQACAYKKGICAMCGKKLL 109 (119)
Q Consensus 65 r~~Py~-~~-~~~C~iCK~~vhq~g~~YCq~CAYkkGiCamCGKki~ 109 (119)
-|+|-- .| ...|+.|...+....+. ++ .++|+ ||++|.
T Consensus 230 g~~P~~GKYh~~~c~~C~~~~~~~~~~-----~~-~~~Cp-CG~~i~ 269 (374)
T TIGR00375 230 GLDPLLGKYHQTACEACGEPAVSEDAE-----TA-CANCP-CGGRIK 269 (374)
T ss_pred eECcCCCccchhhhcccCCcCCchhhh-----hc-CCCCC-CCCcce
Confidence 356643 22 56788887766542211 23 58999 999964
No 36
>KOG0320|consensus
Probab=32.93 E-value=11 Score=30.42 Aligned_cols=36 Identities=33% Similarity=0.843 Sum_probs=27.0
Q ss_pred ccchhhhhhccc-------CCCccCcccc---ccc-ccccccCcccc
Q psy8320 74 ESCKICRQKVHQ-------VGSHYCQACA---YKK-GICAMCGKKLL 109 (119)
Q Consensus 74 ~~C~iCK~~vhq-------~g~~YCq~CA---Ykk-GiCamCGKki~ 109 (119)
-+|.||--.+.+ =||-||..|+ .++ ..|..|+|+|.
T Consensus 132 ~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 132 YKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred cCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 489999654432 3788999997 333 48999999886
No 37
>PRK00420 hypothetical protein; Validated
Probab=26.72 E-value=30 Score=25.58 Aligned_cols=22 Identities=18% Similarity=0.528 Sum_probs=15.5
Q ss_pred Cccchhhhhhccc--CCCccCccc
Q psy8320 73 FESCKICRQKVHQ--VGSHYCQAC 94 (119)
Q Consensus 73 ~~~C~iCK~~vhq--~g~~YCq~C 94 (119)
...|..|...+-. .|..||+.|
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
>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=26.43 E-value=27 Score=24.66 Aligned_cols=11 Identities=36% Similarity=1.038 Sum_probs=9.0
Q ss_pred ccccccCcccc
Q psy8320 99 GICAMCGKKLL 109 (119)
Q Consensus 99 GiCamCGKki~ 109 (119)
|+|-.||..|-
T Consensus 81 G~C~~Cge~I~ 91 (110)
T TIGR02420 81 GYCEECGEEIG 91 (110)
T ss_pred CchhccCCccc
Confidence 68999998874
No 39
>PHA02929 N1R/p28-like protein; Provisional
Probab=26.33 E-value=28 Score=28.60 Aligned_cols=40 Identities=28% Similarity=0.697 Sum_probs=29.7
Q ss_pred Cccchhhhhhcc-------------cCCCccCccccc----ccccccccCccccccc
Q psy8320 73 FESCKICRQKVH-------------QVGSHYCQACAY----KKGICAMCGKKLLDVK 112 (119)
Q Consensus 73 ~~~C~iCK~~vh-------------q~g~~YCq~CAY----kkGiCamCGKki~Dt~ 112 (119)
...|.||-..+. .=+|.||..|-- .+..|++|-..+.-+.
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 358999987643 237889999972 5679999998877543
No 40
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=24.66 E-value=30 Score=29.11 Aligned_cols=33 Identities=21% Similarity=0.627 Sum_probs=25.3
Q ss_pred hhccCCCcccCccchhhhhhc-----ccCCCccCcccc
Q psy8320 63 KARFNPYTQKFESCKICRQKV-----HQVGSHYCQACA 95 (119)
Q Consensus 63 k~r~~Py~~~~~~C~iCK~~v-----hq~g~~YCq~CA 95 (119)
..++.-|+.....|+.|.+.+ .+-+.+||..|-
T Consensus 235 q~~l~VYgR~GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 235 QQELKVYGRAGEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred ceeEEEecCCCCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 346677887788999997654 566889999983
No 41
>smart00746 TRASH metallochaperone-like domain.
Probab=24.61 E-value=36 Score=16.91 Aligned_cols=9 Identities=44% Similarity=1.435 Sum_probs=7.6
Q ss_pred ccccCcccc
Q psy8320 101 CAMCGKKLL 109 (119)
Q Consensus 101 CamCGKki~ 109 (119)
|+.||..|.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 788999886
No 42
>KOG4458|consensus
Probab=24.52 E-value=28 Score=24.47 Aligned_cols=33 Identities=30% Similarity=0.634 Sum_probs=21.6
Q ss_pred hhccCCCcccCccchhhhhhcccCCCccCccccccccccc
Q psy8320 63 KARFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKGICA 102 (119)
Q Consensus 63 k~r~~Py~~~~~~C~iCK~~vhq~g~~YCq~CAYkkGiCa 102 (119)
|.+++||.-...-=-.|+-.+|... ||+.|||-
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 4577888632222335666888754 89999994
No 43
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=24.34 E-value=20 Score=19.86 Aligned_cols=21 Identities=19% Similarity=0.654 Sum_probs=7.8
Q ss_pred cchhhhhhccc-----CCCccCcccc
Q psy8320 75 SCKICRQKVHQ-----VGSHYCQACA 95 (119)
Q Consensus 75 ~C~iCK~~vhq-----~g~~YCq~CA 95 (119)
+|..|...+.. ....||..|.
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred cCccCCCcceEeEecCCCCeECcCCc
Confidence 56666554422 2235555553
No 44
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=24.21 E-value=33 Score=27.84 Aligned_cols=30 Identities=30% Similarity=0.730 Sum_probs=21.1
Q ss_pred ccCCCcccCccchhhhhhcc-----cCCCccCccc
Q psy8320 65 RFNPYTQKFESCKICRQKVH-----QVGSHYCQAC 94 (119)
Q Consensus 65 r~~Py~~~~~~C~iCK~~vh-----q~g~~YCq~C 94 (119)
++.-|+.....|..|.+.|. +-...||..|
T Consensus 236 ~~~Vy~R~g~pCprCG~~I~~~~~~gR~t~~CP~C 270 (272)
T PRK14810 236 SHRVYQRTGEPCLNCKTPIRRVVVAGRSSHYCPHC 270 (272)
T ss_pred hEeecCCCCCcCCCCCCeeEEEEECCCccEECcCC
Confidence 45567655778999987664 3356788877
No 45
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=24.21 E-value=31 Score=27.89 Aligned_cols=30 Identities=20% Similarity=0.669 Sum_probs=19.8
Q ss_pred cCCCcccCccchhhhhhcc-----cCCCccCcccc
Q psy8320 66 FNPYTQKFESCKICRQKVH-----QVGSHYCQACA 95 (119)
Q Consensus 66 ~~Py~~~~~~C~iCK~~vh-----q~g~~YCq~CA 95 (119)
+.-|+.....|..|.+.|. .-+..||+.|-
T Consensus 238 l~Vy~R~g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 238 LQVYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred eEEcCCCCCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 4456545668999987664 22567888873
No 46
>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=24.15 E-value=18 Score=23.90 Aligned_cols=23 Identities=39% Similarity=0.518 Sum_probs=17.5
Q ss_pred hhhhhccchhHHHhhhcc---ccCCC
Q psy8320 14 EEIYFIMVCSKCEKKLGK---VITPD 36 (119)
Q Consensus 14 ~~~~~~MVC~KCEKKL~k---latPD 36 (119)
.+|+....|+-|.|.|+. ++-||
T Consensus 73 v~i~~~~~C~vC~k~l~~~~f~~~p~ 98 (109)
T PF10367_consen 73 VVITESTKCSVCGKPLGNSVFVVFPC 98 (109)
T ss_pred EEECCCCCccCcCCcCCCceEEEeCC
Confidence 356688999999999985 45554
No 47
>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=24.09 E-value=34 Score=25.96 Aligned_cols=35 Identities=29% Similarity=0.622 Sum_probs=23.0
Q ss_pred CCcccCccchhhhh-------hcccCCCccCcccccccccccccCccc
Q psy8320 68 PYTQKFESCKICRQ-------KVHQVGSHYCQACAYKKGICAMCGKKL 108 (119)
Q Consensus 68 Py~~~~~~C~iCK~-------~vhq~g~~YCq~CAYkkGiCamCGKki 108 (119)
|-|.+..-|.+|-. .+.++ .. +-+.|.|.|||++-
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 66666677777743 34442 23 23889999999974
No 48
>PHA03096 p28-like protein; Provisional
Probab=23.36 E-value=22 Score=29.82 Aligned_cols=25 Identities=44% Similarity=0.897 Sum_probs=19.7
Q ss_pred cccccccc-cccccCccccccccccc
Q psy8320 92 QACAYKKG-ICAMCGKKLLDVKNYKQ 116 (119)
Q Consensus 92 q~CAYkkG-iCamCGKki~Dt~~ykq 116 (119)
..|.|-.| +|.|||+..++...+.|
T Consensus 135 ~~c~~lHg~lC~~C~k~~Lhp~d~eq 160 (284)
T PHA03096 135 KYCEYLHGDICDICEKYLLHPTDIKQ 160 (284)
T ss_pred cCcHHHHHHHHHhhcchhcCCcCHHH
Confidence 45777666 69999999998877655
No 49
>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=22.77 E-value=45 Score=22.94 Aligned_cols=23 Identities=35% Similarity=0.624 Sum_probs=18.8
Q ss_pred hccchhHHHhhhc-cccCCCCCCC
Q psy8320 18 FIMVCSKCEKKLG-KVITPDNWKS 40 (119)
Q Consensus 18 ~~MVC~KCEKKL~-klatPD~~k~ 40 (119)
+.=+|.+|.|-|+ ..--|-+||+
T Consensus 53 fs~pC~~C~klL~~~~~LPP~~r~ 76 (90)
T PF11571_consen 53 FSTPCKKCGKLLSSKAFLPPVRRP 76 (90)
T ss_pred ccchhhHHHhHhhhcccCCCeeec
Confidence 5568999999996 5778888884
No 50
>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=22.27 E-value=46 Score=22.15 Aligned_cols=11 Identities=45% Similarity=1.026 Sum_probs=8.4
Q ss_pred ccccccccCcc
Q psy8320 97 KKGICAMCGKK 107 (119)
Q Consensus 97 kkGiCamCGKk 107 (119)
.+++|..||.+
T Consensus 4 ~~~~C~~Cg~r 14 (69)
T PF09706_consen 4 KKYNCIFCGER 14 (69)
T ss_pred CCCcCcCCCCc
Confidence 46789999944
No 51
>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=21.89 E-value=38 Score=25.69 Aligned_cols=24 Identities=25% Similarity=0.667 Sum_probs=19.9
Q ss_pred ccCccchhhhhhcccCCCccCccccc
Q psy8320 71 QKFESCKICRQKVHQVGSHYCQACAY 96 (119)
Q Consensus 71 ~~~~~C~iCK~~vhq~g~~YCq~CAY 96 (119)
...-.|..|.+.+.. | .||..|+-
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 345699999999998 5 99999973
No 52
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.77 E-value=51 Score=30.18 Aligned_cols=22 Identities=32% Similarity=0.851 Sum_probs=17.2
Q ss_pred CccCcccccccc---cccccCcccc
Q psy8320 88 SHYCQACAYKKG---ICAMCGKKLL 109 (119)
Q Consensus 88 ~~YCq~CAYkkG---iCamCGKki~ 109 (119)
.-.|+.|.|... .|.-||...+
T Consensus 408 ~l~Ch~Cg~~~~~~~~Cp~Cg~~~l 432 (679)
T PRK05580 408 RLRCHHCGYQEPIPKACPECGSTDL 432 (679)
T ss_pred eEECCCCcCCCCCCCCCCCCcCCee
Confidence 346999999865 7999988754
No 53
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=21.68 E-value=37 Score=21.93 Aligned_cols=28 Identities=25% Similarity=0.624 Sum_probs=17.9
Q ss_pred cchhhhhhcccCCCccCcccccccccccccCcccc
Q psy8320 75 SCKICRQKVHQVGSHYCQACAYKKGICAMCGKKLL 109 (119)
Q Consensus 75 ~C~iCK~~vhq~g~~YCq~CAYkkGiCamCGKki~ 109 (119)
+|..|...+.... ++.--.|.-||-+|+
T Consensus 8 ~C~~Cg~~~~~~~-------~~~~irCp~Cg~rIl 35 (49)
T COG1996 8 KCARCGREVELDQ-------ETRGIRCPYCGSRIL 35 (49)
T ss_pred EhhhcCCeeehhh-------ccCceeCCCCCcEEE
Confidence 7888888876432 344456666666665
No 54
>KOG1734|consensus
Probab=21.47 E-value=31 Score=29.96 Aligned_cols=16 Identities=25% Similarity=0.706 Sum_probs=12.8
Q ss_pred ccccccccCccccccc
Q psy8320 97 KKGICAMCGKKLLDVK 112 (119)
Q Consensus 97 kkGiCamCGKki~Dt~ 112 (119)
..++||.||+++.++-
T Consensus 223 ~d~vCaVCg~~~~~s~ 238 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSV 238 (328)
T ss_pred CcchhHhhcchheeec
Confidence 4469999999998653
No 55
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=21.36 E-value=38 Score=25.88 Aligned_cols=24 Identities=25% Similarity=0.885 Sum_probs=16.9
Q ss_pred ccchhhhhhcc-cCCCccCcccccc
Q psy8320 74 ESCKICRQKVH-QVGSHYCQACAYK 97 (119)
Q Consensus 74 ~~C~iCK~~vh-q~g~~YCq~CAYk 97 (119)
..|..|++.+- -+|.-||+.|-|.
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~~~ 53 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCGYR 53 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCCce
Confidence 48999999773 3377777766553
No 56
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.15 E-value=40 Score=27.42 Aligned_cols=33 Identities=21% Similarity=0.615 Sum_probs=22.6
Q ss_pred ccCCCcccCccchhhhhhcc-----cCCCccCcccccc
Q psy8320 65 RFNPYTQKFESCKICRQKVH-----QVGSHYCQACAYK 97 (119)
Q Consensus 65 r~~Py~~~~~~C~iCK~~vh-----q~g~~YCq~CAYk 97 (119)
++.-|+.....|..|.+.|. +-+..||..|--.
T Consensus 227 ~~~Vy~R~g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 227 QHAVYGREGQPCPRCGTPIEKIVVGGRGTHFCPQCQPL 264 (269)
T ss_pred eEEecCCCcCCCCcCCCeeEEEEECCCCcEECCCCcCC
Confidence 34567655678999988664 3367889888543
No 57
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=21.08 E-value=44 Score=26.31 Aligned_cols=14 Identities=36% Similarity=0.942 Sum_probs=11.1
Q ss_pred cccccccccCcccc
Q psy8320 96 YKKGICAMCGKKLL 109 (119)
Q Consensus 96 YkkGiCamCGKki~ 109 (119)
-+.|.|++||..+.
T Consensus 18 ~Q~G~CaiC~~~l~ 31 (157)
T PHA02565 18 AQNGICPLCKRELD 31 (157)
T ss_pred HhCCcCCCCCCccC
Confidence 45679999999865
Done!