Query psy8090
Match_columns 242
No_of_seqs 360 out of 1593
Neff 7.3
Searched_HMMs 46136
Date Fri Aug 16 18:11:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8090.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8090hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06297 PET: PET Domain; Int 100.0 1.3E-33 2.8E-38 213.8 7.9 84 1-84 23-106 (106)
2 KOG1701|consensus 99.9 3.4E-26 7.4E-31 206.5 -1.1 128 88-234 276-406 (468)
3 KOG1701|consensus 99.8 4E-20 8.6E-25 167.4 4.1 129 87-225 335-467 (468)
4 KOG2272|consensus 99.7 4.4E-18 9.6E-23 145.0 -2.9 116 87-220 13-130 (332)
5 KOG4577|consensus 99.6 4E-17 8.7E-22 141.4 -2.3 126 88-231 35-164 (383)
6 KOG2272|consensus 99.6 5.4E-16 1.2E-20 132.3 0.1 111 88-218 197-310 (332)
7 KOG1703|consensus 99.5 3.7E-15 8.1E-20 141.4 5.2 125 87-230 304-430 (479)
8 PF00412 LIM: LIM domain; Int 99.5 1.5E-14 3.2E-19 98.3 3.6 58 89-150 1-58 (58)
9 KOG1703|consensus 99.5 6.4E-15 1.4E-19 139.8 2.2 114 86-217 363-478 (479)
10 KOG1044|consensus 99.3 8.3E-13 1.8E-17 123.9 1.3 87 87-193 134-220 (670)
11 KOG1044|consensus 99.1 2.6E-11 5.7E-16 114.0 2.7 112 109-233 82-203 (670)
12 smart00132 LIM Zinc-binding do 98.5 3.8E-08 8.2E-13 60.7 2.1 38 88-129 1-38 (39)
13 PF00412 LIM: LIM domain; Int 98.5 8.5E-08 1.8E-12 64.7 2.5 56 154-221 1-58 (58)
14 KOG1700|consensus 98.1 5.9E-07 1.3E-11 76.2 0.8 62 87-153 8-69 (200)
15 KOG4577|consensus 97.7 8.9E-06 1.9E-10 71.4 0.4 64 87-154 93-158 (383)
16 KOG1700|consensus 97.7 1.5E-05 3.2E-10 67.7 1.1 59 87-150 109-167 (200)
17 KOG1702|consensus 97.2 3.3E-05 7.1E-10 64.9 -2.2 59 88-151 6-64 (264)
18 KOG0490|consensus 96.1 0.001 2.3E-08 56.7 -1.1 112 91-220 1-119 (235)
19 smart00132 LIM Zinc-binding do 95.3 0.014 3.1E-07 35.2 2.2 30 153-194 1-30 (39)
20 PF10367 Vps39_2: Vacuolar sor 88.5 0.76 1.7E-05 34.1 4.1 31 85-119 77-107 (109)
21 PRK14890 putative Zn-ribbon RN 83.6 1.2 2.6E-05 30.3 2.6 48 87-158 8-55 (59)
22 PF14446 Prok-RING_1: Prokaryo 79.6 1.3 2.8E-05 29.6 1.6 33 150-192 4-36 (54)
23 cd06535 CIDE_N_CAD CIDE_N doma 74.9 0.74 1.6E-05 33.1 -0.6 23 12-34 54-76 (77)
24 PF07754 DUF1610: Domain of un 74.8 2.1 4.5E-05 23.8 1.4 15 89-103 1-15 (24)
25 smart00504 Ubox Modified RING 74.0 3 6.4E-05 27.8 2.3 45 119-164 2-48 (63)
26 cd06536 CIDE_N_ICAD CIDE_N dom 72.8 0.92 2E-05 32.8 -0.5 24 11-34 56-79 (80)
27 PF14835 zf-RING_6: zf-RING of 72.2 3.4 7.5E-05 28.6 2.2 47 119-165 8-54 (65)
28 PF11781 RRN7: RNA polymerase 71.1 2.4 5.2E-05 25.9 1.1 25 119-147 9-33 (36)
29 cd06538 CIDE_N_FSP27 CIDE_N do 71.0 1 2.2E-05 32.5 -0.6 24 11-34 53-76 (79)
30 COG1645 Uncharacterized Zn-fin 70.6 2.2 4.8E-05 33.7 1.2 22 120-146 30-51 (131)
31 PF09943 DUF2175: Uncharacteri 70.3 1.3 2.8E-05 33.5 -0.3 33 87-123 3-35 (101)
32 cd06539 CIDE_N_A CIDE_N domain 70.1 1.1 2.4E-05 32.2 -0.6 24 11-34 54-77 (78)
33 cd01615 CIDE_N CIDE_N domain, 69.1 1.2 2.7E-05 32.0 -0.5 23 12-34 55-77 (78)
34 smart00266 CAD Domains present 69.0 1.2 2.7E-05 31.7 -0.5 23 11-33 52-74 (74)
35 COG2888 Predicted Zn-ribbon RN 67.2 5.8 0.00013 27.0 2.4 28 87-128 10-37 (61)
36 cd06537 CIDE_N_B CIDE_N domain 67.2 1.4 3.1E-05 31.9 -0.5 24 11-34 53-76 (81)
37 PF08394 Arc_trans_TRASH: Arch 66.6 1.7 3.7E-05 26.8 -0.2 32 89-127 1-32 (37)
38 PF13920 zf-C3HC4_3: Zinc fing 62.9 11 0.00025 24.0 3.2 43 119-162 3-48 (50)
39 PF00645 zf-PARP: Poly(ADP-rib 59.8 2.5 5.4E-05 30.2 -0.4 45 146-193 2-47 (82)
40 COG2191 Formylmethanofuran deh 58.4 4.2 9.1E-05 34.5 0.7 31 119-149 173-203 (206)
41 PF10235 Cript: Microtubule-as 54.5 8.8 0.00019 28.4 1.7 42 114-163 40-81 (90)
42 PF06677 Auto_anti-p27: Sjogre 53.9 4.8 0.0001 25.3 0.2 9 136-144 31-39 (41)
43 PF12773 DZR: Double zinc ribb 52.9 21 0.00044 22.7 3.2 13 152-164 30-42 (50)
44 KOG1813|consensus 51.2 9.3 0.0002 34.3 1.7 44 119-163 242-287 (313)
45 PF01258 zf-dskA_traR: Prokary 51.2 3.9 8.4E-05 24.6 -0.5 10 89-98 6-15 (36)
46 PRK14559 putative protein seri 50.3 15 0.00032 36.8 3.1 12 88-99 3-14 (645)
47 PF02591 DUF164: Putative zinc 50.3 8.4 0.00018 25.5 1.0 54 64-128 3-56 (56)
48 KOG0320|consensus 47.1 11 0.00023 31.6 1.3 49 116-164 129-180 (187)
49 PF10367 Vps39_2: Vacuolar sor 46.8 13 0.00027 27.4 1.6 28 120-147 80-108 (109)
50 COG5152 Uncharacterized conser 45.8 7.3 0.00016 33.1 0.2 43 119-162 197-241 (259)
51 PF02017 CIDE-N: CIDE-N domain 44.4 2.9 6.2E-05 30.1 -2.1 23 12-34 55-77 (78)
52 cd00162 RING RING-finger (Real 43.5 16 0.00034 21.7 1.4 24 137-160 18-44 (45)
53 PF12674 Zn_ribbon_2: Putative 43.4 13 0.00027 26.9 1.1 29 120-148 2-35 (81)
54 PF14634 zf-RING_5: zinc-RING 42.8 23 0.0005 22.0 2.1 38 121-158 2-43 (44)
55 COG4357 Zinc finger domain con 41.7 5 0.00011 30.0 -1.3 45 89-138 38-82 (105)
56 PF13923 zf-C3HC4_2: Zinc fing 40.5 16 0.00035 22.0 1.1 37 121-157 1-39 (39)
57 PRK14873 primosome assembly pr 39.4 17 0.00037 36.5 1.7 39 119-160 393-431 (665)
58 COG4847 Uncharacterized protei 37.9 9.6 0.00021 28.4 -0.3 37 88-128 8-44 (103)
59 KOG0978|consensus 37.7 12 0.00026 37.6 0.2 14 152-165 679-692 (698)
60 KOG4739|consensus 36.5 24 0.00053 30.7 1.9 41 123-163 8-49 (233)
61 PF14471 DUF4428: Domain of un 35.6 24 0.00052 23.1 1.4 29 120-149 1-30 (51)
62 PF02069 Metallothio_Pro: Prok 34.4 24 0.00051 23.4 1.2 25 120-144 9-33 (52)
63 PLN03208 E3 ubiquitin-protein 34.3 33 0.00071 29.0 2.3 15 151-165 68-82 (193)
64 KOG1702|consensus 34.1 5.8 0.00013 33.9 -2.2 61 151-224 4-66 (264)
65 PRK04023 DNA polymerase II lar 33.0 43 0.00093 35.2 3.3 39 119-165 639-677 (1121)
66 cd02249 ZZ Zinc finger, ZZ typ 32.5 35 0.00076 21.5 1.8 9 140-148 24-32 (46)
67 PRK00398 rpoP DNA-directed RNA 32.2 33 0.00071 21.6 1.6 27 88-128 5-31 (46)
68 PRK00420 hypothetical protein; 32.1 21 0.00046 27.5 0.8 9 88-96 25-33 (112)
69 TIGR02420 dksA RNA polymerase- 30.7 30 0.00064 26.2 1.4 13 88-100 82-94 (110)
70 KOG0490|consensus 30.2 21 0.00045 30.0 0.5 48 184-232 16-69 (235)
71 cd02336 ZZ_RSC8 Zinc finger, Z 28.5 46 0.001 21.2 1.8 30 119-148 1-32 (45)
72 PF06906 DUF1272: Protein of u 27.9 77 0.0017 21.4 2.8 24 140-163 30-53 (57)
73 PF07191 zinc-ribbons_6: zinc- 27.3 19 0.00042 25.4 -0.2 10 88-97 3-12 (70)
74 TIGR00595 priA primosomal prot 27.1 37 0.0008 32.8 1.7 38 120-160 224-262 (505)
75 PRK11595 DNA utilization prote 26.5 56 0.0012 27.9 2.6 9 88-96 7-15 (227)
76 smart00291 ZnF_ZZ Zinc-binding 26.4 55 0.0012 20.4 1.9 9 140-148 28-36 (44)
77 PRK14714 DNA polymerase II lar 25.5 76 0.0016 34.3 3.6 50 87-164 668-722 (1337)
78 COG2075 RPL24A Ribosomal prote 22.8 67 0.0015 22.3 1.9 24 152-177 4-27 (66)
79 PRK10445 endonuclease VIII; Pr 22.6 1.4E+02 0.0031 26.1 4.5 42 29-75 167-210 (263)
80 PF04570 DUF581: Protein of un 22.6 47 0.001 22.5 1.0 24 120-143 18-43 (58)
81 PF01844 HNH: HNH endonuclease 22.4 29 0.00062 21.4 -0.0 33 187-222 14-46 (47)
82 PF15135 UPF0515: Uncharacteri 22.0 95 0.0021 27.4 3.0 54 88-164 134-187 (278)
83 PRK14810 formamidopyrimidine-D 21.8 1.5E+02 0.0034 26.1 4.5 43 29-75 170-213 (272)
84 COG4306 Uncharacterized protei 21.6 1.1E+02 0.0024 24.1 3.1 38 88-128 41-78 (160)
85 TIGR00577 fpg formamidopyrimid 20.9 1.7E+02 0.0037 25.8 4.6 44 29-75 171-214 (272)
86 PF00628 PHD: PHD-finger; Int 20.5 96 0.0021 19.4 2.2 34 180-218 17-50 (51)
87 PRK13945 formamidopyrimidine-D 20.5 1.6E+02 0.0036 26.0 4.4 27 49-75 197-223 (282)
No 1
>PF06297 PET: PET Domain; InterPro: IPR010442 The PET domain is a ~110 amino acid motif in the N-terminal part of LIM domain proteins. The domain was described in Drosophila proteins involved in cell differentiation and is named after Prickle, Espinas and Testin. PET domain proteins contain about three zinc-binding LIM domains (see PDOC00382 from INTERPRO, IPR001781 from INTERPRO) and are found among metazoans. The PET domain has been suggested to play a role in protein-protein interactions with proteins involved in planar polarity signalling or organisation of the cytoskeleton []. Some proteins known to contain a PET domain: Mammalian testin protein (Q9UGI8 from SWISSPROT), which may function as a tumour suppressor. Mammalian LIM domain only protein 6 (LMO6/Prickle3, O43900 from SWISSPROT). Fruit fly prickle (A1Z6W3 from SWISSPROT) and espinas (Q9U1I1 from SWISSPROT) proteins encoded by the tissue polarity gene prickle (pk), involved in the control of orientation of bristles and hairs. Mammalian prickle-like proteins 1 (Q96MT3 from SWISSPROT) and 2 (Q7Z3G6 from SWISSPROT). ; GO: 0008270 zinc ion binding
Probab=100.00 E-value=1.3e-33 Score=213.84 Aligned_cols=84 Identities=60% Similarity=0.924 Sum_probs=82.2
Q ss_pred CCCCCCChHHHHHHHhcCCCCCCCCcCChhHHHHHHHHhhhCCCCCCCchhcccCCHHHHHHHHHHHHHhhhhccCCCcc
Q psy8090 1 MLKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSAQRKREALGRGFV 80 (242)
Q Consensus 1 w~p~~~~~~~~~~y~~~lp~~~~p~~~s~g~~~r~~ql~~qlP~~d~~~~~c~~l~e~e~~~~~~f~~~~~~~~~g~g~v 80 (242)
||||||++++|++||++||++++|++||+||+||++||++|||+||.|++||++|+++|+++|++|+++|+++++|+|.|
T Consensus 23 WvPpgl~~~~v~~Ym~~LP~~~vP~~gS~Ge~~R~~QL~~QLP~hD~d~~~C~~Lse~E~k~l~~F~~~rk~~alG~G~V 102 (106)
T PF06297_consen 23 WVPPGLSPELVEQYMSCLPEEKVPVVGSPGEKYRRRQLLYQLPPHDLDPRYCHSLSEEEKKELEDFVKQRKEEALGVGTV 102 (106)
T ss_pred ecCCCCChHHHHHHHHhCCCcCCCCCCCHHHHHHHHHHHHcCCcccCCHHHHhhCCHHHHHHHHHHHHHHHHHcCCeeEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccc
Q psy8090 81 KQLV 84 (242)
Q Consensus 81 ~~~~ 84 (242)
+.+|
T Consensus 103 ~~~~ 106 (106)
T PF06297_consen 103 KELP 106 (106)
T ss_pred EeCC
Confidence 8754
No 2
>KOG1701|consensus
Probab=99.91 E-value=3.4e-26 Score=206.53 Aligned_cols=128 Identities=16% Similarity=0.292 Sum_probs=116.3
Q ss_pred ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCcc
Q psy8090 88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQD 167 (242)
Q Consensus 88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~~ 167 (242)
+|.+|+|.|.+...++. ||++.||..||+|.+|++.|.+..||..|+++||+.||.+. ..||..|+++|++.+
T Consensus 276 iC~~C~K~V~g~~~ac~----Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t-lekC~~Cg~~I~d~i-- 348 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAVE----AMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT-LEKCNKCGEPIMDRI-- 348 (468)
T ss_pred hhhhcCCcccCcchHHH----HhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHH-HHHHhhhhhHHHHHH--
Confidence 69999999999999987 89999999999999999999999999999999999999965 489999999999755
Q ss_pred eeeeeecCCCCCCCCCCCcccCCCccC--CCCCCCCCCccc-CCCCCCCHHHHhhhhcccccCCCCCCCC
Q psy8090 168 ILYYLTRDSERDLPDEYRTERLEHQRD--LPESYGTHRNSL-NKEQNHSFDNLLKSNLKKLSLADSDDVS 234 (242)
Q Consensus 168 ~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g~~~f~~-~d~~~yC~~cy~~~~a~kc~~~~~~~~~ 234 (242)
+.|+++.+|..||.+ +.+.+++..|++ .++++||++||+++||+||++|...++-
T Consensus 349 ------------LrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P 406 (468)
T KOG1701|consen 349 ------------LRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILP 406 (468)
T ss_pred ------------HHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccC
Confidence 578999999999943 457889998885 6999999999999999999999887653
No 3
>KOG1701|consensus
Probab=99.79 E-value=4e-20 Score=167.39 Aligned_cols=129 Identities=22% Similarity=0.392 Sum_probs=104.4
Q ss_pred cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCcccee-eCCeeccHhhhhcccCCCcccCCCcccCCC
Q psy8090 87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFY-RGDKLYCGRHHAETLKPRCSACDEECQTSS 165 (242)
Q Consensus 87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~-~dg~~yC~~~y~~~~~prC~~C~~~I~~~~ 165 (242)
.+|..|++.|.+ +++. |+|+.||+.||+|.+|++.|.+..|.+ .++++||..||+++|+|||+.|+++|++.+
T Consensus 335 ekC~~Cg~~I~d--~iLr----A~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~ 408 (468)
T KOG1701|consen 335 EKCNKCGEPIMD--RILR----ALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRD 408 (468)
T ss_pred HHHhhhhhHHHH--HHHH----hcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCC
Confidence 359999999986 6665 899999999999999999999888876 689999999999999999999999999876
Q ss_pred cc--eeeeeecCCCCCCCCCCCcccCCCccCCC-CCCCCCCcccCCCCCCCHHHHhhhhcccc
Q psy8090 166 QD--ILYYLTRDSERDLPDEYRTERLEHQRDLP-ESYGTHRNSLNKEQNHSFDNLLKSNLKKL 225 (242)
Q Consensus 166 ~~--~~~~~~~~~~~~~~~~~~~~h~~~f~~~~-~~~g~~~f~~~d~~~yC~~cy~~~~a~kc 225 (242)
.. ..++|..|+.+++. ||++..+. ..++ +..|..+|.+ |++.+|..|..+.....+
T Consensus 409 G~~etvRvvamdr~fHv~-CY~CEDCg--~~LS~e~e~qgCyPl-d~HllCk~Ch~~Rl~~~~ 467 (468)
T KOG1701|consen 409 GKDETVRVVAMDRDFHVN-CYKCEDCG--LLLSSEEEGQGCYPL-DGHLLCKTCHLKRLQAGS 467 (468)
T ss_pred CCcceEEEEEcccccccc-ceehhhcC--ccccccCCCCcceec-cCceeechhhhhhhcccC
Confidence 43 34555566666655 88776544 3443 6677788877 889999999998866554
No 4
>KOG2272|consensus
Probab=99.65 E-value=4.4e-18 Score=145.01 Aligned_cols=116 Identities=20% Similarity=0.365 Sum_probs=103.8
Q ss_pred cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCc
Q psy8090 87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQ 166 (242)
Q Consensus 87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~ 166 (242)
+.|.+|.....+.+.++. ..+..||..||+|+.|-+++.+.+||..+|+.||+.+|..+|+|-|..|++.|.++.
T Consensus 13 ~~C~RC~~gF~~~e~~vn----s~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGrV- 87 (332)
T KOG2272|consen 13 MVCERCRDGFEPAEKIVN----SNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGRV- 87 (332)
T ss_pred HHHHHHhccCCchhhhhc----cCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhHH-
Confidence 479999999999988886 678999999999999999999999999999999999999999999999999999753
Q ss_pred ceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCCCCCcccCCCCCCCHHHHhhh
Q psy8090 167 DILYYLTRDSERDLPDEYRTERLEHQRD--LPESYGTHRNSLNKEQNHSFDNLLKS 220 (242)
Q Consensus 167 ~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g~~~f~~~d~~~yC~~cy~~~ 220 (242)
+.+++..||+.||++ +.+.+...-|+-+.|+.+|.+|-.+.
T Consensus 88 -------------ikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~ 130 (332)
T KOG2272|consen 88 -------------IKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKE 130 (332)
T ss_pred -------------HHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhh
Confidence 466889999999943 34577888899999999999998884
No 5
>KOG4577|consensus
Probab=99.60 E-value=4e-17 Score=141.40 Aligned_cols=126 Identities=19% Similarity=0.374 Sum_probs=100.7
Q ss_pred ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCcc
Q psy8090 88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQD 167 (242)
Q Consensus 88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~~ 167 (242)
+|++|.+.|.+.. +.. .+++.||..|++|+.|...|.+ .+|.++|.+||+.+|.++|+.+|++|++.|.+..+
T Consensus 35 ~CagC~q~IlDrF-ilK----vl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqV- 107 (383)
T KOG4577|consen 35 ICAGCDQHILDRF-ILK----VLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQV- 107 (383)
T ss_pred cccchHHHHHHHH-HHH----HHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHH-
Confidence 7999999998753 333 6899999999999999999977 89999999999999999999999999999988652
Q ss_pred eeeeeecCCCCCCCCCCCcccCCCc----cCCCCCCCCCCcccCCCCCCCHHHHhhhhcccccCCCCC
Q psy8090 168 ILYYLTRDSERDLPDEYRTERLEHQ----RDLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLSLADSD 231 (242)
Q Consensus 168 ~~~~~~~~~~~~~~~~~~~~h~~~f----~~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~~~~~~ 231 (242)
|. .|..-.+|..|| |...-..|...|...|.+.+|.++|+..-++.|..++++
T Consensus 108 ----VR-------kAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd 164 (383)
T KOG4577|consen 108 ----VR-------KAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGD 164 (383)
T ss_pred ----HH-------HhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccccccc
Confidence 11 334566788888 333234455555567899999999999888888655554
No 6
>KOG2272|consensus
Probab=99.55 E-value=5.4e-16 Score=132.34 Aligned_cols=111 Identities=13% Similarity=0.239 Sum_probs=94.3
Q ss_pred ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCcc
Q psy8090 88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQD 167 (242)
Q Consensus 88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~~ 167 (242)
+|..|.++|.. .++. ++|+.||.++|+|+.|.+|+-+-..|++.|..||+.||.++|+..|..|+..|.++.
T Consensus 197 iCgaC~rpIee--rvi~----amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~v-- 268 (332)
T KOG2272|consen 197 ICGACRRPIEE--RVIF----AMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDV-- 268 (332)
T ss_pred ccccccCchHH--HHHH----HhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccH--
Confidence 68999999984 5565 899999999999999999999999999999999999999999999999999998653
Q ss_pred eeeeeecCCCCCCCCCCCcccCCCccCC---CCCCCCCCcccCCCCCCCHHHHh
Q psy8090 168 ILYYLTRDSERDLPDEYRTERLEHQRDL---PESYGTHRNSLNKEQNHSFDNLL 218 (242)
Q Consensus 168 ~~~~~~~~~~~~~~~~~~~~h~~~f~~~---~~~~g~~~f~~~d~~~yC~~cy~ 218 (242)
+.+.++.|-.+||.+. .+-.-...|.+-|..|+|..||.
T Consensus 269 ------------v~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~ 310 (332)
T KOG2272|consen 269 ------------VSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYD 310 (332)
T ss_pred ------------HHHhhhhhccccccccccccccccccceeeeccchHHHHHHh
Confidence 4668899999999321 12222346788899999999997
No 7
>KOG1703|consensus
Probab=99.55 E-value=3.7e-15 Score=141.43 Aligned_cols=125 Identities=17% Similarity=0.238 Sum_probs=109.5
Q ss_pred cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCc
Q psy8090 87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQ 166 (242)
Q Consensus 87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~ 166 (242)
..|..|++.|.....++ ++++.||+.+|.|..|...+....|...+|++||..||.+.++|+|.+|.++|.+..
T Consensus 304 p~c~~c~~~i~~~~~i~-----~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~- 377 (479)
T KOG1703|consen 304 PLCLSCNQKIRSVKVIV-----ALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEG- 377 (479)
T ss_pred ccccccccCcccceeEe-----eccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhH-
Confidence 47999999998843333 789999999999999999999888889999999999999999999999999999754
Q ss_pred ceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCCCCCcccCCCCCCCHHHHhhhhcccccCCCC
Q psy8090 167 DILYYLTRDSERDLPDEYRTERLEHQRD--LPESYGTHRNSLNKEQNHSFDNLLKSNLKKLSLADS 230 (242)
Q Consensus 167 ~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~~~~~ 230 (242)
+.+.++.||.+||.+ +...+....|...++.+||..||+++|.++|..+.-
T Consensus 378 -------------v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~ 430 (479)
T KOG1703|consen 378 -------------VCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKK 430 (479)
T ss_pred -------------hhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccc
Confidence 345689999999932 367888999999999999999999999989876643
No 8
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.50 E-value=1.5e-14 Score=98.32 Aligned_cols=58 Identities=26% Similarity=0.695 Sum_probs=53.0
Q ss_pred cccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhccc
Q psy8090 89 CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETL 150 (242)
Q Consensus 89 C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~ 150 (242)
|.+|+++|.+++.++. +.++.||++||+|..|+++|.+..|+..||++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~----~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIK----AMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEE----ETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEE----eCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 8899999998877654 679999999999999999999888999999999999999875
No 9
>KOG1703|consensus
Probab=99.49 E-value=6.4e-15 Score=139.81 Aligned_cols=114 Identities=17% Similarity=0.360 Sum_probs=97.9
Q ss_pred ccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCC
Q psy8090 86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSS 165 (242)
Q Consensus 86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~ 165 (242)
...|.+|+++|.+. .|. +++..||++||+|..|+++|....||..||.+||+.||.+++.++|..|+.+|+.+.
T Consensus 363 ~p~C~~C~~~i~~~--~v~----a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~ 436 (479)
T KOG1703|consen 363 RPNCKRCLLPILEE--GVC----ALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGS 436 (479)
T ss_pred CccccccCCchHHh--Hhh----hccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhh
Confidence 34799999999874 344 679999999999999999999999999999999999999999999999999988654
Q ss_pred cceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCCCCCcccCCCCCCCHHHH
Q psy8090 166 QDILYYLTRDSERDLPDEYRTERLEHQRD--LPESYGTHRNSLNKEQNHSFDNL 217 (242)
Q Consensus 166 ~~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g~~~f~~~d~~~yC~~cy 217 (242)
. .+.+.+..||..||.+ +...+.++.|..+.++|+|..|+
T Consensus 437 ~------------~ie~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 437 R------------QIEADGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHF 478 (479)
T ss_pred h------------HhhccCccccccceehhhhhccccCCceeecCCccccccCC
Confidence 3 2456889999999932 34577888899999999998775
No 10
>KOG1044|consensus
Probab=99.28 E-value=8.3e-13 Score=123.87 Aligned_cols=87 Identities=21% Similarity=0.532 Sum_probs=77.2
Q ss_pred cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCc
Q psy8090 87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQ 166 (242)
Q Consensus 87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~ 166 (242)
..|++|++.|..+..++ |+++.||..||+|..|...|.+ .|..+||.+||++||.+.|+-+|..|.+.|.++.
T Consensus 134 s~cagc~~~lk~gq~ll-----ald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fisgkv- 206 (670)
T KOG1044|consen 134 STCAGCGEELKNGQALL-----ALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKV- 206 (670)
T ss_pred ccccchhhhhhccceee-----eeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhhhhh-
Confidence 46999999999887766 8999999999999999999965 8999999999999999999999999999999753
Q ss_pred ceeeeeecCCCCCCCCCCCcccCCCcc
Q psy8090 167 DILYYLTRDSERDLPDEYRTERLEHQR 193 (242)
Q Consensus 167 ~~~~~~~~~~~~~~~~~~~~~h~~~f~ 193 (242)
+.|-++.+|+.|-+
T Consensus 207 -------------Lqag~kh~HPtCAR 220 (670)
T KOG1044|consen 207 -------------LQAGDKHFHPTCAR 220 (670)
T ss_pred -------------hhccCcccCcchhh
Confidence 45567788888873
No 11
>KOG1044|consensus
Probab=99.11 E-value=2.6e-11 Score=113.96 Aligned_cols=112 Identities=13% Similarity=0.153 Sum_probs=85.2
Q ss_pred CCCCcccCCcccccccCCCCCCc-cceeeCCeeccHhhhhc-------c-cCCCcccCCCcccCCCcceeeeeecCCCCC
Q psy8090 109 GPNSCWHPGCFTCSVCNELLVDL-IYFYRGDKLYCGRHHAE-------T-LKPRCSACDEECQTSSQDILYYLTRDSERD 179 (242)
Q Consensus 109 ~~~~~wH~~CF~C~~C~~~L~~~-~~~~~dg~~yC~~~y~~-------~-~~prC~~C~~~I~~~~~~~~~~~~~~~~~~ 179 (242)
++|+.||+.||.|++|..++... ....-.....|..|-.- . ....|++|++.|..+..
T Consensus 82 a~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~------------- 148 (670)
T KOG1044|consen 82 TLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQA------------- 148 (670)
T ss_pred cccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccce-------------
Confidence 78999999999999999998533 33334445677777642 1 22579999999987652
Q ss_pred CCCCCCcccCCCc-cCCCCCCCCCCcccCCCCCCCHHHHhhhhcccccCCCCCCC
Q psy8090 180 LPDEYRTERLEHQ-RDLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLSLADSDDV 233 (242)
Q Consensus 180 ~~~~~~~~h~~~f-~~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~~~~~~~~ 233 (242)
+.|.++.||..|| |......-...|..+|+.|||..||..+|.-||..|...+.
T Consensus 149 llald~qwhv~cfkc~~c~~vL~gey~skdg~pyce~dy~~~fgvkc~~c~~fis 203 (670)
T KOG1044|consen 149 LLALDKQWHVSCFKCKSCSAVLNGEYMSKDGVPYCEKDYQAKFGVKCEECEKFIS 203 (670)
T ss_pred eeeeccceeeeeeehhhhcccccceeeccCCCcchhhhhhhhcCeehHHhhhhhh
Confidence 4568899999999 43222344556899999999999999999999988876554
No 12
>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=98.55 E-value=3.8e-08 Score=60.71 Aligned_cols=38 Identities=29% Similarity=0.823 Sum_probs=32.4
Q ss_pred ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCC
Q psy8090 88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV 129 (242)
Q Consensus 88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~ 129 (242)
+|.+|+++|.+++..+. +.+..||+.||+|..|+++|.
T Consensus 1 ~C~~C~~~i~~~~~~~~----~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLR----ALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEE----eCCccccccCCCCcccCCcCc
Confidence 48999999998744554 679999999999999999985
No 13
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=98.48 E-value=8.5e-08 Score=64.73 Aligned_cols=56 Identities=11% Similarity=-0.009 Sum_probs=44.5
Q ss_pred cccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhh
Q psy8090 154 CSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSN 221 (242)
Q Consensus 154 C~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~ 221 (242)
|++|+++|.+....+ .+.++.||.+||. .+..++....|...++++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~------------~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVI------------KAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEE------------EETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEE------------EeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 789999999765311 2378899999993 2446777777999999999999999876
No 14
>KOG1700|consensus
Probab=98.15 E-value=5.9e-07 Score=76.22 Aligned_cols=62 Identities=21% Similarity=0.442 Sum_probs=52.6
Q ss_pred cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCC
Q psy8090 87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPR 153 (242)
Q Consensus 87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~pr 153 (242)
..|..|++.+...+.+. ..+..||..||.|..|.+.|....+..+++.+||..+|...++|+
T Consensus 8 ~kc~~c~k~vy~~e~~~-----~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~ 69 (200)
T KOG1700|consen 8 DKCNACGKTVYFVEKVQ-----KDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPK 69 (200)
T ss_pred chhhhccCcchHHHHHh-----ccCcchhhhHHhccccccccccccccccccccccccchHhhhCcc
Confidence 36999999998766543 568899999999999999999889999999999999776666543
No 15
>KOG4577|consensus
Probab=97.71 E-value=8.9e-06 Score=71.39 Aligned_cols=64 Identities=19% Similarity=0.593 Sum_probs=51.5
Q ss_pred cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCC-Cccce-eeCCeeccHhhhhcccCCCc
Q psy8090 87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV-DLIYF-YRGDKLYCGRHHAETLKPRC 154 (242)
Q Consensus 87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~-~~~~~-~~dg~~yC~~~y~~~~~prC 154 (242)
.+|..|...|.+..++ |-|.+..||..||.|..|++.|. +..|| ..|+++.|+++|.+.-..-|
T Consensus 93 TKCsaC~~GIpPtqVV----RkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 93 TKCSACQEGIPPTQVV----RKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC 158 (383)
T ss_pred CcchhhcCCCChHHHH----HHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence 3699999999986544 34889999999999999999995 44555 57899999999986544444
No 16
>KOG1700|consensus
Probab=97.66 E-value=1.5e-05 Score=67.65 Aligned_cols=59 Identities=25% Similarity=0.559 Sum_probs=52.7
Q ss_pred cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhccc
Q psy8090 87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETL 150 (242)
Q Consensus 87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~ 150 (242)
..|..|.+.+++.+.+. +.+..||..||+|+.|+..|....|...+|.+||..++.+.+
T Consensus 109 ~~c~~c~k~vy~~Ek~~-----~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 109 EKCARCQKTVYPLEKVT-----GNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF 167 (200)
T ss_pred cccccccceeeehHHHh-----hhhhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence 46999999999887765 678999999999999999999999999999999988877655
No 17
>KOG1702|consensus
Probab=97.21 E-value=3.3e-05 Score=64.94 Aligned_cols=59 Identities=25% Similarity=0.494 Sum_probs=51.0
Q ss_pred ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccC
Q psy8090 88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLK 151 (242)
Q Consensus 88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~ 151 (242)
.|..|++.+.+-+.+- -+++.||..||.|..|+..|....|--.|.++||..||-...+
T Consensus 6 n~~~cgk~vYPvE~v~-----cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 6 NREDCGKTVYPVEEVK-----CLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred hhhhhccccccHHHHh-----hHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence 5889999998866543 4689999999999999999988888888999999999987664
No 18
>KOG0490|consensus
Probab=96.07 E-value=0.001 Score=56.71 Aligned_cols=112 Identities=16% Similarity=0.275 Sum_probs=75.5
Q ss_pred cCCCceecCccccccccCCCCCcccCCcccccccCCCCC-CccceeeCCeeccHhhhhc--ccCCCcccCCCcccCCCcc
Q psy8090 91 NCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV-DLIYFYRGDKLYCGRHHAE--TLKPRCSACDEECQTSSQD 167 (242)
Q Consensus 91 ~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~-~~~~~~~dg~~yC~~~y~~--~~~prC~~C~~~I~~~~~~ 167 (242)
+|+..|.+.... . ..+..||..|..|..|...|. ....|..+|.+||..+|.. .+..+|..|...|...+..
T Consensus 1 ~~~~~~~~~~~l-~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~l 75 (235)
T KOG0490|consen 1 GCGRQILDRYLL-R----VLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDEL 75 (235)
T ss_pred CCCccccchHHh-h----cccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhccccccCCCCCcCHHHHH
Confidence 366677664332 2 448899999999999999996 3455555999999999998 7889999999998654421
Q ss_pred eeeeeecCCCCCCCCCCCcccCCCcc---CCCCCCCCCCcccCCC-CCCCHHHHhhh
Q psy8090 168 ILYYLTRDSERDLPDEYRTERLEHQR---DLPESYGTHRNSLNKE-QNHSFDNLLKS 220 (242)
Q Consensus 168 ~~~~~~~~~~~~~~~~~~~~h~~~f~---~~~~~~g~~~f~~~d~-~~yC~~cy~~~ 220 (242)
+.. ..+. |.-||. +....+.+..+.+.+. +++|-..+...
T Consensus 76 er~------------f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 76 ERA------------FEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred HHh------------hcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 111 1223 666662 1222344555555555 88998877544
No 19
>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=95.30 E-value=0.014 Score=35.16 Aligned_cols=30 Identities=13% Similarity=0.193 Sum_probs=22.0
Q ss_pred CcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCccC
Q psy8090 153 RCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQRD 194 (242)
Q Consensus 153 rC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~~ 194 (242)
+|.+|+++|.++.. + +.+.++.||.+||.+
T Consensus 1 ~C~~C~~~i~~~~~----~--------~~~~~~~~H~~Cf~C 30 (39)
T smart00132 1 KCAGCGKPIRGGEL----V--------LRALGKVWHPECFKC 30 (39)
T ss_pred CccccCCcccCCcE----E--------EEeCCccccccCCCC
Confidence 68999999987532 1 233678999999943
No 20
>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=88.47 E-value=0.76 Score=34.11 Aligned_cols=31 Identities=26% Similarity=0.422 Sum_probs=23.5
Q ss_pred cccccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090 85 APMFCENCEDELQTSDMSVFASRAGPNSCWHPGCF 119 (242)
Q Consensus 85 ~~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF 119 (242)
....|..|+++|.....+++ ..|..+|..|+
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~----p~~~v~H~~C~ 107 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVF----PCGHVVHYSCI 107 (109)
T ss_pred CCCCccCcCCcCCCceEEEe----CCCeEEecccc
Confidence 34579999999988666554 56777898886
No 21
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=83.57 E-value=1.2 Score=30.28 Aligned_cols=48 Identities=23% Similarity=0.610 Sum_probs=30.0
Q ss_pred cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCC
Q psy8090 87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACD 158 (242)
Q Consensus 87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~ 158 (242)
.+|..|+..|.+.+..+. |.|-.|++.+.. -|.+|-.....-+|..|+
T Consensus 8 ~~CtSCg~~i~~~~~~~~--------------F~CPnCG~~~I~----------RC~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVK--------------FLCPNCGEVIIY----------RCEKCRKQSNPYTCPKCG 55 (59)
T ss_pred ccccCCCCcccCCCccCE--------------eeCCCCCCeeEe----------echhHHhcCCceECCCCC
Confidence 369999999987664442 888888876321 155554444344555554
No 22
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=79.60 E-value=1.3 Score=29.62 Aligned_cols=33 Identities=9% Similarity=0.156 Sum_probs=25.6
Q ss_pred cCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090 150 LKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ 192 (242)
Q Consensus 150 ~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f 192 (242)
.+.+|..|++.|.+++- .+ .++.|+.++|.+|.
T Consensus 4 ~~~~C~~Cg~~~~~~dD---iV-------vCp~CgapyHR~C~ 36 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDD---IV-------VCPECGAPYHRDCW 36 (54)
T ss_pred cCccChhhCCcccCCCC---EE-------ECCCCCCcccHHHH
Confidence 46899999999975541 12 38899999999887
No 23
>cd06535 CIDE_N_CAD CIDE_N domain of CAD nuclease. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of CAD/DFF40 and ICAD/DFF45 during apoptosis. In normal cells, DFF exists in the nucleus as a heterodimer composed of CAD/DFF40 as a latent nuclease and its chaperone and inhibitor subunit ICAD/DFF45. Apoptotic activation of caspase-3 results in the cleavage of DFF45/ICAD and the release of active DFF40/CAD nuclease.
Probab=74.87 E-value=0.74 Score=33.07 Aligned_cols=23 Identities=26% Similarity=0.690 Sum_probs=21.2
Q ss_pred HHHHhcCCCCCCCCcCChhHHHH
Q psy8090 12 HLYFSSLPEDKVPYVNSPGEQYR 34 (242)
Q Consensus 12 ~~y~~~lp~~~~p~~~s~g~~~r 34 (242)
++||.+||.+-+-++=.+|+.|+
T Consensus 54 EeyF~tLp~nT~lmvL~~gq~W~ 76 (77)
T cd06535 54 EEYFPTLPDNTELVLLTPGQSWQ 76 (77)
T ss_pred HHHHhcCCCCcEEEEEcCCCccC
Confidence 89999999999999999998875
No 24
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=74.83 E-value=2.1 Score=23.79 Aligned_cols=15 Identities=20% Similarity=0.687 Sum_probs=9.4
Q ss_pred cccCCCceecCcccc
Q psy8090 89 CENCEDELQTSDMSV 103 (242)
Q Consensus 89 C~~C~~~I~~~~~~v 103 (242)
|..|+..|.+.+..+
T Consensus 1 C~sC~~~i~~r~~~v 15 (24)
T PF07754_consen 1 CTSCGRPIAPREQAV 15 (24)
T ss_pred CccCCCcccCcccCc
Confidence 567777777655433
No 25
>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=73.95 E-value=3 Score=27.77 Aligned_cols=45 Identities=16% Similarity=0.214 Sum_probs=34.1
Q ss_pred ccccccCCCCCCccceeeCCeeccHhhhhccc--CCCcccCCCcccCC
Q psy8090 119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETL--KPRCSACDEECQTS 164 (242)
Q Consensus 119 F~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~--~prC~~C~~~I~~~ 164 (242)
|.|..|++.+.+ ......|..||..+..+.+ ...|-.|++++...
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~~ 48 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTHE 48 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCChh
Confidence 678899988876 5556789999998887544 36788888887543
No 26
>cd06536 CIDE_N_ICAD CIDE_N domain of ICAD. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD (DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40 and ICAD/DFF45 during apoptosis. In normal cells, DFF exists in the nucleus as a heterodimer composed of CAD/DFF40 as a latent nuclease and its chaperone and inhibitor subunit ICAD/DFF45. Apoptotic activation of caspase-3 results in the cleavage of DFF45/ICAD and release of active DFF40/CAD nuclease.
Probab=72.78 E-value=0.92 Score=32.83 Aligned_cols=24 Identities=21% Similarity=0.300 Sum_probs=21.4
Q ss_pred HHHHHhcCCCCCCCCcCChhHHHH
Q psy8090 11 VHLYFSSLPEDKVPYVNSPGEQYR 34 (242)
Q Consensus 11 ~~~y~~~lp~~~~p~~~s~g~~~r 34 (242)
-++||.+||.+-+-++=.+|+.|+
T Consensus 56 dEeyF~tLp~nT~l~~L~~gq~W~ 79 (80)
T cd06536 56 DEDYFLCLPPNTKFVLLAENEKWA 79 (80)
T ss_pred cHHHHhhCCCCcEEEEECCCCccC
Confidence 389999999999999989998874
No 27
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=72.19 E-value=3.4 Score=28.62 Aligned_cols=47 Identities=15% Similarity=0.550 Sum_probs=21.0
Q ss_pred ccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCC
Q psy8090 119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSS 165 (242)
Q Consensus 119 F~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~ 165 (242)
.+|+.|..-|..--....=+.+||..|-.+.++..|..|..+-...+
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD 54 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQD 54 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHH
Confidence 35666665553322223345677777777788888999998876655
No 28
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=71.09 E-value=2.4 Score=25.86 Aligned_cols=25 Identities=24% Similarity=0.602 Sum_probs=18.2
Q ss_pred ccccccCCCCCCccceeeCCeeccHhhhh
Q psy8090 119 FTCSVCNELLVDLIYFYRGDKLYCGRHHA 147 (242)
Q Consensus 119 F~C~~C~~~L~~~~~~~~dg~~yC~~~y~ 147 (242)
+.|..|+.. .|...||..||.+|..
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCce
Confidence 447778753 5667899999977754
No 29
>cd06538 CIDE_N_FSP27 CIDE_N domain of FSP27 proteins. The CIDE-N (cell death-inducing DFF45-like effector, N-terminal) domain is found in the FSP27/CIDE-C protein, which has been identified as a n adipocyte lipid droplet protein that negatively regulates lipolysis and promotes triglyceride accumulation. The CIDE protein family includes 3 members: CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence similarity with DFF40 and DFF45, CIDE proteins were initially characterized as mitochondrial activators of apoptosis. The CIDE-N domain of FSP27 is sufficient to increase apoptosis in vitro when overexpressed.
Probab=71.02 E-value=1 Score=32.48 Aligned_cols=24 Identities=21% Similarity=0.508 Sum_probs=21.5
Q ss_pred HHHHHhcCCCCCCCCcCChhHHHH
Q psy8090 11 VHLYFSSLPEDKVPYVNSPGEQYR 34 (242)
Q Consensus 11 ~~~y~~~lp~~~~p~~~s~g~~~r 34 (242)
-++||.+||.+.+-++=.+|+.|+
T Consensus 53 ~EeyF~tLp~nt~l~vL~~gq~W~ 76 (79)
T cd06538 53 TEEFFQALADNTVFMVLGKGQKWK 76 (79)
T ss_pred cHHHHhhCCCCcEEEEECCCCccC
Confidence 389999999999999999998885
No 30
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=70.64 E-value=2.2 Score=33.73 Aligned_cols=22 Identities=23% Similarity=0.679 Sum_probs=16.2
Q ss_pred cccccCCCCCCccceeeCCeeccHhhh
Q psy8090 120 TCSVCNELLVDLIYFYRGDKLYCGRHH 146 (242)
Q Consensus 120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y 146 (242)
.|..|+.|| |.+||.+||..|-
T Consensus 30 hCp~Cg~PL-----F~KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPL-----FRKDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcc-----eeeCCeEECCCCC
Confidence 477888877 5589999985553
No 31
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=70.30 E-value=1.3 Score=33.50 Aligned_cols=33 Identities=18% Similarity=0.336 Sum_probs=25.2
Q ss_pred cccccCCCceecCccccccccCCCCCcccCCcccccc
Q psy8090 87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSV 123 (242)
Q Consensus 87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~ 123 (242)
..|.-|+++|..|+.+.+ ..+..-|-.||+=..
T Consensus 3 WkC~iCg~~I~~gqlFTF----~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTF----TKKGPVHYECFREKA 35 (101)
T ss_pred eEEEecCCeeeecceEEE----ecCCcEeHHHHHHHH
Confidence 369999999999888766 455778888886443
No 32
>cd06539 CIDE_N_A CIDE_N domain of CIDE-A proteins. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins. These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40, ICAD/DFF45, and CIDE nucleases during apoptosis. The CIDE protein family includes 3 members: CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence similarity with DFF40 and DFF45, the CIDE proteins were initially characterized as mitochondrial activators of apoptosis. However, strong metabolic phenotypes of mice lacking CIDE-A and CIDE-B indicated that this family may play critical roles in energy balance.
Probab=70.12 E-value=1.1 Score=32.24 Aligned_cols=24 Identities=17% Similarity=0.369 Sum_probs=21.2
Q ss_pred HHHHHhcCCCCCCCCcCChhHHHH
Q psy8090 11 VHLYFSSLPEDKVPYVNSPGEQYR 34 (242)
Q Consensus 11 ~~~y~~~lp~~~~p~~~s~g~~~r 34 (242)
-++||.+||.+.+-++=.+|+.|+
T Consensus 54 ~EeyF~~LpdnT~lm~L~~gq~W~ 77 (78)
T cd06539 54 TEEFFQTLGDNTHFMVLEKGQKWT 77 (78)
T ss_pred cHHHHhhCCCCCEEEEECCCCccC
Confidence 389999999999999888998874
No 33
>cd01615 CIDE_N CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein.
Probab=69.14 E-value=1.2 Score=32.03 Aligned_cols=23 Identities=30% Similarity=0.752 Sum_probs=20.6
Q ss_pred HHHHhcCCCCCCCCcCChhHHHH
Q psy8090 12 HLYFSSLPEDKVPYVNSPGEQYR 34 (242)
Q Consensus 12 ~~y~~~lp~~~~p~~~s~g~~~r 34 (242)
++||.+||.+-+-++=.+|++|.
T Consensus 55 EeYF~tLp~nT~l~~l~~gq~W~ 77 (78)
T cd01615 55 EEYFQTLPDNTVLMLLEPGQKWT 77 (78)
T ss_pred HHHHhcCCCCcEEEEECCCCCcC
Confidence 89999999999999888888774
No 34
>smart00266 CAD Domains present in proteins implicated in post-mortem DNA fragmentation.
Probab=68.98 E-value=1.2 Score=31.71 Aligned_cols=23 Identities=26% Similarity=0.521 Sum_probs=19.7
Q ss_pred HHHHHhcCCCCCCCCcCChhHHH
Q psy8090 11 VHLYFSSLPEDKVPYVNSPGEQY 33 (242)
Q Consensus 11 ~~~y~~~lp~~~~p~~~s~g~~~ 33 (242)
-++||.+||.+-+-++=.+|+.|
T Consensus 52 dEeyF~tLp~nt~l~~L~~gq~W 74 (74)
T smart00266 52 DEEYFQTLPDNTELMALEKGEKW 74 (74)
T ss_pred cHHHHhcCCCCcEEEEEcCCCCC
Confidence 38999999999998888888765
No 35
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=67.21 E-value=5.8 Score=27.03 Aligned_cols=28 Identities=29% Similarity=0.734 Sum_probs=21.1
Q ss_pred cccccCCCceecCccccccccCCCCCcccCCcccccccCCCC
Q psy8090 87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELL 128 (242)
Q Consensus 87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L 128 (242)
.+|..|+..|..++..+. |.|-.|++.+
T Consensus 10 ~~CtSCg~~i~p~e~~v~--------------F~CPnCGe~~ 37 (61)
T COG2888 10 PVCTSCGREIAPGETAVK--------------FPCPNCGEVE 37 (61)
T ss_pred ceeccCCCEeccCCceeE--------------eeCCCCCcee
Confidence 379999999977766553 8888888544
No 36
>cd06537 CIDE_N_B CIDE_N domain of CIDE-B proteins. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins. These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40, ICAD/DFF45 and CIDE nucleases during apoptosis. The CIDE protein family includes 3 members: CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence similarity with DFF40 and DFF45, CIDE proteins were initially characterized as mitochondrial activators of apoptosis. However, strong metabolic phenotypes of mice lacking CIDE-A and CIDE-B indicated that this family may play critical roles in energy balance.
Probab=67.19 E-value=1.4 Score=31.85 Aligned_cols=24 Identities=21% Similarity=0.375 Sum_probs=21.6
Q ss_pred HHHHHhcCCCCCCCCcCChhHHHH
Q psy8090 11 VHLYFSSLPEDKVPYVNSPGEQYR 34 (242)
Q Consensus 11 ~~~y~~~lp~~~~p~~~s~g~~~r 34 (242)
-++||.+||.+-+-++=..|+.|+
T Consensus 53 ~EeyF~tLpdnT~lm~L~~gq~W~ 76 (81)
T cd06537 53 SEDFFELLEDDTCLMVLEQGQSWS 76 (81)
T ss_pred cHHHHhhCCCCCEEEEECCCCccC
Confidence 389999999999999999999886
No 37
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=66.55 E-value=1.7 Score=26.76 Aligned_cols=32 Identities=25% Similarity=0.576 Sum_probs=22.2
Q ss_pred cccCCCceecCccccccccCCCCCcccCCcccccccCCC
Q psy8090 89 CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNEL 127 (242)
Q Consensus 89 C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~ 127 (242)
|.-|+++|.+...++. ..++.|| |-|.+|.+.
T Consensus 1 Cd~CG~~I~~eP~~~k----~~~~~y~---fCC~tC~~~ 32 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVK----IGNKVYY---FCCPTCLSQ 32 (37)
T ss_pred CCccCCcccCCEEEEE----ECCeEEE---EECHHHHHH
Confidence 6789999988666554 4578888 556666543
No 38
>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=62.90 E-value=11 Score=24.01 Aligned_cols=43 Identities=23% Similarity=0.565 Sum_probs=29.2
Q ss_pred ccccccCCCCCCccceeeCCee-ccHhhhhccc--CCCcccCCCccc
Q psy8090 119 FTCSVCNELLVDLIYFYRGDKL-YCGRHHAETL--KPRCSACDEECQ 162 (242)
Q Consensus 119 F~C~~C~~~L~~~~~~~~dg~~-yC~~~y~~~~--~prC~~C~~~I~ 162 (242)
+.|..|.....+ ..+..=|.. +|..|..+.+ ..+|..|..+|.
T Consensus 3 ~~C~iC~~~~~~-~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 3 EECPICFENPRD-VVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp SB-TTTSSSBSS-EEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCCccCCccCCc-eEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 356677776655 334445666 9999998763 589999999986
No 39
>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=59.76 E-value=2.5 Score=30.20 Aligned_cols=45 Identities=9% Similarity=0.130 Sum_probs=25.8
Q ss_pred hhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcc-cCCCcc
Q psy8090 146 HAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTE-RLEHQR 193 (242)
Q Consensus 146 y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~-h~~~f~ 193 (242)
|+..-..+|.+|++.|..+.+.+-..+..... ......| |..||.
T Consensus 2 yAks~Ra~Ck~C~~~I~kg~lRiG~~~~~~~~---~~~~~~W~H~~C~~ 47 (82)
T PF00645_consen 2 YAKSGRAKCKGCKKKIAKGELRIGKIVPSPEG---DGDIPKWYHWDCFF 47 (82)
T ss_dssp E-SSSTEBETTTSCBE-TTSEEEEEEEEETTS---SCEEEEEEEHHHHH
T ss_pred cCCCCCccCcccCCcCCCCCEEEEEEeccccc---CCCCCceECccccc
Confidence 34445678999999999888665554443222 1112234 777774
No 40
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=58.37 E-value=4.2 Score=34.54 Aligned_cols=31 Identities=23% Similarity=0.395 Sum_probs=23.4
Q ss_pred ccccccCCCCCCccceeeCCeeccHhhhhcc
Q psy8090 119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAET 149 (242)
Q Consensus 119 F~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~ 149 (242)
-+|+.|++......--..+|++.|..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVCKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceecccccccc
Confidence 5788888877655555678899999988753
No 41
>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=54.53 E-value=8.8 Score=28.41 Aligned_cols=42 Identities=19% Similarity=0.502 Sum_probs=29.2
Q ss_pred ccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccC
Q psy8090 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQT 163 (242)
Q Consensus 114 wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~ 163 (242)
|-+.=-.|..|...+.. .|.-||..|..+ .-.|+.|++.|.+
T Consensus 40 y~~~~~~C~~CK~~v~q------~g~~YCq~CAYk--kGiCamCGKki~d 81 (90)
T PF10235_consen 40 YAPYSSKCKICKTKVHQ------PGAKYCQTCAYK--KGICAMCGKKILD 81 (90)
T ss_pred ccccCcccccccccccc------CCCccChhhhcc--cCcccccCCeecc
Confidence 33333467888766632 367899999654 3589999999964
No 42
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=53.87 E-value=4.8 Score=25.30 Aligned_cols=9 Identities=33% Similarity=0.914 Sum_probs=4.6
Q ss_pred eCCeeccHh
Q psy8090 136 RGDKLYCGR 144 (242)
Q Consensus 136 ~dg~~yC~~ 144 (242)
++|++||..
T Consensus 31 k~g~~~Cv~ 39 (41)
T PF06677_consen 31 KDGKIYCVS 39 (41)
T ss_pred cCCCEECCC
Confidence 455555543
No 43
>PF12773 DZR: Double zinc ribbon
Probab=52.90 E-value=21 Score=22.73 Aligned_cols=13 Identities=23% Similarity=0.585 Sum_probs=8.9
Q ss_pred CCcccCCCcccCC
Q psy8090 152 PRCSACDEECQTS 164 (242)
Q Consensus 152 prC~~C~~~I~~~ 164 (242)
..|..|+..+..+
T Consensus 30 ~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 30 KICPNCGAENPPN 42 (50)
T ss_pred CCCcCCcCCCcCC
Confidence 4688888876543
No 44
>KOG1813|consensus
Probab=51.21 E-value=9.3 Score=34.32 Aligned_cols=44 Identities=14% Similarity=0.520 Sum_probs=33.5
Q ss_pred ccccccCCCCCCccceeeCCeeccHhhhhcccC--CCcccCCCcccC
Q psy8090 119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLK--PRCSACDEECQT 163 (242)
Q Consensus 119 F~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~--prC~~C~~~I~~ 163 (242)
|.|..|++.... .-...-+..||+.|....+. ++|..|++.+.+
T Consensus 242 f~c~icr~~f~~-pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 242 FKCFICRKYFYR-PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred cccccccccccc-chhhcCCceeehhhhccccccCCcceeccccccc
Confidence 778888876644 33345677889999987774 899999999875
No 45
>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=51.16 E-value=3.9 Score=24.61 Aligned_cols=10 Identities=30% Similarity=1.089 Sum_probs=4.9
Q ss_pred cccCCCceec
Q psy8090 89 CENCEDELQT 98 (242)
Q Consensus 89 C~~C~~~I~~ 98 (242)
|..|+++|..
T Consensus 6 C~~CGe~I~~ 15 (36)
T PF01258_consen 6 CEDCGEPIPE 15 (36)
T ss_dssp -TTTSSBEEH
T ss_pred ccccCChHHH
Confidence 5555555544
No 46
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=50.31 E-value=15 Score=36.77 Aligned_cols=12 Identities=25% Similarity=0.645 Sum_probs=8.2
Q ss_pred ccccCCCceecC
Q psy8090 88 FCENCEDELQTS 99 (242)
Q Consensus 88 ~C~~C~~~I~~~ 99 (242)
+|..|+..+..+
T Consensus 3 ~Cp~Cg~~n~~~ 14 (645)
T PRK14559 3 ICPQCQFENPNN 14 (645)
T ss_pred cCCCCCCcCCCC
Confidence 588888776543
No 47
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=50.30 E-value=8.4 Score=25.48 Aligned_cols=54 Identities=22% Similarity=0.413 Sum_probs=28.3
Q ss_pred HHHHHHhhhhccCCCcccccccccccccCCCceecCccccccccCCCCCcccCCcccccccCCCC
Q psy8090 64 RLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELL 128 (242)
Q Consensus 64 ~~f~~~~~~~~~g~g~v~~~~~~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L 128 (242)
..|.+.++. .-|.+.+... ...|.+|+-.|.+....-. + .+ ..=..|..|++-|
T Consensus 3 ~~Y~rl~~~-~~g~~va~v~--~~~C~gC~~~l~~~~~~~i--~--~~----~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 3 AEYERLRKR-KGGVAVARVE--GGTCSGCHMELPPQELNEI--R--KG----DEIVFCPNCGRIL 56 (56)
T ss_pred HHHHHHHhh-cCCcEEEEee--CCccCCCCEEcCHHHHHHH--H--cC----CCeEECcCCCccC
Confidence 344444444 2244433322 2379999999987543211 1 11 3346677777644
No 48
>KOG0320|consensus
Probab=47.08 E-value=11 Score=31.55 Aligned_cols=49 Identities=14% Similarity=0.582 Sum_probs=38.4
Q ss_pred CCcccccccCCCCCCcc-ceeeCCeeccHhhhhccc--CCCcccCCCcccCC
Q psy8090 116 PGCFTCSVCNELLVDLI-YFYRGDKLYCGRHHAETL--KPRCSACDEECQTS 164 (242)
Q Consensus 116 ~~CF~C~~C~~~L~~~~-~~~~dg~~yC~~~y~~~~--~prC~~C~~~I~~~ 164 (242)
..+|.|-.|-....... +-.+=|.+||..|-...+ +.+|-.|++.|+..
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITHK 180 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccchh
Confidence 46899999977775444 446789999999997655 47999999988753
No 49
>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=46.83 E-value=13 Score=27.36 Aligned_cols=28 Identities=18% Similarity=0.300 Sum_probs=21.0
Q ss_pred cccccCCCCCCcccee-eCCeeccHhhhh
Q psy8090 120 TCSVCNELLVDLIYFY-RGDKLYCGRHHA 147 (242)
Q Consensus 120 ~C~~C~~~L~~~~~~~-~dg~~yC~~~y~ 147 (242)
.|..|+++|....|.. .+|.++...|..
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEeccccc
Confidence 5899999998766664 567887766653
No 50
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=45.82 E-value=7.3 Score=33.09 Aligned_cols=43 Identities=14% Similarity=0.439 Sum_probs=32.2
Q ss_pred ccccccCCCCCCccceeeCCeeccHhhhhcccC--CCcccCCCccc
Q psy8090 119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLK--PRCSACDEECQ 162 (242)
Q Consensus 119 F~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~--prC~~C~~~I~ 162 (242)
|.|..|.+.... .-...-|.-||..|+...+. +.|..|++..-
T Consensus 197 F~C~iCKkdy~s-pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~ 241 (259)
T COG5152 197 FLCGICKKDYES-PVVTECGHSFCSLCAIRKYQKGDECGVCGKATY 241 (259)
T ss_pred eeehhchhhccc-hhhhhcchhHHHHHHHHHhccCCcceecchhhc
Confidence 788888876533 33334578899999987774 89999998754
No 51
>PF02017 CIDE-N: CIDE-N domain; InterPro: IPR003508 This domain consists of caspase-activated (CAD) nucleases, which induce DNA fragmentation and chromatin condensation during apoptosis, and the cell death activator proteins CIDE-A and CIDE-B, which are inhibitors of CAD nuclease. The two proteins interact through the region defined by the method signatures.; GO: 0006915 apoptosis, 0005622 intracellular; PDB: 1IBX_A 2EEL_A 1F2R_I 1C9F_A 1D4B_A.
Probab=44.36 E-value=2.9 Score=30.14 Aligned_cols=23 Identities=30% Similarity=0.661 Sum_probs=18.1
Q ss_pred HHHHhcCCCCCCCCcCChhHHHH
Q psy8090 12 HLYFSSLPEDKVPYVNSPGEQYR 34 (242)
Q Consensus 12 ~~y~~~lp~~~~p~~~s~g~~~r 34 (242)
++||.+||.+-+-++=..|+.|.
T Consensus 55 EeyF~tLp~nT~lm~L~~ge~W~ 77 (78)
T PF02017_consen 55 EEYFQTLPDNTVLMLLEKGEKWT 77 (78)
T ss_dssp CHHHCCSSSSEEEEEEESSS--S
T ss_pred HHHHhhCCCCCEEEEECCCCccC
Confidence 58999999999888888888773
No 52
>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=43.49 E-value=16 Score=21.67 Aligned_cols=24 Identities=21% Similarity=0.518 Sum_probs=12.5
Q ss_pred CCeeccHhhhhccc---CCCcccCCCc
Q psy8090 137 GDKLYCGRHHAETL---KPRCSACDEE 160 (242)
Q Consensus 137 dg~~yC~~~y~~~~---~prC~~C~~~ 160 (242)
=|..||..|....+ ..+|..|...
T Consensus 18 C~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 18 CGHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CCChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 34556666554332 3456666543
No 53
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=43.44 E-value=13 Score=26.94 Aligned_cols=29 Identities=21% Similarity=0.289 Sum_probs=20.0
Q ss_pred cccccCCCCCCcccee--eCC---eeccHhhhhc
Q psy8090 120 TCSVCNELLVDLIYFY--RGD---KLYCGRHHAE 148 (242)
Q Consensus 120 ~C~~C~~~L~~~~~~~--~dg---~~yC~~~y~~ 148 (242)
.|..|+.||.....+- .|| .-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 4888999997655332 333 5699998874
No 54
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=42.84 E-value=23 Score=21.98 Aligned_cols=38 Identities=16% Similarity=0.454 Sum_probs=22.9
Q ss_pred ccccCCCCC-Cccce-eeCCeeccHhhhhccc--CCCcccCC
Q psy8090 121 CSVCNELLV-DLIYF-YRGDKLYCGRHHAETL--KPRCSACD 158 (242)
Q Consensus 121 C~~C~~~L~-~~~~~-~~dg~~yC~~~y~~~~--~prC~~C~ 158 (242)
|..|.+.+. ...++ ..=|.++|..|..... ...|..|+
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~ 43 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICR 43 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCC
Confidence 555666552 22222 3457788888887766 45676665
No 55
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=41.67 E-value=5 Score=30.02 Aligned_cols=45 Identities=29% Similarity=0.558 Sum_probs=29.0
Q ss_pred cccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCC
Q psy8090 89 CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGD 138 (242)
Q Consensus 89 C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg 138 (242)
|..|+..+..-...- ..-..+++.+..|-.|...|.-..|.....
T Consensus 38 Cy~CHdel~~Hpf~p-----~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~ 82 (105)
T COG4357 38 CYHCHDELEDHPFEP-----WGLQEFNPKAIICGVCRKLLTRAEYGMCGS 82 (105)
T ss_pred HHHHHhHHhcCCCcc-----CChhhcCCccEEhhhhhhhhhHHHHhhcCC
Confidence 677777765532221 223568888999999998886555554444
No 56
>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=40.45 E-value=16 Score=21.97 Aligned_cols=37 Identities=24% Similarity=0.667 Sum_probs=20.6
Q ss_pred ccccCCCCCCccceeeCCeeccHhhhhccc--CCCcccC
Q psy8090 121 CSVCNELLVDLIYFYRGDKLYCGRHHAETL--KPRCSAC 157 (242)
Q Consensus 121 C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~--~prC~~C 157 (242)
|..|.+.+.+......=|..||..|..+.+ ..+|..|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLEKNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHHCTSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHHCcCCCcCC
Confidence 455666665533455668888888876543 2444443
No 57
>PRK14873 primosome assembly protein PriA; Provisional
Probab=39.40 E-value=17 Score=36.47 Aligned_cols=39 Identities=21% Similarity=0.356 Sum_probs=27.1
Q ss_pred ccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCc
Q psy8090 119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEE 160 (242)
Q Consensus 119 F~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~ 160 (242)
++|..|+-+| .|...++.+.|..|-......+|..|+..
T Consensus 393 ~~C~~C~~~L---~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPL---GLPSAGGTPRCRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCce---eEecCCCeeECCCCcCCCcCccCCCCcCC
Confidence 4555666555 45445678889888766666799999875
No 58
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=37.93 E-value=9.6 Score=28.44 Aligned_cols=37 Identities=16% Similarity=0.206 Sum_probs=27.6
Q ss_pred ccccCCCceecCccccccccCCCCCcccCCcccccccCCCC
Q psy8090 88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELL 128 (242)
Q Consensus 88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L 128 (242)
.|..|+++|..|+.+.+ .....-|-+||.=+.-+++-
T Consensus 8 kC~VCg~~iieGqkFTF----~~kGsVH~eCl~~s~~~k~~ 44 (103)
T COG4847 8 KCYVCGGTIIEGQKFTF----TKKGSVHYECLAESKRKKPG 44 (103)
T ss_pred eEeeeCCEeeeccEEEE----eeCCcchHHHHHHHHhcCcC
Confidence 69999999988888766 34567788888776655544
No 59
>KOG0978|consensus
Probab=37.66 E-value=12 Score=37.60 Aligned_cols=14 Identities=14% Similarity=0.648 Sum_probs=11.0
Q ss_pred CCcccCCCcccCCC
Q psy8090 152 PRCSACDEECQTSS 165 (242)
Q Consensus 152 prC~~C~~~I~~~~ 165 (242)
-+|..|+.+..+.+
T Consensus 679 RKCP~Cn~aFganD 692 (698)
T KOG0978|consen 679 RKCPKCNAAFGAND 692 (698)
T ss_pred CCCCCCCCCCCccc
Confidence 57999998887654
No 60
>KOG4739|consensus
Probab=36.46 E-value=24 Score=30.66 Aligned_cols=41 Identities=12% Similarity=0.351 Sum_probs=30.1
Q ss_pred ccCCCCCCcccee-eCCeeccHhhhhcccCCCcccCCCcccC
Q psy8090 123 VCNELLVDLIYFY-RGDKLYCGRHHAETLKPRCSACDEECQT 163 (242)
Q Consensus 123 ~C~~~L~~~~~~~-~dg~~yC~~~y~~~~~prC~~C~~~I~~ 163 (242)
.|+..=....||. -=..++|..|.....++.|..|++.|..
T Consensus 8 ~C~~~~~~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 8 KCFRFPSQDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIRI 49 (233)
T ss_pred cccccCCCCceeeeechhhhhhhhcccCCccccccccceeee
Confidence 3433333446665 4578999999998888899999999764
No 61
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=35.58 E-value=24 Score=23.12 Aligned_cols=29 Identities=10% Similarity=0.368 Sum_probs=20.3
Q ss_pred cccccCCCCCCcc-ceeeCCeeccHhhhhcc
Q psy8090 120 TCSVCNELLVDLI-YFYRGDKLYCGRHHAET 149 (242)
Q Consensus 120 ~C~~C~~~L~~~~-~~~~dg~~yC~~~y~~~ 149 (242)
.|..|+..+.-.. +-..|| ..|..|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 4788888875333 446777 6899998764
No 62
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=34.44 E-value=24 Score=23.42 Aligned_cols=25 Identities=20% Similarity=0.587 Sum_probs=14.0
Q ss_pred cccccCCCCCCccceeeCCeeccHh
Q psy8090 120 TCSVCNELLVDLIYFYRGDKLYCGR 144 (242)
Q Consensus 120 ~C~~C~~~L~~~~~~~~dg~~yC~~ 144 (242)
-|..|...+....-+.+||+.||..
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~YCS~ 33 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYYCSE 33 (52)
T ss_dssp SSTT----B-TTTSEESSS-EESSH
T ss_pred cCCCCEeEECchHhHHhCCEeeecH
Confidence 3667777776567788999999953
No 63
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=34.34 E-value=33 Score=29.01 Aligned_cols=15 Identities=20% Similarity=0.873 Sum_probs=12.1
Q ss_pred CCCcccCCCcccCCC
Q psy8090 151 KPRCSACDEECQTSS 165 (242)
Q Consensus 151 ~prC~~C~~~I~~~~ 165 (242)
.++|-.|...|....
T Consensus 68 ~~~CPvCR~~Is~~~ 82 (193)
T PLN03208 68 PPKCPVCKSDVSEAT 82 (193)
T ss_pred CCcCCCCCCcCChhc
Confidence 368999999997654
No 64
>KOG1702|consensus
Probab=34.14 E-value=5.8 Score=33.88 Aligned_cols=61 Identities=5% Similarity=-0.099 Sum_probs=42.5
Q ss_pred CCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc-cC-CCCCCCCCCcccCCCCCCCHHHHhhhhccc
Q psy8090 151 KPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ-RD-LPESYGTHRNSLNKEQNHSFDNLLKSNLKK 224 (242)
Q Consensus 151 ~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f-~~-~~~~~g~~~f~~~d~~~yC~~cy~~~~a~k 224 (242)
.+-|..|++.+-+-+. +.-..+.||.-|| |. +...+-.+.|..-+.+|||-..|-+..|.-
T Consensus 4 k~n~~~cgk~vYPvE~-------------v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~at~ 66 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVEE-------------VKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVATV 66 (264)
T ss_pred cchhhhhccccccHHH-------------HhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccceeee
Confidence 3556778877765331 2324678999999 42 345677788888899999999988776543
No 65
>PRK04023 DNA polymerase II large subunit; Validated
Probab=33.02 E-value=43 Score=35.19 Aligned_cols=39 Identities=23% Similarity=0.431 Sum_probs=25.9
Q ss_pred ccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCC
Q psy8090 119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSS 165 (242)
Q Consensus 119 F~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~ 165 (242)
|+|..|+.. .....+|..|-...-...|..|+..+.+..
T Consensus 639 frCP~CG~~--------Te~i~fCP~CG~~~~~y~CPKCG~El~~~s 677 (1121)
T PRK04023 639 RRCPFCGTH--------TEPVYRCPRCGIEVEEDECEKCGREPTPYS 677 (1121)
T ss_pred ccCCCCCCC--------CCcceeCccccCcCCCCcCCCCCCCCCccc
Confidence 667777665 123456778866555577999988776654
No 66
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=32.53 E-value=35 Score=21.50 Aligned_cols=9 Identities=22% Similarity=0.290 Sum_probs=5.4
Q ss_pred eccHhhhhc
Q psy8090 140 LYCGRHHAE 148 (242)
Q Consensus 140 ~yC~~~y~~ 148 (242)
-+|..||..
T Consensus 24 dLC~~Cf~~ 32 (46)
T cd02249 24 DLCSSCYAK 32 (46)
T ss_pred cCHHHHHCc
Confidence 457777663
No 67
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=32.15 E-value=33 Score=21.59 Aligned_cols=27 Identities=19% Similarity=0.582 Sum_probs=17.3
Q ss_pred ccccCCCceecCccccccccCCCCCcccCCcccccccCCCC
Q psy8090 88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELL 128 (242)
Q Consensus 88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L 128 (242)
.|..|+..+...+.. . -++|..|+..+
T Consensus 5 ~C~~CG~~~~~~~~~--------~------~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGREVELDEYG--------T------GVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCEEEECCCC--------C------ceECCCCCCeE
Confidence 688888877543211 1 37788887655
No 68
>PRK00420 hypothetical protein; Validated
Probab=32.09 E-value=21 Score=27.50 Aligned_cols=9 Identities=33% Similarity=0.700 Sum_probs=4.7
Q ss_pred ccccCCCce
Q psy8090 88 FCENCEDEL 96 (242)
Q Consensus 88 ~C~~C~~~I 96 (242)
.|+.|+-++
T Consensus 25 ~CP~Cg~pL 33 (112)
T PRK00420 25 HCPVCGLPL 33 (112)
T ss_pred CCCCCCCcc
Confidence 455555444
No 69
>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=30.75 E-value=30 Score=26.22 Aligned_cols=13 Identities=31% Similarity=0.976 Sum_probs=11.0
Q ss_pred ccccCCCceecCc
Q psy8090 88 FCENCEDELQTSD 100 (242)
Q Consensus 88 ~C~~C~~~I~~~~ 100 (242)
.|..|+++|....
T Consensus 82 ~C~~Cge~I~~~R 94 (110)
T TIGR02420 82 YCEECGEEIGLRR 94 (110)
T ss_pred chhccCCcccHHH
Confidence 7999999998753
No 70
>KOG0490|consensus
Probab=30.19 E-value=21 Score=30.03 Aligned_cols=48 Identities=8% Similarity=-0.133 Sum_probs=36.1
Q ss_pred CCcccCCCc-c-CCCCCCC--CCCcccCCCCCCCHHHHhh--hhcccccCCCCCC
Q psy8090 184 YRTERLEHQ-R-DLPESYG--THRNSLNKEQNHSFDNLLK--SNLKKLSLADSDD 232 (242)
Q Consensus 184 ~~~~h~~~f-~-~~~~~~g--~~~f~~~d~~~yC~~cy~~--~~a~kc~~~~~~~ 232 (242)
...||..|. | .+...++ ...|.. ++..||..+|.+ .+.++|+.+.-.+
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~ 69 (235)
T KOG0490|consen 16 DRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTI 69 (235)
T ss_pred cHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCc
Confidence 678888877 2 2233444 667777 999999999999 8888988877654
No 71
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=28.50 E-value=46 Score=21.22 Aligned_cols=30 Identities=17% Similarity=0.318 Sum_probs=18.3
Q ss_pred ccccccCCCCCCcccee--eCCeeccHhhhhc
Q psy8090 119 FTCSVCNELLVDLIYFY--RGDKLYCGRHHAE 148 (242)
Q Consensus 119 F~C~~C~~~L~~~~~~~--~dg~~yC~~~y~~ 148 (242)
+.|..|+..+....|.. ..+..+|..||.+
T Consensus 1 y~C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~ 32 (45)
T cd02336 1 YHCFTCGNDCTRVRYHNLKAKKYDLCPSCYQE 32 (45)
T ss_pred CcccCCCCccCceEEEecCCCccccChHHHhC
Confidence 35777777776433332 1246778888875
No 72
>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=27.95 E-value=77 Score=21.36 Aligned_cols=24 Identities=21% Similarity=0.511 Sum_probs=17.1
Q ss_pred eccHhhhhcccCCCcccCCCcccC
Q psy8090 140 LYCGRHHAETLKPRCSACDEECQT 163 (242)
Q Consensus 140 ~yC~~~y~~~~~prC~~C~~~I~~ 163 (242)
-||..|....+...|..|+..+..
T Consensus 30 TFC~~C~e~~l~~~CPNCgGelv~ 53 (57)
T PF06906_consen 30 TFCADCAETMLNGVCPNCGGELVR 53 (57)
T ss_pred cccHHHHHHHhcCcCcCCCCcccc
Confidence 456777777777888888776654
No 73
>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=27.33 E-value=19 Score=25.35 Aligned_cols=10 Identities=40% Similarity=1.099 Sum_probs=4.6
Q ss_pred ccccCCCcee
Q psy8090 88 FCENCEDELQ 97 (242)
Q Consensus 88 ~C~~C~~~I~ 97 (242)
.|..|..++.
T Consensus 3 ~CP~C~~~L~ 12 (70)
T PF07191_consen 3 TCPKCQQELE 12 (70)
T ss_dssp B-SSS-SBEE
T ss_pred cCCCCCCccE
Confidence 4666666653
No 74
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.09 E-value=37 Score=32.80 Aligned_cols=38 Identities=26% Similarity=0.606 Sum_probs=26.2
Q ss_pred cccccCCCCCCccceeeCCeeccHhhhhc-ccCCCcccCCCc
Q psy8090 120 TCSVCNELLVDLIYFYRGDKLYCGRHHAE-TLKPRCSACDEE 160 (242)
Q Consensus 120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~-~~~prC~~C~~~ 160 (242)
+|..|+-+| .|...++.+.|..|-.. .+..+|..|+..
T Consensus 224 ~C~~C~~~l---~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~ 262 (505)
T TIGR00595 224 CCPNCDVSL---TYHKKEGKLRCHYCGYQEPIPKTCPQCGSE 262 (505)
T ss_pred CCCCCCCce---EEecCCCeEEcCCCcCcCCCCCCCCCCCCC
Confidence 444555444 66677889999888654 345799999864
No 75
>PRK11595 DNA utilization protein GntX; Provisional
Probab=26.54 E-value=56 Score=27.89 Aligned_cols=9 Identities=33% Similarity=0.689 Sum_probs=5.6
Q ss_pred ccccCCCce
Q psy8090 88 FCENCEDEL 96 (242)
Q Consensus 88 ~C~~C~~~I 96 (242)
.|..|++.|
T Consensus 7 ~C~~C~~~~ 15 (227)
T PRK11595 7 LCWLCRMPL 15 (227)
T ss_pred cCccCCCcc
Confidence 466666655
No 76
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=26.38 E-value=55 Score=20.42 Aligned_cols=9 Identities=22% Similarity=0.316 Sum_probs=5.8
Q ss_pred eccHhhhhc
Q psy8090 140 LYCGRHHAE 148 (242)
Q Consensus 140 ~yC~~~y~~ 148 (242)
-+|..||.+
T Consensus 28 dlC~~Cf~~ 36 (44)
T smart00291 28 DLCQSCFAK 36 (44)
T ss_pred cchHHHHhC
Confidence 347777764
No 77
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=25.55 E-value=76 Score=34.26 Aligned_cols=50 Identities=24% Similarity=0.434 Sum_probs=28.4
Q ss_pred cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhccc-----CCCcccCCCcc
Q psy8090 87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETL-----KPRCSACDEEC 161 (242)
Q Consensus 87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~-----~prC~~C~~~I 161 (242)
..|..|+..+.. +.|..|+.++.. ...|..|-.+.- +..|..|+.+.
T Consensus 668 rkCPkCG~~t~~--------------------~fCP~CGs~te~--------vy~CPsCGaev~~des~a~~CP~CGtpl 719 (1337)
T PRK14714 668 RRCPSCGTETYE--------------------NRCPDCGTHTEP--------VYVCPDCGAEVPPDESGRVECPRCDVEL 719 (1337)
T ss_pred EECCCCCCcccc--------------------ccCcccCCcCCC--------ceeCccCCCccCCCccccccCCCCCCcc
Confidence 469999976432 156666665522 124555554332 23788888766
Q ss_pred cCC
Q psy8090 162 QTS 164 (242)
Q Consensus 162 ~~~ 164 (242)
.+.
T Consensus 720 v~~ 722 (1337)
T PRK14714 720 TPY 722 (1337)
T ss_pred ccc
Confidence 543
No 78
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=22.80 E-value=67 Score=22.33 Aligned_cols=24 Identities=21% Similarity=0.594 Sum_probs=17.7
Q ss_pred CCcccCCCcccCCCcceeeeeecCCC
Q psy8090 152 PRCSACDEECQTSSQDILYYLTRDSE 177 (242)
Q Consensus 152 prC~~C~~~I~~~~~~~~~~~~~~~~ 177 (242)
..|+-|+..|.+|.. ..||.+|+.
T Consensus 4 ~~CsFcG~~I~PGtG--~m~Vr~Dg~ 27 (66)
T COG2075 4 RVCSFCGKKIEPGTG--IMYVRNDGK 27 (66)
T ss_pred eEecCcCCccCCCce--EEEEecCCe
Confidence 469999999999874 456666554
No 79
>PRK10445 endonuclease VIII; Provisional
Probab=22.62 E-value=1.4e+02 Score=26.11 Aligned_cols=42 Identities=21% Similarity=0.228 Sum_probs=24.1
Q ss_pred hhHHHHHHHHhhh-C-CCCCCCchhcccCCHHHHHHHHHHHHHhhhhcc
Q psy8090 29 PGEQYRIRQLLHQ-L-PPHDNEVRYCHALSEDERKELRLFSAQRKREAL 75 (242)
Q Consensus 29 ~g~~~r~~ql~~q-l-P~~d~~~~~c~~l~e~e~~~~~~f~~~~~~~~~ 75 (242)
-|-.|+.--|.+. + | .+.+..|++++.+.+-.-...--+.++
T Consensus 167 IGNiyadEiLf~A~I~P-----~~~~~~Ls~~~~~~L~~~i~~vl~~ai 210 (263)
T PRK10445 167 LGNYLRVEILWQAGLTP-----QHKAKDLNEAQLDALAHALLDIPRLSY 210 (263)
T ss_pred ccHHHHHHHHHHcCCCc-----CCCcccCCHHHHHHHHHHHHHHHHHHH
Confidence 4555665555332 2 3 345678888888777665555444444
No 80
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=22.61 E-value=47 Score=22.51 Aligned_cols=24 Identities=46% Similarity=1.032 Sum_probs=17.7
Q ss_pred cccccCCCCC--CccceeeCCeeccH
Q psy8090 120 TCSVCNELLV--DLIYFYRGDKLYCG 143 (242)
Q Consensus 120 ~C~~C~~~L~--~~~~~~~dg~~yC~ 143 (242)
.|..|++.|. ..+|..++.+.||.
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS 43 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCS 43 (58)
T ss_pred HHHccCCCCCCCCCeeeecccccccc
Confidence 5677888886 24677788888885
No 81
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=22.41 E-value=29 Score=21.37 Aligned_cols=33 Identities=12% Similarity=-0.107 Sum_probs=18.1
Q ss_pred ccCCCccCCCCCCCCCCcccCCCCCCCHHHHhhhhc
Q psy8090 187 ERLEHQRDLPESYGTHRNSLNKEQNHSFDNLLKSNL 222 (242)
Q Consensus 187 ~h~~~f~~~~~~~g~~~f~~~d~~~yC~~cy~~~~a 222 (242)
|+.+|.-... . +..+...+-.+.|..|...+.+
T Consensus 14 ~~v~Hi~~~~--~-gg~~~~~Nl~~lC~~Ch~~k~~ 46 (47)
T PF01844_consen 14 LHVHHIIPRS--K-GGKNDLENLILLCPSCHRKKHD 46 (47)
T ss_dssp EEEEESS-TT--T-T---STTTEEEEEHHHHHHHH-
T ss_pred eEeECcCchh--c-CCCCCHHHHHHHhHHHHHHhcC
Confidence 4444544432 2 4445677888899999877643
No 82
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=21.98 E-value=95 Score=27.41 Aligned_cols=54 Identities=19% Similarity=0.505 Sum_probs=38.7
Q ss_pred ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCC
Q psy8090 88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTS 164 (242)
Q Consensus 88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~ 164 (242)
.|.+|.+.-.+ | ..++.|-..=|.|..|+..+.+ | -.......|.+|+.++.+.
T Consensus 134 RCr~C~~rYDP----V-----P~dkmwG~aef~C~~C~h~F~G--~------------~qm~v~sPCy~C~~~v~P~ 187 (278)
T PF15135_consen 134 RCRKCRKRYDP----V-----PCDKMWGIAEFHCPKCRHNFRG--F------------AQMGVPSPCYGCGNPVYPS 187 (278)
T ss_pred cccccccccCC----C-----ccccccceeeeecccccccchh--h------------hhcCCCCCccCCCCccCcc
Confidence 58888887654 2 3477888888999999988764 1 1123457899999988764
No 83
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.79 E-value=1.5e+02 Score=26.07 Aligned_cols=43 Identities=23% Similarity=0.309 Sum_probs=23.3
Q ss_pred hhHHHHHHHHhh-hCCCCCCCchhcccCCHHHHHHHHHHHHHhhhhcc
Q psy8090 29 PGEQYRIRQLLH-QLPPHDNEVRYCHALSEDERKELRLFSAQRKREAL 75 (242)
Q Consensus 29 ~g~~~r~~ql~~-qlP~~d~~~~~c~~l~e~e~~~~~~f~~~~~~~~~ 75 (242)
-|-.|+.--|.. .+ .-...+..|+++|.+.+..-.+.--+.++
T Consensus 170 iGNiya~EiLf~a~i----~P~~~~~~l~~~~~~~l~~a~~~vl~~ai 213 (272)
T PRK14810 170 VGNIYADEALFRAGI----RPQRLASSLSRERLRKLHDAIGEVLREAI 213 (272)
T ss_pred ccHhHHHHHHHHcCC----CCCCCcccCCHHHHHHHHHHHHHHHHHHH
Confidence 345566555543 22 22445678888887766554444333333
No 84
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.58 E-value=1.1e+02 Score=24.12 Aligned_cols=38 Identities=18% Similarity=0.447 Sum_probs=25.7
Q ss_pred ccccCCCceecCccccccccCCCCCcccCCcccccccCCCC
Q psy8090 88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELL 128 (242)
Q Consensus 88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L 128 (242)
.|..|+.+|.++..+ .. -.++|.-|.+.-| |..|+.++
T Consensus 41 qcp~csasirgd~~v-eg-vlglg~dye~psf-chncgs~f 78 (160)
T COG4306 41 QCPICSASIRGDYYV-EG-VLGLGGDYEPPSF-CHNCGSRF 78 (160)
T ss_pred cCCccCCccccccee-ee-eeccCCCCCCcch-hhcCCCCC
Confidence 599999999886543 11 1256777777655 78887765
No 85
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.90 E-value=1.7e+02 Score=25.77 Aligned_cols=44 Identities=23% Similarity=0.224 Sum_probs=22.7
Q ss_pred hhHHHHHHHHhhhCCCCCCCchhcccCCHHHHHHHHHHHHHhhhhcc
Q psy8090 29 PGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSAQRKREAL 75 (242)
Q Consensus 29 ~g~~~r~~ql~~qlP~~d~~~~~c~~l~e~e~~~~~~f~~~~~~~~~ 75 (242)
.|-.|+.--|-.. .=.-.+....|+++|.+.+-.-++.--+.++
T Consensus 171 IGNiyadEiLf~a---~I~P~~~~~~Ls~~~~~~L~~~i~~vL~~ai 214 (272)
T TIGR00577 171 IGNIYADEVLFRA---GIHPERLANSLSKEECELLHRAIKEVLRKAI 214 (272)
T ss_pred ccHHHHHHHHHHc---CCCcchhhccCCHHHHHHHHHHHHHHHHHHH
Confidence 4555665555332 1111345577788877766555554333333
No 86
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=20.53 E-value=96 Score=19.41 Aligned_cols=34 Identities=6% Similarity=-0.215 Sum_probs=18.4
Q ss_pred CCCCCCcccCCCccCCCCCCCCCCcccCCCCCCCHHHHh
Q psy8090 180 LPDEYRTERLEHQRDLPESYGTHRNSLNKEQNHSFDNLL 218 (242)
Q Consensus 180 ~~~~~~~~h~~~f~~~~~~~g~~~f~~~d~~~yC~~cy~ 218 (242)
+..|.+.+|..|.-.. ........+.-+|..|-.
T Consensus 17 C~~C~~~~H~~C~~~~-----~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 17 CDSCNRWYHQECVGPP-----EKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp BSTTSCEEETTTSTSS-----HSHHSHHSSSBSSHHHHH
T ss_pred cCCCChhhCcccCCCC-----hhhccCCCCcEECcCCcC
Confidence 6678888888765221 111112222667877753
No 87
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.52 E-value=1.6e+02 Score=26.02 Aligned_cols=27 Identities=11% Similarity=0.096 Sum_probs=16.8
Q ss_pred chhcccCCHHHHHHHHHHHHHhhhhcc
Q psy8090 49 VRYCHALSEDERKELRLFSAQRKREAL 75 (242)
Q Consensus 49 ~~~c~~l~e~e~~~~~~f~~~~~~~~~ 75 (242)
.+....|+++|.+.|-.-++.--+.++
T Consensus 197 ~~~~~~Ls~~~~~~L~~~i~~vl~~ai 223 (282)
T PRK13945 197 TTPAGQLKKKQLERLREAIIEVLKTSI 223 (282)
T ss_pred cCccccCCHHHHHHHHHHHHHHHHHHH
Confidence 344678888887776665554444444
Done!