Query 034393
Match_columns 96
No_of_seqs 101 out of 103
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 12:58:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034393.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034393hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3476 Microtubule-associated 100.0 5.1E-55 1.1E-59 302.5 2.0 96 1-96 1-100 (100)
2 PF10235 Cript: Microtubule-as 100.0 1.4E-47 3E-52 262.4 4.3 85 11-96 1-90 (90)
3 PF10217 DUF2039: Uncharacteri 95.8 0.0012 2.5E-08 45.8 -1.5 40 45-84 48-90 (92)
4 PF12773 DZR: Double zinc ribb 92.3 0.1 2.2E-06 30.6 1.8 35 54-88 1-42 (50)
5 KOG3241 Uncharacterized conser 91.1 0.014 3.1E-07 45.8 -3.6 44 45-88 60-106 (227)
6 COG5152 Uncharacterized conser 83.1 0.43 9.3E-06 38.2 0.4 48 35-85 183-240 (259)
7 PRK14559 putative protein seri 80.1 1.2 2.5E-05 39.5 2.0 35 53-87 3-39 (645)
8 PF13240 zinc_ribbon_2: zinc-r 79.3 0.97 2.1E-05 23.8 0.8 20 53-72 1-20 (23)
9 PF13248 zf-ribbon_3: zinc-rib 78.6 1.2 2.6E-05 23.6 1.0 21 53-73 4-24 (26)
10 KOG3799 Rab3 effector RIM1 and 73.4 1.4 3.1E-05 33.4 0.6 36 52-89 66-103 (169)
11 PF10571 UPF0547: Uncharacteri 62.6 4 8.8E-05 22.1 0.8 22 53-74 2-23 (26)
12 PF06906 DUF1272: Protein of u 59.8 3.9 8.4E-05 26.4 0.5 34 53-86 7-52 (57)
13 PF14634 zf-RING_5: zinc-RING 58.8 2.4 5.3E-05 24.3 -0.5 20 64-83 21-44 (44)
14 PRK12496 hypothetical protein; 55.4 5.2 0.00011 29.4 0.7 22 65-86 127-154 (164)
15 PF13920 zf-C3HC4_3: Zinc fing 49.5 3.2 7E-05 24.2 -1.0 36 53-88 4-50 (50)
16 PF00645 zf-PARP: Poly(ADP-rib 49.4 6.9 0.00015 24.8 0.5 19 46-64 2-20 (82)
17 TIGR00570 cdk7 CDK-activating 47.8 7.7 0.00017 31.9 0.6 35 53-87 5-55 (309)
18 PF14471 DUF4428: Domain of un 45.6 10 0.00022 23.2 0.8 16 77-92 1-16 (51)
19 PF02318 FYVE_2: FYVE-type zin 45.1 9.7 0.00021 26.2 0.7 36 47-84 50-88 (118)
20 KOG1813 Predicted E3 ubiquitin 44.0 13 0.00027 31.0 1.3 36 53-88 243-288 (313)
21 PF14446 Prok-RING_1: Prokaryo 42.4 12 0.00026 23.7 0.7 14 73-86 3-16 (54)
22 PF01258 zf-dskA_traR: Prokary 42.1 11 0.00024 21.0 0.5 12 76-87 4-15 (36)
23 PF10764 Gin: Inhibitor of sig 40.0 20 0.00042 21.7 1.4 17 2-18 20-36 (46)
24 PF13894 zf-C2H2_4: C2H2-type 39.2 7.1 0.00015 18.4 -0.6 15 77-91 2-16 (24)
25 PF05715 zf-piccolo: Piccolo Z 35.4 16 0.00034 23.9 0.5 30 53-84 4-39 (61)
26 PF03660 PHF5: PHF5-like prote 33.9 13 0.00029 26.5 -0.0 31 52-82 28-62 (106)
27 COG1545 Predicted nucleic-acid 33.3 16 0.00035 26.2 0.3 32 32-73 20-51 (140)
28 PF11532 HnRNP_M: Heterogeneou 31.9 18 0.00039 20.7 0.3 9 43-51 18-26 (30)
29 COG1996 RPC10 DNA-directed RNA 31.3 18 0.00039 22.5 0.3 15 76-90 7-21 (49)
30 TIGR02420 dksA RNA polymerase- 30.2 22 0.00047 24.2 0.5 11 76-86 81-91 (110)
31 PHA02094 hypothetical protein 29.8 26 0.00056 23.8 0.8 11 13-23 65-75 (81)
32 KOG0153 Predicted RNA-binding 29.5 13 0.00028 31.6 -0.8 45 33-81 26-83 (377)
33 PF07191 zinc-ribbons_6: zinc- 29.4 10 0.00023 25.1 -1.1 35 53-87 3-42 (70)
34 PF11571 Med27: Mediator compl 29.0 30 0.00066 22.9 1.0 20 2-21 56-76 (90)
35 KOG1705 Uncharacterized conser 28.7 27 0.0006 25.0 0.8 32 52-83 28-63 (110)
36 PRK11595 DNA utilization prote 27.8 34 0.00074 25.7 1.3 33 53-85 7-44 (227)
37 smart00746 TRASH metallochaper 27.3 30 0.00064 16.6 0.6 10 78-87 1-10 (39)
38 KOG1734 Predicted RING-contain 27.1 21 0.00045 29.8 -0.0 16 74-89 223-238 (328)
39 PHA02565 49 recombination endo 26.4 33 0.00072 26.0 1.0 14 73-86 18-31 (157)
40 PF09706 Cas_CXXC_CXXC: CRISPR 25.6 37 0.00081 21.7 1.0 11 74-84 4-14 (69)
41 PF10367 Vps39_2: Vacuolar sor 25.4 34 0.00074 21.7 0.8 11 77-87 80-90 (109)
42 PF02945 Endonuclease_7: Recom 25.1 27 0.00059 23.2 0.3 14 73-86 20-33 (81)
43 COG1439 Predicted nucleic acid 24.2 36 0.00078 26.1 0.8 24 53-86 141-164 (177)
44 PF10621 FpoO: F420H2 dehydrog 24.0 35 0.00077 24.9 0.7 29 52-85 35-70 (119)
45 PHA03096 p28-like protein; Pro 23.7 19 0.00041 29.0 -0.8 24 70-93 136-160 (284)
46 PF10417 1-cysPrx_C: C-termina 23.2 50 0.0011 19.1 1.1 13 12-24 9-21 (40)
47 cd00162 RING RING-finger (Real 23.1 34 0.00074 17.7 0.4 20 65-84 20-44 (45)
48 PF10146 zf-C4H2: Zinc finger- 22.7 38 0.00082 26.5 0.7 20 52-71 195-214 (230)
49 TIGR00375 conserved hypothetic 22.0 38 0.00083 28.3 0.6 28 52-86 241-269 (374)
50 KOG4217 Nuclear receptors of t 21.6 33 0.00072 30.7 0.2 29 47-75 282-331 (605)
51 PRK05580 primosome assembly pr 21.6 61 0.0013 28.5 1.8 43 44-86 376-432 (679)
52 COG2995 PqiA Uncharacterized p 21.4 53 0.0012 28.4 1.4 37 44-86 205-246 (418)
53 PF12874 zf-met: Zinc-finger o 20.9 23 0.0005 17.4 -0.6 15 78-92 3-17 (25)
54 PF07649 C1_3: C1-like domain; 20.8 29 0.00064 18.4 -0.2 21 53-73 2-23 (30)
55 KOG2272 Focal adhesion protein 20.4 71 0.0015 26.7 1.8 49 37-86 149-206 (332)
56 PF00096 zf-C2H2: Zinc finger, 20.3 23 0.00051 17.1 -0.6 15 77-91 2-16 (23)
No 1
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=100.00 E-value=5.1e-55 Score=302.51 Aligned_cols=96 Identities=74% Similarity=1.273 Sum_probs=91.8
Q ss_pred CcchHHHHhhcCcccCCccCCCCCccccCCCceecccccc-ccccCCCCCCC--ccccchhhhcCCC-CCcccccccccC
Q 034393 1 MVCEKCEKKLSKVIVPDKWKEGASNTTEAGGRKVNENKLL-SKKKRWTPYGN--TKCIICKQQVHQD-AKYCHTCAYSKG 76 (96)
Q Consensus 1 MVC~KCeKKl~klatPd~~k~g~~~~~~~g~r~i~eNKlL-s~k~r~~py~~--~~C~~CK~~v~q~-~~YCq~CAYkkg 76 (96)
|||++|||||++|++|||||+|+||++++|+|+|+|||.| |+++||+||+. .+|+|||+.|||+ +||||.|||+||
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 9999999999999999999999999999999999999955 45999999994 5999999999999 799999999999
Q ss_pred ccccCCccccccccccccCC
Q 034393 77 VCAMCGKQVLDTKFYKQSNV 96 (96)
Q Consensus 77 iCamCGKki~dt~~y~qS~~ 96 (96)
|||||||+|+||++|+||++
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=1.4e-47 Score=262.36 Aligned_cols=85 Identities=67% Similarity=1.227 Sum_probs=79.9
Q ss_pred cCcccCCccCCCC--CccccCCCceecccccccc--ccCCCCCCCccccchhhhcCC-CCCcccccccccCccccCCccc
Q 034393 11 SKVIVPDKWKEGA--SNTTEAGGRKVNENKLLSK--KKRWTPYGNTKCIICKQQVHQ-DAKYCHTCAYSKGVCAMCGKQV 85 (96)
Q Consensus 11 ~klatPd~~k~g~--~~~~~~g~r~i~eNKlLs~--k~r~~py~~~~C~~CK~~v~q-~~~YCq~CAYkkgiCamCGKki 85 (96)
++||||||||+|+ +++.++|+|+||||||||+ ++||+||.+ +|++||++||| ++||||.|||++||||||||+|
T Consensus 1 tklatPd~~k~~~~~~~~~~~g~r~i~eNKlLs~~~~nPy~~~~~-~C~~CK~~v~q~g~~YCq~CAYkkGiCamCGKki 79 (90)
T PF10235_consen 1 TKLATPDPWKKGAMYRNTAESGGRKIGENKLLSKKKKNPYAPYSS-KCKICKTKVHQPGAKYCQTCAYKKGICAMCGKKI 79 (90)
T ss_pred CccccCCccccCcccccccCCCCccccceeeecccccCcccccCc-cccccccccccCCCccChhhhcccCcccccCCee
Confidence 4799999999999 8999999999999999999 567777777 99999999999 6999999999999999999999
Q ss_pred cccccccccCC
Q 034393 86 LDTKFYKQSNV 96 (96)
Q Consensus 86 ~dt~~y~qS~~ 96 (96)
+||++|+||+|
T Consensus 80 ~dtk~ykqs~v 90 (90)
T PF10235_consen 80 LDTKNYKQSSV 90 (90)
T ss_pred cccccccccCC
Confidence 99999999987
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=95.82 E-value=0.0012 Score=45.83 Aligned_cols=40 Identities=38% Similarity=0.826 Sum_probs=32.9
Q ss_pred CCCCCCC-ccccchhh-hcCCC-CCcccccccccCccccCCcc
Q 034393 45 RWTPYGN-TKCIICKQ-QVHQD-AKYCHTCAYSKGVCAMCGKQ 84 (96)
Q Consensus 45 r~~py~~-~~C~~CK~-~v~q~-~~YCq~CAYkkgiCamCGKk 84 (96)
+|.|-+. .+|-.|.+ .|.+. +..|+.||-..++||.||++
T Consensus 48 KYKpLt~p~kC~~C~qktVk~AYh~iC~~Ca~~~~vCaKC~k~ 90 (92)
T PF10217_consen 48 KYKPLTQPKKCNKCQQKTVKHAYHVICDPCAKELKVCAKCGKP 90 (92)
T ss_pred CcccCCCCccccccccchHHHHHHHHHHHHHHhhccCcccCCC
Confidence 4555553 69999997 55665 99999999999999999986
No 4
>PF12773 DZR: Double zinc ribbon
Probab=92.34 E-value=0.1 Score=30.58 Aligned_cols=35 Identities=29% Similarity=0.707 Sum_probs=23.9
Q ss_pred ccchhhhcCCCCCcccccccccC-------ccccCCcccccc
Q 034393 54 CIICKQQVHQDAKYCHTCAYSKG-------VCAMCGKQVLDT 88 (96)
Q Consensus 54 C~~CK~~v~q~~~YCq~CAYkkg-------iCamCGKki~dt 88 (96)
|..|.+.+..++.||..|-..-. +|.-||..+...
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPLPPPDQSKKICPNCGAENPPN 42 (50)
T ss_pred CCCcCCcCCccccCChhhcCChhhccCCCCCCcCCcCCCcCC
Confidence 55677777777777777766554 577777765543
No 5
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=91.12 E-value=0.014 Score=45.81 Aligned_cols=44 Identities=36% Similarity=0.754 Sum_probs=35.8
Q ss_pred CCCCCCC-ccccchhh-hcCCC-CCcccccccccCccccCCcccccc
Q 034393 45 RWTPYGN-TKCIICKQ-QVHQD-AKYCHTCAYSKGVCAMCGKQVLDT 88 (96)
Q Consensus 45 r~~py~~-~~C~~CK~-~v~q~-~~YCq~CAYkkgiCamCGKki~dt 88 (96)
+|.|.+. .+|..|+. .|.|. |..|..||-...+||-|+|.+.++
T Consensus 60 KYKpLt~akkC~kC~~r~Vk~aYH~~Cr~CA~e~~vCAKC~ks~~~i 106 (227)
T KOG3241|consen 60 KYKPLTEAKKCQKCTKRNVKQAYHKLCRGCAKEQKVCAKCCKSVDQI 106 (227)
T ss_pred cccccchhHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHhccHHHh
Confidence 4555553 68999987 67777 999999999999999999976554
No 6
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=83.09 E-value=0.43 Score=38.22 Aligned_cols=48 Identities=35% Similarity=0.823 Sum_probs=32.6
Q ss_pred ccccccccccCCCCCCCccccchhhhcC------CCCCcccccc---cccC-ccccCCccc
Q 034393 35 NENKLLSKKKRWTPYGNTKCIICKQQVH------QDAKYCHTCA---YSKG-VCAMCGKQV 85 (96)
Q Consensus 35 ~eNKlLs~k~r~~py~~~~C~~CK~~v~------q~~~YCq~CA---Ykkg-iCamCGKki 85 (96)
-|.++++-...=-|| .|.|||.... =+|++|..|| |++| .|-.||+..
T Consensus 183 Ee~~v~~~~~e~IPF---~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t 240 (259)
T COG5152 183 EEAPVISGPGEKIPF---LCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKAT 240 (259)
T ss_pred hhcccccCCCCCCce---eehhchhhccchhhhhcchhHHHHHHHHHhccCCcceecchhh
Confidence 344555443222344 9999997432 2489999999 6776 799999864
No 7
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=80.05 E-value=1.2 Score=39.53 Aligned_cols=35 Identities=26% Similarity=0.696 Sum_probs=28.7
Q ss_pred cccchhhhcCCCCCccccccccc--CccccCCccccc
Q 034393 53 KCIICKQQVHQDAKYCHTCAYSK--GVCAMCGKQVLD 87 (96)
Q Consensus 53 ~C~~CK~~v~q~~~YCq~CAYkk--giCamCGKki~d 87 (96)
.|..|...+..+++||+.|-.+- ..|+-||..+..
T Consensus 3 ~Cp~Cg~~n~~~akFC~~CG~~l~~~~Cp~CG~~~~~ 39 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKCGTSLTHKPCPQCGTEVPV 39 (645)
T ss_pred cCCCCCCcCCCCCccccccCCCCCCCcCCCCCCCCCc
Confidence 68999999988999999998774 368888887643
No 8
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=79.34 E-value=0.97 Score=23.75 Aligned_cols=20 Identities=35% Similarity=0.976 Sum_probs=15.4
Q ss_pred cccchhhhcCCCCCcccccc
Q 034393 53 KCIICKQQVHQDAKYCHTCA 72 (96)
Q Consensus 53 ~C~~CK~~v~q~~~YCq~CA 72 (96)
.|..|...+..++++|+.|-
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG 20 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCG 20 (23)
T ss_pred CCcccCCCCCCcCcchhhhC
Confidence 37788888888888877664
No 9
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=78.56 E-value=1.2 Score=23.62 Aligned_cols=21 Identities=33% Similarity=0.858 Sum_probs=17.0
Q ss_pred cccchhhhcCCCCCccccccc
Q 034393 53 KCIICKQQVHQDAKYCHTCAY 73 (96)
Q Consensus 53 ~C~~CK~~v~q~~~YCq~CAY 73 (96)
.|..|-+.+..+++||+.|-.
T Consensus 4 ~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 4 FCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred CCcccCCcCCcccccChhhCC
Confidence 788899988888998888743
No 10
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=73.38 E-value=1.4 Score=33.41 Aligned_cols=36 Identities=31% Similarity=0.690 Sum_probs=27.8
Q ss_pred ccccch-hhhcCCC-CCcccccccccCccccCCccccccc
Q 034393 52 TKCIIC-KQQVHQD-AKYCHTCAYSKGVCAMCGKQVLDTK 89 (96)
Q Consensus 52 ~~C~~C-K~~v~q~-~~YCq~CAYkkgiCamCGKki~dt~ 89 (96)
..|.|| |++...+ +|-|..|-.+ .||.||=++.--+
T Consensus 66 atC~IC~KTKFADG~GH~C~YCq~r--~CARCGGrv~lrs 103 (169)
T KOG3799|consen 66 ATCGICHKTKFADGCGHNCSYCQTR--FCARCGGRVSLRS 103 (169)
T ss_pred cchhhhhhcccccccCcccchhhhh--HHHhcCCeeeecc
Confidence 589999 4577777 9988888544 8999998775433
No 11
>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=62.58 E-value=4 Score=22.07 Aligned_cols=22 Identities=36% Similarity=0.966 Sum_probs=18.4
Q ss_pred cccchhhhcCCCCCcccccccc
Q 034393 53 KCIICKQQVHQDAKYCHTCAYS 74 (96)
Q Consensus 53 ~C~~CK~~v~q~~~YCq~CAYk 74 (96)
.|..|.+.|....+.|..|-|.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCC
Confidence 6889999998889988888763
No 12
>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=59.84 E-value=3.9 Score=26.43 Aligned_cols=34 Identities=32% Similarity=0.963 Sum_probs=26.8
Q ss_pred cccchhhhcCCCC----------Cccccccccc--CccccCCcccc
Q 034393 53 KCIICKQQVHQDA----------KYCHTCAYSK--GVCAMCGKQVL 86 (96)
Q Consensus 53 ~C~~CK~~v~q~~----------~YCq~CAYkk--giCamCGKki~ 86 (96)
.|..|-+.|.+++ .||..||-.. ++|.-||=-+.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGelv 52 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGELV 52 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCccc
Confidence 6888888887775 6888888665 99999996553
No 13
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=58.85 E-value=2.4 Score=24.31 Aligned_cols=20 Identities=25% Similarity=0.762 Sum_probs=15.3
Q ss_pred CCCcccccccccC----ccccCCc
Q 034393 64 DAKYCHTCAYSKG----VCAMCGK 83 (96)
Q Consensus 64 ~~~YCq~CAYkkg----iCamCGK 83 (96)
+|.+|+.|+.+.- .|+.|++
T Consensus 21 gH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 21 GHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCHHHHHHHHhhcCCCCCCcCCCC
Confidence 4778888887766 8888875
No 14
>PRK12496 hypothetical protein; Provisional
Probab=55.38 E-value=5.2 Score=29.39 Aligned_cols=22 Identities=41% Similarity=1.046 Sum_probs=16.6
Q ss_pred CCcccccc--c----ccCccccCCcccc
Q 034393 65 AKYCHTCA--Y----SKGVCAMCGKQVL 86 (96)
Q Consensus 65 ~~YCq~CA--Y----kkgiCamCGKki~ 86 (96)
.++|++|- | ..+.|.+||-++.
T Consensus 127 ~~~C~gC~~~~~~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 127 RKVCKGCKKKYPEDYPDDVCEICGSPVK 154 (164)
T ss_pred eEECCCCCccccCCCCCCcCCCCCChhh
Confidence 45688887 6 4467999998764
No 15
>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=49.46 E-value=3.2 Score=24.16 Aligned_cols=36 Identities=22% Similarity=0.662 Sum_probs=24.0
Q ss_pred cccchhhhcCC------CCC-ccccccccc----CccccCCcccccc
Q 034393 53 KCIICKQQVHQ------DAK-YCHTCAYSK----GVCAMCGKQVLDT 88 (96)
Q Consensus 53 ~C~~CK~~v~q------~~~-YCq~CAYkk----giCamCGKki~dt 88 (96)
.|.+|...... +|. +|..|+.+- ..|++|-..|.++
T Consensus 4 ~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~V 50 (50)
T PF13920_consen 4 ECPICFENPRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIESV 50 (50)
T ss_dssp B-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SEE
T ss_pred CCccCCccCCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcCC
Confidence 56666664322 255 789998766 8999999988754
No 16
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=49.45 E-value=6.9 Score=24.83 Aligned_cols=19 Identities=26% Similarity=0.691 Sum_probs=12.9
Q ss_pred CCCCCCccccchhhhcCCC
Q 034393 46 WTPYGNTKCIICKQQVHQD 64 (96)
Q Consensus 46 ~~py~~~~C~~CK~~v~q~ 64 (96)
|+|-+..+|+.|++++..+
T Consensus 2 yAks~Ra~Ck~C~~~I~kg 20 (82)
T PF00645_consen 2 YAKSGRAKCKGCKKKIAKG 20 (82)
T ss_dssp E-SSSTEBETTTSCBE-TT
T ss_pred cCCCCCccCcccCCcCCCC
Confidence 4555557999999988765
No 17
>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=47.82 E-value=7.7 Score=31.94 Aligned_cols=35 Identities=26% Similarity=0.657 Sum_probs=24.5
Q ss_pred cccchhhh----------cC-CCCCcccccccc-----cCccccCCccccc
Q 034393 53 KCIICKQQ----------VH-QDAKYCHTCAYS-----KGVCAMCGKQVLD 87 (96)
Q Consensus 53 ~C~~CK~~----------v~-q~~~YCq~CAYk-----kgiCamCGKki~d 87 (96)
.|.+|++. |+ =+|.+|.+|-=. .+.|+.|++.+.-
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 68888872 33 148899999633 3489999987653
No 18
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=45.58 E-value=10 Score=23.18 Aligned_cols=16 Identities=44% Similarity=0.798 Sum_probs=11.5
Q ss_pred ccccCCcccccccccc
Q 034393 77 VCAMCGKQVLDTKFYK 92 (96)
Q Consensus 77 iCamCGKki~dt~~y~ 92 (96)
+|++||++|-=.+.++
T Consensus 1 ~C~iCg~kigl~~~~k 16 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFK 16 (51)
T ss_pred CCCcccccccccccee
Confidence 5899999886555443
No 19
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=45.12 E-value=9.7 Score=26.19 Aligned_cols=36 Identities=28% Similarity=0.766 Sum_probs=24.8
Q ss_pred CCCCCccccchhhhc---CCCCCcccccccccCccccCCcc
Q 034393 47 TPYGNTKCIICKQQV---HQDAKYCHTCAYSKGVCAMCGKQ 84 (96)
Q Consensus 47 ~py~~~~C~~CK~~v---~q~~~YCq~CAYkkgiCamCGKk 84 (96)
..|+...|..|-+.+ -..+..|..|.+ -+|+.||..
T Consensus 50 ~~~~~~~C~~C~~~fg~l~~~~~~C~~C~~--~VC~~C~~~ 88 (118)
T PF02318_consen 50 QKYGERHCARCGKPFGFLFNRGRVCVDCKH--RVCKKCGVY 88 (118)
T ss_dssp TTHCCSB-TTTS-BCSCTSTTCEEETTTTE--EEETTSEEE
T ss_pred cccCCcchhhhCCcccccCCCCCcCCcCCc--cccCccCCc
Confidence 345656999997753 333889999954 499999876
No 20
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.99 E-value=13 Score=31.01 Aligned_cols=36 Identities=33% Similarity=0.894 Sum_probs=28.2
Q ss_pred cccchhhhcCC------CCCcccccc---ccc-CccccCCcccccc
Q 034393 53 KCIICKQQVHQ------DAKYCHTCA---YSK-GVCAMCGKQVLDT 88 (96)
Q Consensus 53 ~C~~CK~~v~q------~~~YCq~CA---Ykk-giCamCGKki~dt 88 (96)
.|.||+..... +|++|-.|| |++ -.|-+|++++...
T Consensus 243 ~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~ 288 (313)
T KOG1813|consen 243 KCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGS 288 (313)
T ss_pred cccccccccccchhhcCCceeehhhhccccccCCcceecccccccc
Confidence 89999875322 388999999 777 5899999987643
No 21
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=42.39 E-value=12 Score=23.73 Aligned_cols=14 Identities=36% Similarity=0.890 Sum_probs=10.9
Q ss_pred cccCccccCCcccc
Q 034393 73 YSKGVCAMCGKQVL 86 (96)
Q Consensus 73 YkkgiCamCGKki~ 86 (96)
|...+|..||+++.
T Consensus 3 ~~~~~C~~Cg~~~~ 16 (54)
T PF14446_consen 3 YEGCKCPVCGKKFK 16 (54)
T ss_pred ccCccChhhCCccc
Confidence 56778888888885
No 22
>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=42.15 E-value=11 Score=20.96 Aligned_cols=12 Identities=33% Similarity=1.132 Sum_probs=9.2
Q ss_pred CccccCCccccc
Q 034393 76 GVCAMCGKQVLD 87 (96)
Q Consensus 76 giCamCGKki~d 87 (96)
|+|..||..|.+
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 679999999875
No 23
>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=39.95 E-value=20 Score=21.71 Aligned_cols=17 Identities=29% Similarity=0.747 Sum_probs=14.6
Q ss_pred cchHHHHhhcCcccCCc
Q 034393 2 VCEKCEKKLSKVIVPDK 18 (96)
Q Consensus 2 VC~KCeKKl~klatPd~ 18 (96)
.|..||++|-.+-+-||
T Consensus 20 IC~~CE~~iv~~~~~d~ 36 (46)
T PF10764_consen 20 ICSDCEKEIVNTETDDP 36 (46)
T ss_pred ehHHHHHHhccCCCCCC
Confidence 59999999998877776
No 24
>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=39.15 E-value=7.1 Score=18.37 Aligned_cols=15 Identities=27% Similarity=0.645 Sum_probs=8.4
Q ss_pred ccccCCccccccccc
Q 034393 77 VCAMCGKQVLDTKFY 91 (96)
Q Consensus 77 iCamCGKki~dt~~y 91 (96)
.|.+||+...+-..+
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 478888877655444
No 25
>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=35.39 E-value=16 Score=23.95 Aligned_cols=30 Identities=30% Similarity=0.858 Sum_probs=17.2
Q ss_pred cccchhhhcCCC------CCcccccccccCccccCCcc
Q 034393 53 KCIICKQQVHQD------AKYCHTCAYSKGVCAMCGKQ 84 (96)
Q Consensus 53 ~C~~CK~~v~q~------~~YCq~CAYkkgiCamCGKk 84 (96)
.|.+||+.+..+ ..-|-.| +.-+|.+||-.
T Consensus 4 ~CPlCkt~~n~gsk~~pNyntCT~C--k~~VCnlCGFN 39 (61)
T PF05715_consen 4 LCPLCKTTLNVGSKDPPNYNTCTEC--KSQVCNLCGFN 39 (61)
T ss_pred cCCcccchhhcCCCCCCCccHHHHH--hhhhhcccCCC
Confidence 566666655222 3345555 45578888854
No 26
>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=33.89 E-value=13 Score=26.55 Aligned_cols=31 Identities=35% Similarity=1.026 Sum_probs=16.4
Q ss_pred ccccchhhhcCCC--CCcccccccc--cCccccCC
Q 034393 52 TKCIICKQQVHQD--AKYCHTCAYS--KGVCAMCG 82 (96)
Q Consensus 52 ~~C~~CK~~v~q~--~~YCq~CAYk--kgiCamCG 82 (96)
.+|.||-+-|.+. -+-|+.|.|- .+.|-|||
T Consensus 28 GkCpiCDS~Vrp~~~VrICdeCs~G~~~~rCIiCg 62 (106)
T PF03660_consen 28 GKCPICDSYVRPCTKVRICDECSFGSLQGRCIICG 62 (106)
T ss_dssp T--TTT-------EE-EEEHHHHTSSTTSB-TTTS
T ss_pred CcccccCCccCCcceEEECCcCCCCCcCceEEEec
Confidence 5889999888876 7889999875 46899999
No 27
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=33.26 E-value=16 Score=26.16 Aligned_cols=32 Identities=38% Similarity=0.778 Sum_probs=22.8
Q ss_pred ceeccccccccccCCCCCCCccccchhhhcCCCCCccccccc
Q 034393 32 RKVNENKLLSKKKRWTPYGNTKCIICKQQVHQDAKYCHTCAY 73 (96)
Q Consensus 32 r~i~eNKlLs~k~r~~py~~~~C~~CK~~v~q~~~YCq~CAY 73 (96)
+.+.++||+ + .+|..|-.-.+.+..+|..|-.
T Consensus 20 ~~l~~~kl~---------g-~kC~~CG~v~~PPr~~Cp~C~~ 51 (140)
T COG1545 20 KGLKEGKLL---------G-TKCKKCGRVYFPPRAYCPKCGS 51 (140)
T ss_pred hhhhhCcEE---------E-EEcCCCCeEEcCCcccCCCCCC
Confidence 345566666 2 3899998888888887777643
No 28
>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=31.88 E-value=18 Score=20.72 Aligned_cols=9 Identities=44% Similarity=1.021 Sum_probs=2.0
Q ss_pred ccCCCCCCC
Q 034393 43 KKRWTPYGN 51 (96)
Q Consensus 43 k~r~~py~~ 51 (96)
-+||.||++
T Consensus 18 g~rfEPY~N 26 (30)
T PF11532_consen 18 GNRFEPYAN 26 (30)
T ss_dssp -----SS--
T ss_pred CcccccccC
Confidence 369999986
No 29
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=31.31 E-value=18 Score=22.49 Aligned_cols=15 Identities=33% Similarity=0.516 Sum_probs=10.7
Q ss_pred CccccCCcccccccc
Q 034393 76 GVCAMCGKQVLDTKF 90 (96)
Q Consensus 76 giCamCGKki~dt~~ 90 (96)
-+|+.||+.+.+...
T Consensus 7 Y~C~~Cg~~~~~~~~ 21 (49)
T COG1996 7 YKCARCGREVELDQE 21 (49)
T ss_pred EEhhhcCCeeehhhc
Confidence 378899988864443
No 30
>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=30.24 E-value=22 Score=24.23 Aligned_cols=11 Identities=36% Similarity=1.051 Sum_probs=8.9
Q ss_pred CccccCCcccc
Q 034393 76 GVCAMCGKQVL 86 (96)
Q Consensus 76 giCamCGKki~ 86 (96)
|+|-.||..|-
T Consensus 81 G~C~~Cge~I~ 91 (110)
T TIGR02420 81 GYCEECGEEIG 91 (110)
T ss_pred CchhccCCccc
Confidence 68899998874
No 31
>PHA02094 hypothetical protein
Probab=29.84 E-value=26 Score=23.84 Aligned_cols=11 Identities=27% Similarity=0.782 Sum_probs=9.7
Q ss_pred cccCCccCCCC
Q 034393 13 VIVPDKWKEGA 23 (96)
Q Consensus 13 latPd~~k~g~ 23 (96)
+|-|+|||||-
T Consensus 65 vakpnpfrdgv 75 (81)
T PHA02094 65 VAKPNPFRDGV 75 (81)
T ss_pred ccCCCCCccce
Confidence 89999999974
No 32
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=29.50 E-value=13 Score=31.62 Aligned_cols=45 Identities=36% Similarity=0.840 Sum_probs=32.6
Q ss_pred eecccccccc-ccCCCCCCCccccchhhhcC---------CC---CCcccccccccCccccC
Q 034393 33 KVNENKLLSK-KKRWTPYGNTKCIICKQQVH---------QD---AKYCHTCAYSKGVCAMC 81 (96)
Q Consensus 33 ~i~eNKlLs~-k~r~~py~~~~C~~CK~~v~---------q~---~~YCq~CAYkkgiCamC 81 (96)
=+|+|-.+.. | .||++ -|+||-.... +. -.-||.||=.|++|.-|
T Consensus 26 CLGdnpyvRMtK---~~~gk-ECKICtrPfT~Frw~pgr~~r~kKTeICqtCaklKNvCQ~C 83 (377)
T KOG0153|consen 26 CLGDNPYVRMTK---EPYGK-ECKICTRPFTIFRWCPGRGARFKKTEICQTCAKLKNVCQTC 83 (377)
T ss_pred hcCCCceeeeec---cccCC-ccceecCcceEEEeccccccccccchHHHHHHHHHhHHHHh
Confidence 3577776655 5 57888 9999976431 11 34699999999999988
No 33
>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=29.35 E-value=10 Score=25.14 Aligned_cols=35 Identities=23% Similarity=0.643 Sum_probs=20.8
Q ss_pred cccchhhhcCCC--CCcccccc---cccCccccCCccccc
Q 034393 53 KCIICKQQVHQD--AKYCHTCA---YSKGVCAMCGKQVLD 87 (96)
Q Consensus 53 ~C~~CK~~v~q~--~~YCq~CA---YkkgiCamCGKki~d 87 (96)
.|..|.+.+... .-+|..|. -+.+.|+-||..+--
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 688888888554 56788876 345789999887753
No 34
>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=28.99 E-value=30 Score=22.90 Aligned_cols=20 Identities=40% Similarity=0.733 Sum_probs=17.0
Q ss_pred cchHHHHhhc-CcccCCccCC
Q 034393 2 VCEKCEKKLS-KVIVPDKWKE 21 (96)
Q Consensus 2 VC~KCeKKl~-klatPd~~k~ 21 (96)
+|.+|.|-|+ ..--|-+||+
T Consensus 56 pC~~C~klL~~~~~LPP~~r~ 76 (90)
T PF11571_consen 56 PCKKCGKLLSSKAFLPPVRRP 76 (90)
T ss_pred hhhHHHhHhhhcccCCCeeec
Confidence 6999999996 5788889994
No 35
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=28.69 E-value=27 Score=24.95 Aligned_cols=32 Identities=38% Similarity=1.064 Sum_probs=21.8
Q ss_pred ccccchhhhcCCC--CCcccccccc--cCccccCCc
Q 034393 52 TKCIICKQQVHQD--AKYCHTCAYS--KGVCAMCGK 83 (96)
Q Consensus 52 ~~C~~CK~~v~q~--~~YCq~CAYk--kgiCamCGK 83 (96)
.+|.||-+-|..- --.|..|+|- .+-|-+||-
T Consensus 28 gkC~ICDS~VRP~tlVRiC~eC~~Gs~q~~ciic~~ 63 (110)
T KOG1705|consen 28 GKCVICDSYVRPCTLVRICDECNYGSYQGRCVICGG 63 (110)
T ss_pred CcccccccccccceeeeeehhcCCccccCceEEecC
Confidence 4777777777665 5567777774 355777765
No 36
>PRK11595 DNA utilization protein GntX; Provisional
Probab=27.77 E-value=34 Score=25.68 Aligned_cols=33 Identities=24% Similarity=0.706 Sum_probs=15.6
Q ss_pred cccchhhhcCCC-CCcccccccc----cCccccCCccc
Q 034393 53 KCIICKQQVHQD-AKYCHTCAYS----KGVCAMCGKQV 85 (96)
Q Consensus 53 ~C~~CK~~v~q~-~~YCq~CAYk----kgiCamCGKki 85 (96)
.|-.|...++.. ...|..|.-+ ...|..||+.+
T Consensus 7 ~C~~C~~~~~~~~~~lC~~C~~~l~~~~~~C~~Cg~~~ 44 (227)
T PRK11595 7 LCWLCRMPLALSHWGICSVCSRALRTLKTCCPQCGLPA 44 (227)
T ss_pred cCccCCCccCCCCCcccHHHHhhCCcccCcCccCCCcC
Confidence 455555555433 2345555311 23466666543
No 37
>smart00746 TRASH metallochaperone-like domain.
Probab=27.25 E-value=30 Score=16.58 Aligned_cols=10 Identities=40% Similarity=1.388 Sum_probs=7.9
Q ss_pred cccCCccccc
Q 034393 78 CAMCGKQVLD 87 (96)
Q Consensus 78 CamCGKki~d 87 (96)
|+.||..|.+
T Consensus 1 c~~C~~~~~~ 10 (39)
T smart00746 1 CSFCGKDIYN 10 (39)
T ss_pred CCCCCCCccC
Confidence 7889998863
No 38
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.15 E-value=21 Score=29.84 Aligned_cols=16 Identities=44% Similarity=0.839 Sum_probs=13.2
Q ss_pred ccCccccCCccccccc
Q 034393 74 SKGVCAMCGKQVLDTK 89 (96)
Q Consensus 74 kkgiCamCGKki~dt~ 89 (96)
..++||.||+++.++-
T Consensus 223 ~d~vCaVCg~~~~~s~ 238 (328)
T KOG1734|consen 223 SDSVCAVCGQQIDVSV 238 (328)
T ss_pred CcchhHhhcchheeec
Confidence 3579999999998764
No 39
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=26.42 E-value=33 Score=25.97 Aligned_cols=14 Identities=21% Similarity=0.850 Sum_probs=11.2
Q ss_pred cccCccccCCcccc
Q 034393 73 YSKGVCAMCGKQVL 86 (96)
Q Consensus 73 YkkgiCamCGKki~ 86 (96)
-+.|.||+||..+.
T Consensus 18 ~Q~G~CaiC~~~l~ 31 (157)
T PHA02565 18 AQNGICPLCKRELD 31 (157)
T ss_pred HhCCcCCCCCCccC
Confidence 35789999998865
No 40
>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=25.62 E-value=37 Score=21.71 Aligned_cols=11 Identities=36% Similarity=0.915 Sum_probs=8.3
Q ss_pred ccCccccCCcc
Q 034393 74 SKGVCAMCGKQ 84 (96)
Q Consensus 74 kkgiCamCGKk 84 (96)
.+++|..||..
T Consensus 4 ~~~~C~~Cg~r 14 (69)
T PF09706_consen 4 KKYNCIFCGER 14 (69)
T ss_pred CCCcCcCCCCc
Confidence 36799999943
No 41
>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=25.37 E-value=34 Score=21.70 Aligned_cols=11 Identities=36% Similarity=1.005 Sum_probs=7.8
Q ss_pred ccccCCccccc
Q 034393 77 VCAMCGKQVLD 87 (96)
Q Consensus 77 iCamCGKki~d 87 (96)
.|+.||++|.+
T Consensus 80 ~C~vC~k~l~~ 90 (109)
T PF10367_consen 80 KCSVCGKPLGN 90 (109)
T ss_pred CccCcCCcCCC
Confidence 57777777765
No 42
>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=25.09 E-value=27 Score=23.24 Aligned_cols=14 Identities=43% Similarity=0.904 Sum_probs=8.4
Q ss_pred cccCccccCCcccc
Q 034393 73 YSKGVCAMCGKQVL 86 (96)
Q Consensus 73 YkkgiCamCGKki~ 86 (96)
.+.|.|++||.+..
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 45689999998443
No 43
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=24.23 E-value=36 Score=26.12 Aligned_cols=24 Identities=29% Similarity=0.749 Sum_probs=16.5
Q ss_pred cccchhhhcCCCCCcccccccccCccccCCcccc
Q 034393 53 KCIICKQQVHQDAKYCHTCAYSKGVCAMCGKQVL 86 (96)
Q Consensus 53 ~C~~CK~~v~q~~~YCq~CAYkkgiCamCGKki~ 86 (96)
.|.-|+.-.+ +.+++|+.||=++.
T Consensus 141 rC~GC~~~f~----------~~~~~Cp~CG~~~~ 164 (177)
T COG1439 141 RCHGCKRIFP----------EPKDFCPICGSPLK 164 (177)
T ss_pred EEecCceecC----------CCCCcCCCCCCceE
Confidence 6777776665 44678888887654
No 44
>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=24.01 E-value=35 Score=24.87 Aligned_cols=29 Identities=31% Similarity=0.882 Sum_probs=19.3
Q ss_pred ccccchhh-------hcCCCCCcccccccccCccccCCccc
Q 034393 52 TKCIICKQ-------QVHQDAKYCHTCAYSKGVCAMCGKQV 85 (96)
Q Consensus 52 ~~C~~CK~-------~v~q~~~YCq~CAYkkgiCamCGKki 85 (96)
+-|.+|-. .+.++..-| +.|.|.|||++-
T Consensus 35 GLC~~CL~sa~~ty~e~~~~~~s~-----~~gKC~LCG~kt 70 (119)
T PF10621_consen 35 GLCETCLDSAEKTYQEVNENESSC-----RSGKCDLCGKKT 70 (119)
T ss_pred hhHHHHHHHHHHHHHHHhcccccc-----cccceeccCCcc
Confidence 37777743 344554433 789999999873
No 45
>PHA03096 p28-like protein; Provisional
Probab=23.67 E-value=19 Score=29.03 Aligned_cols=24 Identities=38% Similarity=0.813 Sum_probs=18.6
Q ss_pred ccccccC-ccccCCccccccccccc
Q 034393 70 TCAYSKG-VCAMCGKQVLDTKFYKQ 93 (96)
Q Consensus 70 ~CAYkkg-iCamCGKki~dt~~y~q 93 (96)
.|.|-.| +|.|||+..++...+.|
T Consensus 136 ~c~~lHg~lC~~C~k~~Lhp~d~eq 160 (284)
T PHA03096 136 YCEYLHGDICDICEKYLLHPTDIKQ 160 (284)
T ss_pred CcHHHHHHHHHhhcchhcCCcCHHH
Confidence 4566555 69999999999877655
No 46
>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=23.16 E-value=50 Score=19.10 Aligned_cols=13 Identities=38% Similarity=0.854 Sum_probs=10.6
Q ss_pred CcccCCccCCCCC
Q 034393 12 KVIVPDKWKEGAS 24 (96)
Q Consensus 12 klatPd~~k~g~~ 24 (96)
.++||.-|+.|..
T Consensus 9 ~v~tPanW~pGd~ 21 (40)
T PF10417_consen 9 GVATPANWKPGDD 21 (40)
T ss_dssp SSBBCTTTCTTSG
T ss_pred CcccCcCCCCCCC
Confidence 4899999998643
No 47
>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=23.13 E-value=34 Score=17.70 Aligned_cols=20 Identities=25% Similarity=0.884 Sum_probs=12.7
Q ss_pred CCccccccc-----ccCccccCCcc
Q 034393 65 AKYCHTCAY-----SKGVCAMCGKQ 84 (96)
Q Consensus 65 ~~YCq~CAY-----kkgiCamCGKk 84 (96)
+.||..|.. ....|.+|...
T Consensus 20 H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 20 HVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred ChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 667777753 24568888654
No 48
>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=22.67 E-value=38 Score=26.49 Aligned_cols=20 Identities=40% Similarity=0.999 Sum_probs=16.9
Q ss_pred ccccchhhhcCCCCCccccc
Q 034393 52 TKCIICKQQVHQDAKYCHTC 71 (96)
Q Consensus 52 ~~C~~CK~~v~q~~~YCq~C 71 (96)
..|..|-|++|.++--|.-|
T Consensus 195 K~C~sC~qqIHRNAPiCPlC 214 (230)
T PF10146_consen 195 KTCQSCHQQIHRNAPICPLC 214 (230)
T ss_pred chhHhHHHHHhcCCCCCccc
Confidence 68999999999998855555
No 49
>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=22.04 E-value=38 Score=28.34 Aligned_cols=28 Identities=25% Similarity=0.617 Sum_probs=19.6
Q ss_pred ccccchhhhcCCC-CCcccccccccCccccCCcccc
Q 034393 52 TKCIICKQQVHQD-AKYCHTCAYSKGVCAMCGKQVL 86 (96)
Q Consensus 52 ~~C~~CK~~v~q~-~~YCq~CAYkkgiCamCGKki~ 86 (96)
..|+.|...+... .. ++ .++|+ ||++|.
T Consensus 241 ~~c~~C~~~~~~~~~~-----~~-~~~Cp-CG~~i~ 269 (374)
T TIGR00375 241 TACEACGEPAVSEDAE-----TA-CANCP-CGGRIK 269 (374)
T ss_pred hhhcccCCcCCchhhh-----hc-CCCCC-CCCcce
Confidence 5888888777644 22 22 58999 999853
No 50
>KOG4217 consensus Nuclear receptors of the nerve growth factor-induced protein B type [Transcription]
Probab=21.56 E-value=33 Score=30.69 Aligned_cols=29 Identities=41% Similarity=0.929 Sum_probs=21.5
Q ss_pred CCCCCccccchhh----hcCCCCCc-----------------cccccccc
Q 034393 47 TPYGNTKCIICKQ----QVHQDAKY-----------------CHTCAYSK 75 (96)
Q Consensus 47 ~py~~~~C~~CK~----~v~q~~~Y-----------------Cq~CAYkk 75 (96)
.-||-..|.-||- .|..+++| ||.|+|+|
T Consensus 282 qHYGvRTCEGCKGFFKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQK 331 (605)
T KOG4217|consen 282 QHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQK 331 (605)
T ss_pred hhcCccccccchHHHHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhH
Confidence 5677678988874 45555666 99999987
No 51
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.55 E-value=61 Score=28.53 Aligned_cols=43 Identities=28% Similarity=0.763 Sum_probs=27.5
Q ss_pred cCCCCCCC-------ccccchhhhc--CCC--CCcccccccccC---ccccCCcccc
Q 034393 44 KRWTPYGN-------TKCIICKQQV--HQD--AKYCHTCAYSKG---VCAMCGKQVL 86 (96)
Q Consensus 44 ~r~~py~~-------~~C~~CK~~v--~q~--~~YCq~CAYkkg---iCamCGKki~ 86 (96)
.-|+|+-. ..|..|-..+ |+. .-.|+.|.|... .|.-||...+
T Consensus 376 rGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l 432 (679)
T PRK05580 376 RGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDL 432 (679)
T ss_pred CCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCCee
Confidence 34777632 2444554443 443 456999999865 7999998654
No 52
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=21.37 E-value=53 Score=28.39 Aligned_cols=37 Identities=22% Similarity=0.613 Sum_probs=26.4
Q ss_pred cCCCCCCCccccchhhhcCCCCCccccccc-----ccCccccCCcccc
Q 034393 44 KRWTPYGNTKCIICKQQVHQDAKYCHTCAY-----SKGVCAMCGKQVL 86 (96)
Q Consensus 44 ~r~~py~~~~C~~CK~~v~q~~~YCq~CAY-----kkgiCamCGKki~ 86 (96)
+||.|+.. . +-..++...|..|-| +++.|..||-++-
T Consensus 205 e~~~pq~~-~-----~~~~~~~~~C~~C~~~~~~~~~~~CpRC~~~Ly 246 (418)
T COG2995 205 ERFYPQTL-A-----TGAREGLRSCLCCHYILPHDAEPRCPRCGSKLY 246 (418)
T ss_pred HhhccccC-C-----CCCcccceecccccccCCHhhCCCCCCCCChhh
Confidence 36666654 1 445556788888876 5889999998763
No 53
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=20.91 E-value=23 Score=17.43 Aligned_cols=15 Identities=20% Similarity=0.625 Sum_probs=9.1
Q ss_pred cccCCcccccccccc
Q 034393 78 CAMCGKQVLDTKFYK 92 (96)
Q Consensus 78 CamCGKki~dt~~y~ 92 (96)
|.+|++...+-..|+
T Consensus 3 C~~C~~~f~s~~~~~ 17 (25)
T PF12874_consen 3 CDICNKSFSSENSLR 17 (25)
T ss_dssp ETTTTEEESSHHHHH
T ss_pred CCCCCCCcCCHHHHH
Confidence 677777666554443
No 54
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=20.76 E-value=29 Score=18.43 Aligned_cols=21 Identities=19% Similarity=0.634 Sum_probs=7.4
Q ss_pred cccchhhhcCC-CCCccccccc
Q 034393 53 KCIICKQQVHQ-DAKYCHTCAY 73 (96)
Q Consensus 53 ~C~~CK~~v~q-~~~YCq~CAY 73 (96)
.|..|+..+.. ..-+|..|-|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf 23 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDF 23 (30)
T ss_dssp --TTTS----S--EEE-TTT--
T ss_pred cCCcCCCcCCCCceEECccCCC
Confidence 46777777766 4666666654
No 55
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=20.40 E-value=71 Score=26.67 Aligned_cols=49 Identities=27% Similarity=0.714 Sum_probs=36.5
Q ss_pred cccccc-ccCCCCCCCccccchhhhcCCC------CCcccccccccC--ccccCCcccc
Q 034393 37 NKLLSK-KKRWTPYGNTKCIICKQQVHQD------AKYCHTCAYSKG--VCAMCGKQVL 86 (96)
Q Consensus 37 NKlLs~-k~r~~py~~~~C~~CK~~v~q~------~~YCq~CAYkkg--iCamCGKki~ 86 (96)
|-+|.- -++|-||-- +|..|+.-+..+ .-||..|-=+-| ||.-|-++|-
T Consensus 149 ~~~l~fr~d~yH~yHF-kCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe 206 (332)
T KOG2272|consen 149 EQPLTFRGDPYHPYHF-KCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE 206 (332)
T ss_pred cccccccCCCCCccce-ecccccccccchhhhhccceeccccccccCCcccccccCchH
Confidence 467766 679999988 999999987543 679999975444 5666666654
No 56
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=20.25 E-value=23 Score=17.06 Aligned_cols=15 Identities=27% Similarity=0.660 Sum_probs=9.4
Q ss_pred ccccCCccccccccc
Q 034393 77 VCAMCGKQVLDTKFY 91 (96)
Q Consensus 77 iCamCGKki~dt~~y 91 (96)
.|..||+...+-..+
T Consensus 2 ~C~~C~~~f~~~~~l 16 (23)
T PF00096_consen 2 KCPICGKSFSSKSNL 16 (23)
T ss_dssp EETTTTEEESSHHHH
T ss_pred CCCCCCCccCCHHHH
Confidence 477788776654443
Done!