Query psy11903
Match_columns 179
No_of_seqs 248 out of 1148
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 21:54:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11903.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11903hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3476|consensus 100.0 4.7E-49 1E-53 286.3 -0.1 100 80-179 1-100 (100)
2 PF10235 Cript: Microtubule-as 100.0 4.9E-43 1.1E-47 257.1 4.3 88 90-179 1-90 (90)
3 KOG1604|consensus 99.8 9.1E-19 2E-23 154.3 8.5 107 10-121 5-124 (353)
4 PRK11055 galM galactose-1-epim 99.7 6.5E-17 1.4E-21 143.2 9.2 88 22-113 5-104 (342)
5 PTZ00485 aldolase 1-epimerase; 99.7 2.9E-16 6.2E-21 141.1 9.2 85 27-114 12-110 (376)
6 TIGR02636 galM_Leloir galactos 99.6 2E-15 4.4E-20 132.9 8.9 85 27-114 3-99 (335)
7 PLN00194 aldose 1-epimerase; P 99.4 1.6E-12 3.5E-17 114.7 9.1 88 22-114 5-104 (337)
8 cd09019 galactose_mutarotase_l 99.3 8.4E-12 1.8E-16 109.1 8.0 83 30-114 1-95 (326)
9 COG2017 GalM Galactose mutarot 99.0 1.9E-09 4.1E-14 94.2 8.2 90 13-114 2-103 (308)
10 PRK15172 putative aldose-1-epi 98.3 1.7E-06 3.6E-11 75.2 7.6 75 28-110 10-95 (300)
11 PF01263 Aldose_epim: Aldose 1 98.0 1.7E-05 3.8E-10 67.1 7.1 80 29-112 1-91 (300)
12 cd09022 Aldose_epim_Ec_YihR Al 97.8 5.2E-05 1.1E-09 64.7 5.9 66 40-111 2-77 (284)
13 cd09024 Aldose_epim_lacX Aldos 95.7 0.019 4.2E-07 49.3 5.2 55 31-90 1-55 (288)
14 cd01081 Aldose_epim aldose 1-e 95.4 0.037 8.1E-07 46.0 5.7 65 40-110 2-79 (284)
15 PF10217 DUF2039: Uncharacteri 95.3 0.0023 4.9E-08 47.6 -1.8 41 126-167 49-90 (92)
16 COG5152 Uncharacterized conser 93.1 0.023 4.9E-07 48.1 -0.4 34 135-168 198-240 (259)
17 KOG3241|consensus 92.3 0.0096 2.1E-07 49.5 -3.6 46 125-171 60-106 (227)
18 PF12773 DZR: Double zinc ribb 89.1 0.26 5.6E-06 31.5 1.7 34 136-170 1-41 (50)
19 PF13248 zf-ribbon_3: zinc-rib 79.8 0.95 2.1E-05 25.6 0.9 22 134-156 3-24 (26)
20 PF13240 zinc_ribbon_2: zinc-r 79.8 0.85 1.8E-05 25.4 0.7 20 135-155 1-20 (23)
21 PF14849 YidC_periplas: YidC p 79.4 3.6 7.8E-05 34.5 4.7 37 30-67 1-41 (270)
22 KOG1813|consensus 69.7 2.3 4.9E-05 37.9 1.1 36 135-170 243-287 (313)
23 PF14634 zf-RING_5: zinc-RING 68.4 1.3 2.7E-05 27.8 -0.5 20 147-166 21-44 (44)
24 cd09021 Aldose_epim_Ec_YphB al 66.9 12 0.00025 31.6 4.9 66 42-111 4-80 (273)
25 TIGR03593 yidC_nterm membrane 64.9 8.3 0.00018 34.2 3.8 29 28-57 73-101 (366)
26 PF07191 zinc-ribbons_6: zinc- 61.2 2.3 5.1E-05 30.1 -0.3 37 135-171 3-43 (70)
27 smart00504 Ubox Modified RING 59.7 3.7 8E-05 26.7 0.5 23 147-169 20-46 (63)
28 PF06750 DiS_P_DiS: Bacterial 58.9 3.4 7.4E-05 30.3 0.2 37 133-169 33-69 (92)
29 KOG2272|consensus 57.2 6.9 0.00015 34.5 1.8 51 116-169 149-206 (332)
30 KOG0320|consensus 54.8 3.3 7.1E-05 34.5 -0.5 36 134-169 132-178 (187)
31 PF10571 UPF0547: Uncharacteri 54.6 6.5 0.00014 22.5 0.9 22 135-157 2-23 (26)
32 PRK12496 hypothetical protein; 54.3 5.8 0.00013 32.0 0.8 21 149-169 128-154 (164)
33 PF13920 zf-C3HC4_3: Zinc fing 53.8 2.7 5.9E-05 26.7 -0.9 37 135-171 4-50 (50)
34 TIGR00599 rad18 DNA repair pro 51.6 6 0.00013 36.5 0.6 36 134-169 27-71 (397)
35 KOG3799|consensus 51.3 6.8 0.00015 31.5 0.8 36 133-170 65-101 (169)
36 PF06906 DUF1272: Protein of u 49.6 7.2 0.00016 26.6 0.6 36 134-169 6-52 (57)
37 PF05715 zf-piccolo: Piccolo Z 48.5 6.8 0.00015 27.0 0.3 32 134-167 3-39 (61)
38 PRK01318 membrane protein inse 47.9 37 0.00079 32.4 5.2 27 30-57 40-66 (521)
39 smart00132 LIM Zinc-binding do 45.2 17 0.00036 20.8 1.7 9 160-168 29-37 (39)
40 PF03660 PHF5: PHF5-like prote 45.2 5.7 0.00012 30.3 -0.5 26 130-155 52-77 (106)
41 PLN03208 E3 ubiquitin-protein 44.4 8 0.00017 32.4 0.2 36 135-170 20-80 (193)
42 cd04476 RPA1_DBD_C RPA1_DBD_C: 44.1 9.4 0.0002 30.0 0.5 22 133-154 34-57 (166)
43 PF14471 DUF4428: Domain of un 43.8 11 0.00024 24.8 0.8 16 160-175 1-16 (51)
44 cd09020 D-hex-6-P-epi_like D-h 42.0 47 0.001 28.2 4.6 32 31-67 2-33 (269)
45 PF14446 Prok-RING_1: Prokaryo 37.5 15 0.00033 24.7 0.7 14 156-169 3-16 (54)
46 TIGR00375 conserved hypothetic 37.0 14 0.00031 33.8 0.6 38 125-169 230-269 (374)
47 KOG1594|consensus 36.1 89 0.0019 27.9 5.3 30 27-56 22-51 (305)
48 PF13923 zf-C3HC4_2: Zinc fing 36.0 5.9 0.00013 23.9 -1.4 10 147-156 18-27 (39)
49 KOG1701|consensus 36.0 6.9 0.00015 36.6 -1.5 36 135-170 304-346 (468)
50 PF14486 DUF4432: Domain of un 35.7 1.1E+02 0.0023 26.9 5.9 41 27-74 3-44 (302)
51 KOG0153|consensus 34.6 10 0.00023 34.6 -0.6 47 112-164 26-83 (377)
52 PF10764 Gin: Inhibitor of sig 34.2 10 0.00022 24.5 -0.6 32 135-172 1-32 (46)
53 PF14315 DUF4380: Domain of un 33.3 1.1E+02 0.0023 26.3 5.4 29 28-57 4-33 (274)
54 cd00162 RING RING-finger (Real 33.1 17 0.00036 21.1 0.3 21 147-167 19-44 (45)
55 PRK05580 primosome assembly pr 33.1 34 0.00074 33.4 2.6 22 148-169 408-432 (679)
56 PHA02929 N1R/p28-like protein; 32.7 20 0.00042 30.9 0.8 41 133-173 174-231 (238)
57 PF01258 zf-dskA_traR: Prokary 32.6 19 0.00042 21.5 0.5 12 159-170 4-15 (36)
58 KOG4458|consensus 32.5 19 0.00042 25.4 0.6 33 123-162 4-36 (78)
59 PF13894 zf-C2H2_4: C2H2-type 32.1 11 0.00024 19.2 -0.5 15 160-174 2-16 (24)
60 COG1996 RPC10 DNA-directed RNA 31.8 20 0.00044 23.6 0.6 28 135-169 8-35 (49)
61 COG0266 Nei Formamidopyrimidin 31.8 20 0.00043 31.5 0.7 32 124-155 236-272 (273)
62 KOG3896|consensus 31.8 20 0.00044 32.9 0.7 41 124-165 16-71 (449)
63 PRK00420 hypothetical protein; 31.6 24 0.00052 27.1 1.0 22 133-154 23-46 (112)
64 PF10621 FpoO: F420H2 dehydrog 30.7 22 0.00047 27.5 0.6 36 128-169 29-71 (119)
65 cd09025 Aldose_epim_Slr1438 Al 30.7 2.2E+02 0.0047 24.0 6.9 55 30-90 3-65 (271)
66 PF00412 LIM: LIM domain; Int 29.8 31 0.00067 21.8 1.2 11 135-145 28-38 (58)
67 PF06827 zf-FPG_IleRS: Zinc fi 29.4 16 0.00035 20.9 -0.2 21 135-155 3-28 (30)
68 COG1439 Predicted nucleic acid 27.7 30 0.00064 28.7 1.0 25 134-169 140-164 (177)
69 PRK14714 DNA polymerase II lar 26.8 34 0.00073 36.2 1.4 31 134-167 668-701 (1337)
70 PRK01103 formamidopyrimidine/5 26.1 31 0.00067 29.7 0.9 31 125-155 237-272 (274)
71 PRK14810 formamidopyrimidine-D 25.8 32 0.00069 29.7 0.9 30 125-154 236-270 (272)
72 COG1645 Uncharacterized Zn-fin 24.9 32 0.00069 27.2 0.7 24 134-157 29-53 (131)
73 PF00643 zf-B_box: B-box zinc 24.6 17 0.00037 21.9 -0.7 29 134-167 4-32 (42)
74 PRK14811 formamidopyrimidine-D 23.3 38 0.00082 29.3 0.9 33 125-157 227-264 (269)
75 PF14835 zf-RING_6: zf-RING of 23.0 57 0.0012 22.8 1.6 42 135-176 9-60 (65)
76 PF09706 Cas_CXXC_CXXC: CRISPR 22.8 43 0.00092 23.2 0.9 11 157-167 4-14 (69)
77 PF07649 C1_3: C1-like domain; 22.1 31 0.00067 19.7 0.1 22 135-156 2-23 (30)
78 PRK06393 rpoE DNA-directed RNA 22.0 41 0.00088 23.4 0.7 22 133-167 5-26 (64)
79 TIGR02420 dksA RNA polymerase- 21.9 37 0.00079 25.3 0.5 11 159-169 81-91 (110)
80 TIGR03826 YvyF flagellar opero 21.9 38 0.00083 26.8 0.6 24 131-156 79-102 (137)
81 TIGR00595 priA primosomal prot 21.7 87 0.0019 29.5 3.0 37 133-169 222-264 (505)
82 COG2888 Predicted Zn-ribbon RN 21.1 50 0.0011 22.8 1.0 29 134-169 10-38 (61)
83 KOG1734|consensus 20.9 32 0.0007 30.6 -0.0 15 158-172 224-238 (328)
84 PF06045 Rhamnogal_lyase: Rham 20.8 1.5E+02 0.0033 25.0 4.0 34 31-70 18-51 (203)
85 KOG1705|consensus 20.4 31 0.00067 26.0 -0.2 33 129-162 51-86 (110)
86 smart00746 TRASH metallochaper 20.2 47 0.001 17.6 0.6 9 161-169 1-9 (39)
87 COG1545 Predicted nucleic-acid 20.2 56 0.0012 25.6 1.2 20 134-154 30-49 (140)
No 1
>KOG3476|consensus
Probab=100.00 E-value=4.7e-49 Score=286.31 Aligned_cols=100 Identities=68% Similarity=1.234 Sum_probs=97.5
Q ss_pred hccccccceecceeccCccCCCCCccccCCceecccceeeeecccccCCCcccCcccchhhcccccCCCccCcccccccC
Q psy11903 80 MVCSKCEKKLGKVITPDNWKSGSRNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKG 159 (179)
Q Consensus 80 mvc~kc~~klg~va~pd~~k~~~~n~l~gG~~gi~~nk~l~~~k~~~~p~~~~~~~c~~ck~~~~~~~~~yc~~cay~~g 159 (179)
|||++||++|+++++||||+++.||+..+|++.|++||.|.+.|+||+||+..+.+|+|||+.|||+|+||||.|||+||
T Consensus 1 MVC~kCEkKLskvi~pd~wr~garn~~~sGgrkinenkaL~s~k~r~~p~gt~~~kC~iCk~~vHQ~GshYC~tCAY~Kg 80 (100)
T KOG3476|consen 1 MVCEKCEKKLSKVIGPDPWRDGARNTTESGGRKINENKALISKKKRATPYGTALAKCRICKQLVHQPGSHYCQTCAYKKG 80 (100)
T ss_pred CchhHHHHHhccccccCcccccccccCCCCCeecchhhhhhhhhhhcCccccccchhHHHHHHhcCCcchhHhHhhhhhh
Confidence 89999999999999999999999999999999999999777778999999999999999999999999999999999999
Q ss_pred cccccCcccccccccccccC
Q psy11903 160 ICAMCGKKLLDVKNYKQSAA 179 (179)
Q Consensus 160 ~c~mcgk~~~d~~~~~~s~~ 179 (179)
|||||||+|+||++|+||++
T Consensus 81 iCAMCGKki~nTK~ykQsst 100 (100)
T KOG3476|consen 81 ICAMCGKKILNTKNYKQSST 100 (100)
T ss_pred HHHHhhhHhhccccccccCC
Confidence 99999999999999999986
No 2
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=100.00 E-value=4.9e-43 Score=257.09 Aligned_cols=88 Identities=66% Similarity=1.194 Sum_probs=83.5
Q ss_pred cceeccCccCCCC--CccccCCceecccceeeeecccccCCCcccCcccchhhcccccCCCccCcccccccCcccccCcc
Q psy11903 90 GKVITPDNWKSGS--RNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKGICAMCGKK 167 (179)
Q Consensus 90 g~va~pd~~k~~~--~n~l~gG~~gi~~nk~l~~~k~~~~p~~~~~~~c~~ck~~~~~~~~~yc~~cay~~g~c~mcgk~ 167 (179)
++||+||||++++ +|+..+|+++|+|||||+++ ++ |||++++++|++||++|||+|+||||.|||+|||||||||+
T Consensus 1 tklatPd~~k~~~~~~~~~~~g~r~i~eNKlLs~~-~~-nPy~~~~~~C~~CK~~v~q~g~~YCq~CAYkkGiCamCGKk 78 (90)
T PF10235_consen 1 TKLATPDPWKKGAMYRNTAESGGRKIGENKLLSKK-KK-NPYAPYSSKCKICKTKVHQPGAKYCQTCAYKKGICAMCGKK 78 (90)
T ss_pred CccccCCccccCcccccccCCCCccccceeeeccc-cc-CcccccCccccccccccccCCCccChhhhcccCcccccCCe
Confidence 4689999999999 99999999999999999873 44 99999999999999999999999999999999999999999
Q ss_pred cccccccccccC
Q psy11903 168 LLDVKNYKQSAA 179 (179)
Q Consensus 168 ~~d~~~~~~s~~ 179 (179)
|+||++|+||+|
T Consensus 79 i~dtk~ykqs~v 90 (90)
T PF10235_consen 79 ILDTKNYKQSSV 90 (90)
T ss_pred ecccccccccCC
Confidence 999999999987
No 3
>KOG1604|consensus
Probab=99.77 E-value=9.1e-19 Score=154.27 Aligned_cols=107 Identities=36% Similarity=0.575 Sum_probs=90.2
Q ss_pred eeccccceeccCCCceecEEEEEEEcCCCeEEEEecCCcEEEEEEeeCCCCcccceEeCcCCchhhh-----hhhhcccc
Q psy11903 10 MEDKFGECINESNGQVLPVRRFTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMREEI-----YFIMVCSK 84 (179)
Q Consensus 10 ~~~~FG~~~~~~~G~~~~v~~~tL~n~~gl~v~vlnyGAtI~sl~vpdr~G~~~dVVLGfd~~e~Y~-----~~gmvc~k 84 (179)
.+..|| -+++...+ .++.|||.|+.+|+|.|++|||+|+||.+||++|+..|||||||+++.|+ |||++.+|
T Consensus 5 ~~~~~~-~~~~~~~~--~~~~~tl~n~~~l~vti~~~GATi~sL~vpd~~gk~~DVVLGfd~v~gY~~~~~~yfGatvGR 81 (353)
T KOG1604|consen 5 VEDVFG-NSNTDQKQ--TIRVYTLGNGKGLQVTIINLGATITSLKVPDKSGKLDDVVLGFDDVDGYLKDDAAYFGATVGR 81 (353)
T ss_pred cccccC-CCcccccC--ceEEEEecCCCeeEEEEeeCCcEEEEEEcCCcCCcccceEecccchhhhccCCcceecceehh
Confidence 345666 23333343 89999999998999999999999999999999999999999999999998 69999999
Q ss_pred ccceecc--------eeccCccCCCCCccccCCceecccceeeee
Q psy11903 85 CEKKLGK--------VITPDNWKSGSRNTIESGGRRIGENKALTA 121 (179)
Q Consensus 85 c~~klg~--------va~pd~~k~~~~n~l~gG~~gi~~nk~l~~ 121 (179)
.++||++ .++..+ |+++|++|||..||+.-...-.
T Consensus 82 vANRI~~G~F~ldgk~y~lt~--N~g~n~lHgg~~gf~~~~w~v~ 124 (353)
T KOG1604|consen 82 VANRIAKGKFSLDGKPYKLTV--NNGKNTLHGGIKGFDKVIWEVV 124 (353)
T ss_pred hhhhcccceEEECCceEEecc--cCCCccccCCcccccceEEEEE
Confidence 9999986 344443 4789999999999998887755
No 4
>PRK11055 galM galactose-1-epimerase; Provisional
Probab=99.69 E-value=6.5e-17 Score=143.16 Aligned_cols=88 Identities=26% Similarity=0.443 Sum_probs=78.0
Q ss_pred CCceecEEEEEEEcCCCeEEEEecCCcEEEEEEeeCCCCcccceEeCcCCchhhh----hhhhccccccceecc------
Q psy11903 22 NGQVLPVRRFTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMREEI----YFIMVCSKCEKKLGK------ 91 (179)
Q Consensus 22 ~G~~~~v~~~tL~n~~gl~v~vlnyGAtI~sl~vpdr~G~~~dVVLGfd~~e~Y~----~~gmvc~kc~~klg~------ 91 (179)
+|+ ++++|||+|++|++|+|++|||+|++|++||++|..+|||||||++++|+ ++|++.+++++||+.
T Consensus 5 ~g~--~v~~~tl~n~~g~~v~i~~~GA~i~~l~vpd~~g~~~dvvlg~~~~~~y~~~~~~~Ga~iGr~anRI~~g~f~~~ 82 (342)
T PRK11055 5 DGQ--PYRLLTLRNNAGMVVTLMDWGATWLSCRVPLSDGSVREVLLGCASPEDYPDQAAYLGASVGRYANRIANSRFTLD 82 (342)
T ss_pred CCC--eEEEEEEECCCCeEEEEeCcCcEEEEEEeECCCCCEeeeEECCCCHHHHhhCCCccCceeCCcCCcccCCEEEEC
Confidence 666 89999999988999999999999999999999999999999999999998 799999999999964
Q ss_pred --eeccCccCCCCCccccCCceec
Q psy11903 92 --VITPDNWKSGSRNTIESGGRRI 113 (179)
Q Consensus 92 --va~pd~~k~~~~n~l~gG~~gi 113 (179)
.+++++ + .+.|+||||..|+
T Consensus 83 G~~y~L~~-N-~~~n~lHGg~~G~ 104 (342)
T PRK11055 83 GETYQLSP-N-QGGNQLHGGPEGF 104 (342)
T ss_pred CEEEEccc-C-CCCcccCCCCccc
Confidence 455554 4 4679999997665
No 5
>PTZ00485 aldolase 1-epimerase; Provisional
Probab=99.66 E-value=2.9e-16 Score=141.09 Aligned_cols=85 Identities=18% Similarity=0.286 Sum_probs=72.7
Q ss_pred cEEEEEEEcCCCeEEEEecCCcEEEEEEeeCC-CCcccceEeCcC-Cchhhh----hhhhccccccceecc--------e
Q psy11903 27 PVRRFTLTNSQRMSVQVIDYGATITTIKVPDK-RGNVDDVVLGFD-DMREEI----YFIMVCSKCEKKLGK--------V 92 (179)
Q Consensus 27 ~v~~~tL~n~~gl~v~vlnyGAtI~sl~vpdr-~G~~~dVVLGfd-~~e~Y~----~~gmvc~kc~~klg~--------v 92 (179)
..++|+|+|+ +|+|+|+||||+|++|++||+ +|.++||||||| ++++|+ ++|++.+|+++||.. .
T Consensus 12 ~~~~~~L~N~-~~~v~i~n~GA~i~si~v~~~~~g~~~dvvLG~d~~~~~Y~~~~~y~Ga~iGr~AnRI~~G~f~ldG~~ 90 (376)
T PTZ00485 12 YDKLVWLETD-RLKVGLTNYAASVASIQVYHPADNKWIEVNCGYPKNPEEAYADPDYMGATVGRCAGRVAGGVFTLDGVK 90 (376)
T ss_pred CCcEEEEEeC-CEEEEEECcCcEEEEEEEEcCCCCcEEeEEECCCCCHHHHhhCCCccCcEeCCCCCeEECCEEEECCEE
Confidence 3668999996 599999999999999999873 399999999997 699998 799999999999964 4
Q ss_pred eccCccCCCCCccccCCceecc
Q psy11903 93 ITPDNWKSGSRNTIESGGRRIG 114 (179)
Q Consensus 93 a~pd~~k~~~~n~l~gG~~gi~ 114 (179)
++++. |.+.|+||||..+|+
T Consensus 91 YqL~~--Neg~n~LHGG~~gf~ 110 (376)
T PTZ00485 91 YYTQK--NRGENTCHCGDDAYH 110 (376)
T ss_pred EEccC--CCCCcccCCCCCccc
Confidence 55553 456799999998887
No 6
>TIGR02636 galM_Leloir galactose mutarotase. Members of this protein family act as galactose mutarotase (D-galactose 1-epimerase) and participate in the Leloir pathway for galactose/glucose interconversion. All members of the seed alignment for this model are found in gene clusters with other enzymes of the Leloir pathway. This enzyme family belongs to the aldose 1-epimerase family, described by pfam model pfam01263. However, the enzyme described as aldose 1-epimerase itself (EC 5.1.3.3) is called broadly specific for D-glucose, L-arabinose, D-xylose, D-galactose, maltose and lactose. The restricted genome context for genes in this family suggests members should act primarily on D-galactose.
Probab=99.61 E-value=2e-15 Score=132.88 Aligned_cols=85 Identities=25% Similarity=0.421 Sum_probs=74.1
Q ss_pred cEEEEEEEcCCCeEEEEecCCcEEEEEEeeCCCCcccceEeCcCCchhhh----hhhhccccccceecc--------eec
Q psy11903 27 PVRRFTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMREEI----YFIMVCSKCEKKLGK--------VIT 94 (179)
Q Consensus 27 ~v~~~tL~n~~gl~v~vlnyGAtI~sl~vpdr~G~~~dVVLGfd~~e~Y~----~~gmvc~kc~~klg~--------va~ 94 (179)
.+++|||+|++||+|+|++|||+|++|.+||++ ..+|||||||++++|+ ++|++.+++++||.. .++
T Consensus 3 ~v~~~~l~n~~g~~v~i~~~GA~i~~l~~pd~~-~~~~vvlg~~~~~~y~~~~~~~Ga~igp~anRI~~g~f~~~G~~y~ 81 (335)
T TIGR02636 3 PAQLITLTNNNGMTISFMDIGATWLSCQVPLAG-ELREVLLGFASMEEYYKQDAYLGATVGRYANRIANGSFEIDGETYQ 81 (335)
T ss_pred eeEEEEEECCCCcEEEEeCcCcEEEEEEeeCCC-CccceEECCCCHHHHhhCCCccCCCcCCCCceecCCEEEECCEEEE
Confidence 789999999889999999999999999999976 7789999999999998 789999999999963 455
Q ss_pred cCccCCCCCccccCCceecc
Q psy11903 95 PDNWKSGSRNTIESGGRRIG 114 (179)
Q Consensus 95 pd~~k~~~~n~l~gG~~gi~ 114 (179)
+++ | .+.|++|||..|++
T Consensus 82 L~~-N-~~~n~lHGg~~G~~ 99 (335)
T TIGR02636 82 LSI-N-QGGNCLHGGPEGFD 99 (335)
T ss_pred ecc-C-CCCcccCCCCcccc
Confidence 553 4 45799999986664
No 7
>PLN00194 aldose 1-epimerase; Provisional
Probab=99.38 E-value=1.6e-12 Score=114.71 Aligned_cols=88 Identities=28% Similarity=0.531 Sum_probs=75.1
Q ss_pred CCceecEEEEEEEcCCCeEEEEecCCcEEEEEEeeCCCCcccceEeCcCCchhhh----hhhhccccccceecc------
Q psy11903 22 NGQVLPVRRFTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMREEI----YFIMVCSKCEKKLGK------ 91 (179)
Q Consensus 22 ~G~~~~v~~~tL~n~~gl~v~vlnyGAtI~sl~vpdr~G~~~dVVLGfd~~e~Y~----~~gmvc~kc~~klg~------ 91 (179)
.|+ .+.+|+|+|+ .++|+|++|||+|++|.++|++|.++||||||++.++|+ ++|++.++.++||..
T Consensus 5 ~~~--~~~~~~L~n~-~l~~~i~~~GA~l~s~~~~~~~g~~~~vvlg~~~~~~y~~~~~~~Ga~lgp~anRI~~g~~~~~ 81 (337)
T PLN00194 5 AEE--KPGIYELKNG-NISVKLTNYGATITSLILPDKNGKLADVVLGFDSVEPYKNDSPYFGAIVGRVANRIKGAKFTLN 81 (337)
T ss_pred CCC--eeEEEEEEeC-CEEEEEECCCcEEEEEEeECCCCCEeeeEECCCCHHHHhhCCCccCCeeCCCCCceeCCEEEEC
Confidence 455 8999999995 699999999999999999999999999999999999998 578999999999853
Q ss_pred --eeccCccCCCCCccccCCceecc
Q psy11903 92 --VITPDNWKSGSRNTIESGGRRIG 114 (179)
Q Consensus 92 --va~pd~~k~~~~n~l~gG~~gi~ 114 (179)
.+..++ +.+.|.+|||..|+.
T Consensus 82 G~~y~l~~--N~~~~~lHGg~~G~~ 104 (337)
T PLN00194 82 GVTYKLPP--NNGPNSLHGGPKGFS 104 (337)
T ss_pred CEEEEecc--CCCCcccCCCCcccC
Confidence 444443 345799999987765
No 8
>cd09019 galactose_mutarotase_like galactose mutarotase_like. Galactose mutarotase catalyzes the conversion of beta-D-galactose to alpha-D-galactose. Beta-D-galactose is produced by the degradation of lactose, a disaccharide composed of beta-D-glucose and beta-D-galactose. This epimerization reaction is the first step in the four-step Leloir pathway, which converts galactose into metabolically important glucose. This epimerization step is followed by the phosophorylation of alpha-D-galactose by galactokinase, an enzyme which can only act on the alpha anomer. A glutamate and a histidine residue of the galactose mutarotase have been shown to be critical for catalysis, the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen. Galactose mutarotase is a member of the aldose-1-epimerase superfamily.
Probab=99.29 E-value=8.4e-12 Score=109.09 Aligned_cols=83 Identities=34% Similarity=0.673 Sum_probs=70.3
Q ss_pred EEEEEcCCCeEEEEecCCcEEEEEEeeCCCCcccceEeCcCCchhhh----hhhhccccccceecc--------eeccCc
Q psy11903 30 RFTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMREEI----YFIMVCSKCEKKLGK--------VITPDN 97 (179)
Q Consensus 30 ~~tL~n~~gl~v~vlnyGAtI~sl~vpdr~G~~~dVVLGfd~~e~Y~----~~gmvc~kc~~klg~--------va~pd~ 97 (179)
+|+|+|+++++|+|+++||+|++|.+++++|..++|||||+++++|+ +++++.++.++||.. .++.++
T Consensus 1 ~~~l~n~~~~~~~i~~~GA~l~~l~~~~~~g~~~~~v~~~~~~~~~~~~~~~~g~~lgp~anRi~~g~~~~~G~~y~l~~ 80 (326)
T cd09019 1 LYTLTNGNGLRVSILNYGATIQSLKVPDKNGKLRDVVLGFDDLEDYLKNSPYFGATVGRVANRIANGRFTLDGKTYQLEA 80 (326)
T ss_pred CEEEECCCCcEEEEECcCcEEEEEEEECCCCCEeeeEECCCCHHHHhhCCCccCCcccCcCCeecCCEEEECCEEEEccC
Confidence 37899966899999999999999999998898899999999999998 578889999999863 455553
Q ss_pred cCCCCCccccCCceecc
Q psy11903 98 WKSGSRNTIESGGRRIG 114 (179)
Q Consensus 98 ~k~~~~n~l~gG~~gi~ 114 (179)
+ .++|+||||..|+.
T Consensus 81 -N-e~~~~LHGg~~G~~ 95 (326)
T cd09019 81 -N-EGPNHLHGGPKGFD 95 (326)
T ss_pred -C-CCCcccCCCCcccc
Confidence 4 44899999986764
No 9
>COG2017 GalM Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]
Probab=98.97 E-value=1.9e-09 Score=94.23 Aligned_cols=90 Identities=32% Similarity=0.539 Sum_probs=75.1
Q ss_pred cccceeccCCCceecEEEEEEEcCCCeEEEEecCCcEEEEEEeeCCCCcccceEeCcCCchhhh----hhhhccccccce
Q psy11903 13 KFGECINESNGQVLPVRRFTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMREEI----YFIMVCSKCEKK 88 (179)
Q Consensus 13 ~FG~~~~~~~G~~~~v~~~tL~n~~gl~v~vlnyGAtI~sl~vpdr~G~~~dVVLGfd~~e~Y~----~~gmvc~kc~~k 88 (179)
.|+..+ +|. .+..+++.|+.++.+.|.+|||+|++|++ +| ++||||+++.++|. +.+++.++.++|
T Consensus 2 ~~~~~~---~~~--~~~~i~~~~~~~~~~~~~~~GA~l~~l~~---~~--~~v~l~~~~~~~~~~~~~~~ga~l~p~anR 71 (308)
T COG2017 2 PFGAAP---DGQ--PVRLLTLGNGGGMVVTVPDWGATLTSLRV---NG--RNLLLGFDDAESYPATRGYGGAILGPYANR 71 (308)
T ss_pred cccccc---CCC--ceEEEEEeCCCeEEEEEccCCcEEEEEEE---CC--ceEEeecCCHHHhccccccccceecCccCc
Confidence 355444 777 89999999988999999999999999999 45 79999999999998 356899999999
Q ss_pred ecc--------eeccCccCCCCCccccCCceecc
Q psy11903 89 LGK--------VITPDNWKSGSRNTIESGGRRIG 114 (179)
Q Consensus 89 lg~--------va~pd~~k~~~~n~l~gG~~gi~ 114 (179)
|.. .+++.+ ++ +.|++|||.+++.
T Consensus 72 I~~g~f~~~G~~y~L~~-N~-~~~~lHG~~~~~~ 103 (308)
T COG2017 72 ISNGRFTLDGKTYQLPP-NE-GGNALHGGARDFD 103 (308)
T ss_pred ccCCEEEECCEEEEeCC-CC-CCccccCCccCCC
Confidence 853 777775 55 7899999987653
No 10
>PRK15172 putative aldose-1-epimerase; Provisional
Probab=98.33 E-value=1.7e-06 Score=75.25 Aligned_cols=75 Identities=12% Similarity=0.127 Sum_probs=58.2
Q ss_pred EEEEEEEcCCCeEEEEecCCcEEEEEEeeCCCCcccceEeCcCCchhhh--hhhhccccccceecc--------eeccCc
Q psy11903 28 VRRFTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMREEI--YFIMVCSKCEKKLGK--------VITPDN 97 (179)
Q Consensus 28 v~~~tL~n~~gl~v~vlnyGAtI~sl~vpdr~G~~~dVVLGfd~~e~Y~--~~gmvc~kc~~klg~--------va~pd~ 97 (179)
-..++|+|+ .++|+|++|||+|++|++. | .+||||++. ++|. ++|.+-+++++||.. .+..++
T Consensus 10 ~~~~~l~~~-~~~v~i~~~Ga~i~~l~~~---~--~~vv~~~~~-~~~~~~~~g~~L~P~anRI~~g~f~~~G~~y~L~~ 82 (300)
T PRK15172 10 GQTISLAAG-DYQATIVTVGAGLAELTFQ---G--RHLVIPHKP-EEMPLAHLGKVLIPWPNRIANGCYRYQGQEYQLPI 82 (300)
T ss_pred cCEEEEeCC-CEEEEEecCCcEEEEEEEC---C--EEEEecCCc-cccCccccccEecccCCeecCCEEEECCEEEECCC
Confidence 346889985 7999999999999999983 4 489999975 6665 577888999999863 555554
Q ss_pred cCCC-CCccccCCc
Q psy11903 98 WKSG-SRNTIESGG 110 (179)
Q Consensus 98 ~k~~-~~n~l~gG~ 110 (179)
|++ ..|.+|||-
T Consensus 83 -N~~~~~~~lHG~~ 95 (300)
T PRK15172 83 -NEHVSKAAIHGLL 95 (300)
T ss_pred -CCCCCCcccCCCc
Confidence 432 478899974
No 11
>PF01263 Aldose_epim: Aldose 1-epimerase; InterPro: IPR008183 Aldose 1-epimerase (5.1.3.3 from EC) (mutarotase) is the enzyme responsible for the anomeric interconversion of D-glucose and other aldoses between their alpha- and beta-forms. The sequence of mutarotase from two bacteria, Acinetobacter calcoaceticus and Streptococcus thermophilus is available []. It has also been shown that, on the basis of extensive sequence similarities, a mutarotase domain seems to be present in the C-terminal half of the fungal GAL10 protein which encodes, in the N-terminal part, UDP-glucose 4-epimerase.; GO: 0016853 isomerase activity, 0005975 carbohydrate metabolic process; PDB: 1YGA_A 3DCD_A 2CIQ_A 2CIS_A 2CIR_A 2HTB_C 2HTA_B 3Q1N_A 1NSZ_B 1NSR_B ....
Probab=98.01 E-value=1.7e-05 Score=67.07 Aligned_cols=80 Identities=19% Similarity=0.141 Sum_probs=60.4
Q ss_pred EEEEEEcCCCeEEEEecCCcEEEEEEeeCCCCcccceEeCcCCchhhhhh---hhccccccceec--------ceeccCc
Q psy11903 29 RRFTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMREEIYF---IMVCSKCEKKLG--------KVITPDN 97 (179)
Q Consensus 29 ~~~tL~n~~gl~v~vlnyGAtI~sl~vpdr~G~~~dVVLGfd~~e~Y~~~---gmvc~kc~~klg--------~va~pd~ 97 (179)
.+|+|+|+.++++.|..+||.|++|.+++ + ..+|+.++++.++|... +.+..+..+||. +.+..+.
T Consensus 1 ~~itL~n~~~~~~~i~~~Ga~l~s~~~~~-~--~~~~l~~~~~~~~~~~~~~~~~~l~p~~~Ri~~g~~~~~g~~~~l~~ 77 (300)
T PF01263_consen 1 DLITLENGNGLSAVIPEYGAELTSLQVKG-N--GREVLWQPDPADAYWSNSFGGPILFPWPNRIRNGRFTFDGKPYCLPW 77 (300)
T ss_dssp EEEEEEETTSEEEEEETBTTEEEEEEETT-T--TEESB-B-STHHHHHHSTCTTCEECSCSSEEGGGEEEETTEEEEBSS
T ss_pred CEEEEECCCceEEEEeccCcEEEEEEECC-C--CeEEecCCCChHHhcccccceeeeecccceEECCEEEECCEEEEeee
Confidence 36899997689999999999999999986 4 47999999998888864 567788888873 3444442
Q ss_pred cCCCCCccccCCcee
Q psy11903 98 WKSGSRNTIESGGRR 112 (179)
Q Consensus 98 ~k~~~~n~l~gG~~g 112 (179)
+....|.+||.-+.
T Consensus 78 -~~~~~~~~HG~~~~ 91 (300)
T PF01263_consen 78 -NGPYPNPIHGFARN 91 (300)
T ss_dssp -SBTTTBEETBSGGG
T ss_pred -ccCCCcCCCCCccc
Confidence 33278999997654
No 12
>cd09022 Aldose_epim_Ec_YihR Aldose 1-epimerase, similar to Escherichia coli YihR. Proteins similar to Escherichia coli YihR are uncharacterized members of aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen.
Probab=97.76 E-value=5.2e-05 Score=64.74 Aligned_cols=66 Identities=17% Similarity=0.096 Sum_probs=50.5
Q ss_pred EEEEecCCcEEEEEEeeCCCCcccceEeCcCCchh-hhhhhhccccccceecc--------eeccCccCCC-CCccccCC
Q psy11903 40 SVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMRE-EIYFIMVCSKCEKKLGK--------VITPDNWKSG-SRNTIESG 109 (179)
Q Consensus 40 ~v~vlnyGAtI~sl~vpdr~G~~~dVVLGfd~~e~-Y~~~gmvc~kc~~klg~--------va~pd~~k~~-~~n~l~gG 109 (179)
+|+|+++||+|++|.+ +| ++||+|+++.+. -.+.|++..++++||.. .+++++ |++ +.|.+||+
T Consensus 2 ~v~i~~~Ga~l~~~~~---~g--~~il~~~~~~~~~~~~~g~~l~p~~nRi~~g~~~~~G~~y~l~~-N~~~~~~~~HG~ 75 (284)
T cd09022 2 RAVVTEVGAGLRSLTV---GG--RDLVEPYPADEVPPGAAGQVLAPWPNRIADGRYTFDGVEHQLPI-TEPERGNAIHGL 75 (284)
T ss_pred EEEEEecCcEEEEEEE---CC--EEEEecCCCccCCccccccEEeeeCCcccCCEEEECCEEEEccC-cCCCCCCCCcCC
Confidence 6899999999999988 45 699999998872 12467899999999863 455553 432 57999997
Q ss_pred ce
Q psy11903 110 GR 111 (179)
Q Consensus 110 ~~ 111 (179)
.+
T Consensus 76 ~~ 77 (284)
T cd09022 76 VR 77 (284)
T ss_pred ee
Confidence 64
No 13
>cd09024 Aldose_epim_lacX Aldose 1-epimerase, similar to Lactococcus lactis lacX. Proteins similar to Lactococcus lactis lacX are uncharacterized members of aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen.
Probab=95.70 E-value=0.019 Score=49.29 Aligned_cols=55 Identities=22% Similarity=0.154 Sum_probs=40.0
Q ss_pred EEEEcCCCeEEEEecCCcEEEEEEeeCCCCcccceEeCcCCchhhhhhhhccccccceec
Q psy11903 31 FTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMREEIYFIMVCSKCEKKLG 90 (179)
Q Consensus 31 ~tL~n~~gl~v~vlnyGAtI~sl~vpdr~G~~~dVVLGfd~~e~Y~~~gmvc~kc~~klg 90 (179)
|+|+|+ .++++|.++||+|+++++.+ +| .+++..++ .+.|.....+|.+..+|+.
T Consensus 1 ~~l~n~-~~~a~v~~~Ga~l~s~~~~~-~g--~e~l~~~~-~~~~~~~~p~l~P~~gri~ 55 (288)
T cd09024 1 ITLENE-FLTVTISEHGAELTSIKDKK-TG--REYLWQGD-PAYWGRHAPILFPIVGRLK 55 (288)
T ss_pred CEEECC-cEEEEEeccCcEEEEEEeCC-CC--CEEEeCCC-hHHcCCCCCEEEeeccCCC
Confidence 578986 59999999999999999964 35 57887664 3334333367777777764
No 14
>cd01081 Aldose_epim aldose 1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism; they catalyze the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate and the histidine as the active site acid to protonate the C-5 ring oxygen.
Probab=95.38 E-value=0.037 Score=45.96 Aligned_cols=65 Identities=17% Similarity=0.122 Sum_probs=46.3
Q ss_pred EEEEecCCcEEEEEEeeCCCCcccceEeCcCCchhh-----hhhhhccccccceecc--------eeccCccCCCCCccc
Q psy11903 40 SVQVIDYGATITTIKVPDKRGNVDDVVLGFDDMREE-----IYFIMVCSKCEKKLGK--------VITPDNWKSGSRNTI 106 (179)
Q Consensus 40 ~v~vlnyGAtI~sl~vpdr~G~~~dVVLGfd~~e~Y-----~~~gmvc~kc~~klg~--------va~pd~~k~~~~n~l 106 (179)
+|+|+++||.|.++++++ ..+|+++++....| .+.+.++....+|+.. .+.+. .++..+.+
T Consensus 2 ~~~i~~~Ga~i~~~~~~~----~~~~l~~~~~~~~~~~~~~~~~~~~l~P~~gri~~g~~~~~g~~~~~~--~~~~~~~l 75 (284)
T cd01081 2 VAVIAPRGANIISLKVKG----DVDLLWGYPDAEEYPLAPTGGGGAILFPFANRISDGRYTFDGKQYPLN--EDEGGNAI 75 (284)
T ss_pred EEEEeCcCcEEEEEEcCC----CceEEecCCChhhhcccCCCCcceEecCcCCcccCCEEeECCEEecCC--CCCCCccc
Confidence 689999999999998863 36999999998876 2455777777777743 11121 23456888
Q ss_pred cCCc
Q psy11903 107 ESGG 110 (179)
Q Consensus 107 ~gG~ 110 (179)
||+-
T Consensus 76 HG~~ 79 (284)
T cd01081 76 HGFV 79 (284)
T ss_pred cCCe
Confidence 9864
No 15
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=95.25 E-value=0.0023 Score=47.57 Aligned_cols=41 Identities=37% Similarity=0.808 Sum_probs=33.4
Q ss_pred cCCCcccCcccchhhc-ccccCCCccCcccccccCcccccCcc
Q psy11903 126 FNPYTQKFESCKICRQ-KVHQVGSHYCQACAYKKGICAMCGKK 167 (179)
Q Consensus 126 ~~p~~~~~~~c~~ck~-~~~~~~~~yc~~cay~~g~c~mcgk~ 167 (179)
|-|..+ .++|-.|.+ +|.+.=|..|+.||-..++||.||++
T Consensus 49 YKpLt~-p~kC~~C~qktVk~AYh~iC~~Ca~~~~vCaKC~k~ 90 (92)
T PF10217_consen 49 YKPLTQ-PKKCNKCQQKTVKHAYHVICDPCAKELKVCAKCGKP 90 (92)
T ss_pred cccCCC-CccccccccchHHHHHHHHHHHHHHhhccCcccCCC
Confidence 344443 469999997 66776788999999999999999986
No 16
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=93.12 E-value=0.023 Score=48.13 Aligned_cols=34 Identities=41% Similarity=1.117 Sum_probs=28.0
Q ss_pred ccchhhccc-----ccCCCccCcccc---cccC-cccccCccc
Q psy11903 135 SCKICRQKV-----HQVGSHYCQACA---YKKG-ICAMCGKKL 168 (179)
Q Consensus 135 ~c~~ck~~~-----~~~~~~yc~~ca---y~~g-~c~mcgk~~ 168 (179)
.|.|||... ..-||++|..|| |+|| .|-.|||..
T Consensus 198 ~C~iCKkdy~spvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t 240 (259)
T COG5152 198 LCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKAT 240 (259)
T ss_pred eehhchhhccchhhhhcchhHHHHHHHHHhccCCcceecchhh
Confidence 899999753 344899999999 6776 799999864
No 17
>KOG3241|consensus
Probab=92.28 E-value=0.0096 Score=49.51 Aligned_cols=46 Identities=28% Similarity=0.755 Sum_probs=37.3
Q ss_pred ccCCCcccCcccchhhc-ccccCCCccCcccccccCcccccCcccccc
Q psy11903 125 RFNPYTQKFESCKICRQ-KVHQVGSHYCQACAYKKGICAMCGKKLLDV 171 (179)
Q Consensus 125 ~~~p~~~~~~~c~~ck~-~~~~~~~~yc~~cay~~g~c~mcgk~~~d~ 171 (179)
+|.|.+. ..+|..|++ .|.|.-|+.|..||-+...||-|+|.+.++
T Consensus 60 KYKpLt~-akkC~kC~~r~Vk~aYH~~Cr~CA~e~~vCAKC~ks~~~i 106 (227)
T KOG3241|consen 60 KYKPLTE-AKKCQKCTKRNVKQAYHKLCRGCAKEQKVCAKCCKSVDQI 106 (227)
T ss_pred cccccch-hHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHhccHHHh
Confidence 4556554 469999987 778888899999999999999999976543
No 18
>PF12773 DZR: Double zinc ribbon
Probab=89.14 E-value=0.26 Score=31.53 Aligned_cols=34 Identities=24% Similarity=0.646 Sum_probs=20.3
Q ss_pred cchhhcccccCCCccCcccccccC-------cccccCccccc
Q psy11903 136 CKICRQKVHQVGSHYCQACAYKKG-------ICAMCGKKLLD 170 (179)
Q Consensus 136 c~~ck~~~~~~~~~yc~~cay~~g-------~c~mcgk~~~d 170 (179)
|..|.+.+.. ++.||..|-.+-. +|.-||..+..
T Consensus 1 Cp~Cg~~~~~-~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 1 CPHCGTPNPD-DAKFCPHCGTPLPPPDQSKKICPNCGAENPP 41 (50)
T ss_pred CCCcCCcCCc-cccCChhhcCChhhccCCCCCCcCCcCCCcC
Confidence 4556666655 5666666655444 57777766543
No 19
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=79.81 E-value=0.95 Score=25.63 Aligned_cols=22 Identities=18% Similarity=0.694 Sum_probs=16.6
Q ss_pred cccchhhcccccCCCccCccccc
Q psy11903 134 ESCKICRQKVHQVGSHYCQACAY 156 (179)
Q Consensus 134 ~~c~~ck~~~~~~~~~yc~~cay 156 (179)
..|..|.+.+.. +++||+.|-.
T Consensus 3 ~~Cp~Cg~~~~~-~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAEIDP-DAKFCPNCGA 24 (26)
T ss_pred CCCcccCCcCCc-ccccChhhCC
Confidence 479999996655 7898887643
No 20
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=79.79 E-value=0.85 Score=25.37 Aligned_cols=20 Identities=20% Similarity=0.866 Sum_probs=15.1
Q ss_pred ccchhhcccccCCCccCcccc
Q psy11903 135 SCKICRQKVHQVGSHYCQACA 155 (179)
Q Consensus 135 ~c~~ck~~~~~~~~~yc~~ca 155 (179)
.|..|..++.. ++++|+.|-
T Consensus 1 ~Cp~CG~~~~~-~~~fC~~CG 20 (23)
T PF13240_consen 1 YCPNCGAEIED-DAKFCPNCG 20 (23)
T ss_pred CCcccCCCCCC-cCcchhhhC
Confidence 48889999976 778876654
No 21
>PF14849 YidC_periplas: YidC periplasmic domain; PDB: 3BS6_B 3BLC_B.
Probab=79.36 E-value=3.6 Score=34.45 Aligned_cols=37 Identities=22% Similarity=0.307 Sum_probs=25.5
Q ss_pred EEEEEcCCCeEEEEecCCcEEEEEEeeCC----CCcccceEe
Q psy11903 30 RFTLTNSQRMSVQVIDYGATITTIKVPDK----RGNVDDVVL 67 (179)
Q Consensus 30 ~~tL~n~~gl~v~vlnyGAtI~sl~vpdr----~G~~~dVVL 67 (179)
+++|+|+ -++|+|.+.||.|.++.+++= ++...+|.|
T Consensus 1 ~v~ven~-~~~~~~s~~GG~i~~~~Lk~y~~~~~~~~~pv~L 41 (270)
T PF14849_consen 1 RVTVEND-LFKVTFSSKGGRIKSVELKKYKNTLDPDSKPVEL 41 (270)
T ss_dssp -EEEE-S-S-EEEEETBTTEEEEEEEEEEESSTT-SS-EEEE
T ss_pred CEEEECC-CEEEEEECCCCeEEEEEcCCCccccCCCCCceEE
Confidence 4789995 799999999999999998742 222236777
No 22
>KOG1813|consensus
Probab=69.70 E-value=2.3 Score=37.93 Aligned_cols=36 Identities=33% Similarity=0.907 Sum_probs=29.4
Q ss_pred ccchhhccc-----ccCCCccCcccc---ccc-CcccccCccccc
Q psy11903 135 SCKICRQKV-----HQVGSHYCQACA---YKK-GICAMCGKKLLD 170 (179)
Q Consensus 135 ~c~~ck~~~-----~~~~~~yc~~ca---y~~-g~c~mcgk~~~d 170 (179)
+|-||++.- ..-+|++|-.|| |++ -.|-.|++++.-
T Consensus 243 ~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 243 KCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred cccccccccccchhhcCCceeehhhhccccccCCcceeccccccc
Confidence 899999853 344889999999 777 589999998763
No 23
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=68.35 E-value=1.3 Score=27.75 Aligned_cols=20 Identities=35% Similarity=0.936 Sum_probs=16.9
Q ss_pred CCccCcccccccC----cccccCc
Q psy11903 147 GSHYCQACAYKKG----ICAMCGK 166 (179)
Q Consensus 147 ~~~yc~~cay~~g----~c~mcgk 166 (179)
||.+|+.|+.+.- .|..|++
T Consensus 21 gH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 21 GHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCHHHHHHHHhhcCCCCCCcCCCC
Confidence 7889999998777 8988875
No 24
>cd09021 Aldose_epim_Ec_YphB aldose 1-epimerase, similar to Escherichia coli YphB. Proteins similar to Escherichia coli YphB are uncharacterized members of the aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen.
Probab=66.94 E-value=12 Score=31.60 Aligned_cols=66 Identities=8% Similarity=0.152 Sum_probs=39.0
Q ss_pred EEecCCcEEEEEEeeCCCCcccceEeCcCCchh--hhhhh-hccccccceec--------ceeccCccCCCCCccccCCc
Q psy11903 42 QVIDYGATITTIKVPDKRGNVDDVVLGFDDMRE--EIYFI-MVCSKCEKKLG--------KVITPDNWKSGSRNTIESGG 110 (179)
Q Consensus 42 ~vlnyGAtI~sl~vpdr~G~~~dVVLGfd~~e~--Y~~~g-mvc~kc~~klg--------~va~pd~~k~~~~n~l~gG~ 110 (179)
.|-.+||.|++|... |...+++...+ .+. ....+ .+-.++++||. +.+...+...++.|.+||+.
T Consensus 4 ~v~~~Ga~l~sl~~~---~~~~~~l~~~~-~~~~~~~~~~~p~LfP~~gRi~~~~~~~~g~~y~l~~n~~~~~~~~HG~a 79 (273)
T cd09021 4 LAPELGGSIAALTSR---GDPTPLLRPAD-PDAADALAMACFPLVPFSNRIRGGRFLFAGREVALPPNTADEPHPLHGDG 79 (273)
T ss_pred eCCCCCceEEEEEeC---CCcceeeecCC-ccccCcccccCceEeccCCcccCCcEeECCEEEecCCCCCCCccCcccch
Confidence 355689999999884 33367877543 222 11222 45556677765 35555542224678899975
Q ss_pred e
Q psy11903 111 R 111 (179)
Q Consensus 111 ~ 111 (179)
+
T Consensus 80 r 80 (273)
T cd09021 80 W 80 (273)
T ss_pred h
Confidence 4
No 25
>TIGR03593 yidC_nterm membrane protein insertase, YidC/Oxa1 family, N-terminal domain. Essentially all bacteria have a member of the YidC family, whose C-terminal domain is modeled by TIGR03592. The two copies are found in endospore-forming bacteria such as Bacillus subtilis appear redundant during vegetative growth, although the member designated spoIIIJ (stage III sporulation protein J) has a distinct role in spore formation. YidC, its mitochondrial homolog Oxa1, and its chloroplast homolog direct insertion into the bacterial/organellar inner (or only) membrane. This model describes an N-terminal sequence region, including a large periplasmic domain lacking in YidC members from Gram-positive species. The multifunctional YidC protein acts both with and independently of the Sec system.
Probab=64.86 E-value=8.3 Score=34.16 Aligned_cols=29 Identities=14% Similarity=0.373 Sum_probs=25.8
Q ss_pred EEEEEEEcCCCeEEEEecCCcEEEEEEeeC
Q psy11903 28 VRRFTLTNSQRMSVQVIDYGATITTIKVPD 57 (179)
Q Consensus 28 v~~~tL~n~~gl~v~vlnyGAtI~sl~vpd 57 (179)
.++++|+|+ -++++|.+.||+|.++.+++
T Consensus 73 ~~~i~v~td-~~~~~is~~Gg~i~~~~Lk~ 101 (366)
T TIGR03593 73 AKRITVKTD-VLRASISTKGGDIDSLELKK 101 (366)
T ss_pred CCeEEEECC-eEEEEEeCCCceeeeecccc
Confidence 457999996 79999999999999999875
No 26
>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=61.18 E-value=2.3 Score=30.10 Aligned_cols=37 Identities=32% Similarity=0.773 Sum_probs=22.4
Q ss_pred ccchhhcccccCC-CccCcccc---cccCcccccCcccccc
Q psy11903 135 SCKICRQKVHQVG-SHYCQACA---YKKGICAMCGKKLLDV 171 (179)
Q Consensus 135 ~c~~ck~~~~~~~-~~yc~~ca---y~~g~c~mcgk~~~d~ 171 (179)
.|..|.+.+...+ ..+|..|. -+.+.|.-||..+--.
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~L 43 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVL 43 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEE
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHH
Confidence 6888998886655 66788886 3567899998887543
No 27
>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=59.67 E-value=3.7 Score=26.74 Aligned_cols=23 Identities=22% Similarity=0.353 Sum_probs=18.2
Q ss_pred CCccCccccc----ccCcccccCcccc
Q psy11903 147 GSHYCQACAY----KKGICAMCGKKLL 169 (179)
Q Consensus 147 ~~~yc~~cay----~~g~c~mcgk~~~ 169 (179)
|+.||..|.- +.+.|.+||+.+.
T Consensus 20 G~v~~~~~i~~~~~~~~~cP~~~~~~~ 46 (63)
T smart00504 20 GQTYERRAIEKWLLSHGTDPVTGQPLT 46 (63)
T ss_pred CCEEeHHHHHHHHHHCCCCCCCcCCCC
Confidence 7788888764 3678999999873
No 28
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=58.90 E-value=3.4 Score=30.29 Aligned_cols=37 Identities=16% Similarity=0.320 Sum_probs=24.3
Q ss_pred CcccchhhcccccCCCccCcccccccCcccccCcccc
Q psy11903 133 FESCKICRQKVHQVGSHYCQACAYKKGICAMCGKKLL 169 (179)
Q Consensus 133 ~~~c~~ck~~~~~~~~~yc~~cay~~g~c~mcgk~~~ 169 (179)
.|.|..|++++.--.--===+=-..+|.|.-|+++|.
T Consensus 33 rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I~ 69 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPIP 69 (92)
T ss_pred CCcCcCCCCcCcccccchHHHHHHhCCCCcccCCCCC
Confidence 4899999999875211000011357899999999885
No 29
>KOG2272|consensus
Probab=57.16 E-value=6.9 Score=34.50 Aligned_cols=51 Identities=31% Similarity=0.705 Sum_probs=38.1
Q ss_pred ceeeeecccccCCCcccCcccchhhccccc-----CCCccCcccccccC--cccccCcccc
Q psy11903 116 NKALTASKARFNPYTQKFESCKICRQKVHQ-----VGSHYCQACAYKKG--ICAMCGKKLL 169 (179)
Q Consensus 116 nk~l~~~k~~~~p~~~~~~~c~~ck~~~~~-----~~~~yc~~cay~~g--~c~mcgk~~~ 169 (179)
+.+|.- |-+||-.|.-+|..|+..+.. .|.-||..|--+-| ||--|-+.|-
T Consensus 149 ~~~l~f---r~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe 206 (332)
T KOG2272|consen 149 EQPLTF---RGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE 206 (332)
T ss_pred cccccc---cCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchH
Confidence 477743 667888888899999987753 36789999987655 6776766664
No 30
>KOG0320|consensus
Probab=54.82 E-value=3.3 Score=34.47 Aligned_cols=36 Identities=33% Similarity=0.843 Sum_probs=27.0
Q ss_pred cccchhhccccc-------CCCccCcccc---ccc-CcccccCcccc
Q psy11903 134 ESCKICRQKVHQ-------VGSHYCQACA---YKK-GICAMCGKKLL 169 (179)
Q Consensus 134 ~~c~~ck~~~~~-------~~~~yc~~ca---y~~-g~c~mcgk~~~ 169 (179)
-+|.||--.+.+ =||-+|..|+ .++ ..|..|+|||.
T Consensus 132 ~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 132 YKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred cCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 489999654433 3788999996 343 48999999986
No 31
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=54.65 E-value=6.5 Score=22.48 Aligned_cols=22 Identities=27% Similarity=0.957 Sum_probs=17.0
Q ss_pred ccchhhcccccCCCccCcccccc
Q psy11903 135 SCKICRQKVHQVGSHYCQACAYK 157 (179)
Q Consensus 135 ~c~~ck~~~~~~~~~yc~~cay~ 157 (179)
.|..|.+.|.. .++.|..|-|.
T Consensus 2 ~CP~C~~~V~~-~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPE-SAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchh-hcCcCCCCCCC
Confidence 68899999987 67877777653
No 32
>PRK12496 hypothetical protein; Provisional
Probab=54.25 E-value=5.8 Score=31.96 Aligned_cols=21 Identities=29% Similarity=1.051 Sum_probs=15.5
Q ss_pred ccCcccc--c----ccCcccccCcccc
Q psy11903 149 HYCQACA--Y----KKGICAMCGKKLL 169 (179)
Q Consensus 149 ~yc~~ca--y----~~g~c~mcgk~~~ 169 (179)
++|++|- | ....|.+||-++.
T Consensus 128 ~~C~gC~~~~~~~~~~~~C~~CG~~~~ 154 (164)
T PRK12496 128 KVCKGCKKKYPEDYPDDVCEICGSPVK 154 (164)
T ss_pred EECCCCCccccCCCCCCcCCCCCChhh
Confidence 5577776 5 4467999998875
No 33
>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=53.81 E-value=2.7 Score=26.73 Aligned_cols=37 Identities=27% Similarity=0.770 Sum_probs=23.8
Q ss_pred ccchhhcccc-----cCCCc-cCccccccc----CcccccCcccccc
Q psy11903 135 SCKICRQKVH-----QVGSH-YCQACAYKK----GICAMCGKKLLDV 171 (179)
Q Consensus 135 ~c~~ck~~~~-----~~~~~-yc~~cay~~----g~c~mcgk~~~d~ 171 (179)
.|.+|..... .=||. +|..|+.+- ..|.+|-++|.++
T Consensus 4 ~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~~V 50 (50)
T PF13920_consen 4 ECPICFENPRDVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIESV 50 (50)
T ss_dssp B-TTTSSSBSSEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-SEE
T ss_pred CCccCCccCCceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhcCC
Confidence 4555555422 22566 888888766 8999999988753
No 34
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=51.55 E-value=6 Score=36.50 Aligned_cols=36 Identities=19% Similarity=0.606 Sum_probs=27.6
Q ss_pred cccchhhcccccC-----CCccCccccc----ccCcccccCcccc
Q psy11903 134 ESCKICRQKVHQV-----GSHYCQACAY----KKGICAMCGKKLL 169 (179)
Q Consensus 134 ~~c~~ck~~~~~~-----~~~yc~~cay----~~g~c~mcgk~~~ 169 (179)
-.|.||+.-+..+ ||.||..|.. ..+.|.+|...+.
T Consensus 27 l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~ 71 (397)
T TIGR00599 27 LRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQ 71 (397)
T ss_pred cCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCccc
Confidence 3788887655433 9999999986 3468999998765
No 35
>KOG3799|consensus
Probab=51.30 E-value=6.8 Score=31.48 Aligned_cols=36 Identities=31% Similarity=0.725 Sum_probs=24.5
Q ss_pred Ccccchhhc-ccccCCCccCcccccccCcccccCccccc
Q psy11903 133 FESCKICRQ-KVHQVGSHYCQACAYKKGICAMCGKKLLD 170 (179)
Q Consensus 133 ~~~c~~ck~-~~~~~~~~yc~~cay~~g~c~mcgk~~~d 170 (179)
-..|-||-. +...--.|-|..|-.+ .||.||-++.-
T Consensus 65 datC~IC~KTKFADG~GH~C~YCq~r--~CARCGGrv~l 101 (169)
T KOG3799|consen 65 DATCGICHKTKFADGCGHNCSYCQTR--FCARCGGRVSL 101 (169)
T ss_pred CcchhhhhhcccccccCcccchhhhh--HHHhcCCeeee
Confidence 458999954 5554335667666544 79999987753
No 36
>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=49.64 E-value=7.2 Score=26.59 Aligned_cols=36 Identities=28% Similarity=0.854 Sum_probs=27.1
Q ss_pred cccchhhcccccCC---------CccCccccccc--CcccccCcccc
Q psy11903 134 ESCKICRQKVHQVG---------SHYCQACAYKK--GICAMCGKKLL 169 (179)
Q Consensus 134 ~~c~~ck~~~~~~~---------~~yc~~cay~~--g~c~mcgk~~~ 169 (179)
..|..|.+.+.++. -.||..||-.. ++|.-||=.+.
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~~CPNCgGelv 52 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTFCADCAETMLNGVCPNCGGELV 52 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcCcCcCCCCccc
Confidence 46888888887744 25788888665 99999996553
No 37
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=48.52 E-value=6.8 Score=27.02 Aligned_cols=32 Identities=25% Similarity=0.850 Sum_probs=15.6
Q ss_pred cccchhhccccc-----CCCccCcccccccCcccccCcc
Q psy11903 134 ESCKICRQKVHQ-----VGSHYCQACAYKKGICAMCGKK 167 (179)
Q Consensus 134 ~~c~~ck~~~~~-----~~~~yc~~cay~~g~c~mcgk~ 167 (179)
+.|..||+.+.- +...-|..| |+-+|.+||-.
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~C--k~~VCnlCGFN 39 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTEC--KSQVCNLCGFN 39 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHH--hhhhhcccCCC
Confidence 355666654421 122234444 34477888753
No 38
>PRK01318 membrane protein insertase; Provisional
Probab=47.86 E-value=37 Score=32.37 Aligned_cols=27 Identities=15% Similarity=0.298 Sum_probs=24.9
Q ss_pred EEEEEcCCCeEEEEecCCcEEEEEEeeC
Q psy11903 30 RFTLTNSQRMSVQVIDYGATITTIKVPD 57 (179)
Q Consensus 30 ~~tL~n~~gl~v~vlnyGAtI~sl~vpd 57 (179)
+++++|+ -++++|.+.||+|.++.+++
T Consensus 40 ~i~v~td-~~~~~is~~Gg~i~~~~Lk~ 66 (521)
T PRK01318 40 RITVETD-VLRLSIDTKGGRIDDLLLKK 66 (521)
T ss_pred EEEEEcC-cEEEEEECCCCeeeeeeccC
Confidence 8999996 79999999999999999875
No 39
>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=45.19 E-value=17 Score=20.80 Aligned_cols=9 Identities=56% Similarity=1.250 Sum_probs=4.8
Q ss_pred cccccCccc
Q psy11903 160 ICAMCGKKL 168 (179)
Q Consensus 160 ~c~mcgk~~ 168 (179)
.|+.|++.|
T Consensus 29 ~C~~C~~~L 37 (39)
T smart00132 29 KCSKCGKPL 37 (39)
T ss_pred CCcccCCcC
Confidence 355555554
No 40
>PF03660 PHF5: PHF5-like protein; InterPro: IPR005345 Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins. At least one example, from Mus musculus (Mouse), may act as a chromatin-associated protein []. The Schizosaccharomyces pombe (Fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.; PDB: 2K0A_A.
Probab=45.18 E-value=5.7 Score=30.27 Aligned_cols=26 Identities=23% Similarity=0.487 Sum_probs=15.2
Q ss_pred cccCcccchhhcccccCCCccCcccc
Q psy11903 130 TQKFESCKICRQKVHQVGSHYCQACA 155 (179)
Q Consensus 130 ~~~~~~c~~ck~~~~~~~~~yc~~ca 155 (179)
+.+..+|.+|........+.||..|-
T Consensus 52 G~~~~rCIiCg~~~g~sdAYYC~eC~ 77 (106)
T PF03660_consen 52 GSLQGRCIICGSGPGVSDAYYCWECV 77 (106)
T ss_dssp SSTTSB-TTTSSSB--EE-EE-HHHH
T ss_pred CCcCceEEEecCCCCcccceehhhhH
Confidence 34457999999555445689999983
No 41
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=44.37 E-value=8 Score=32.38 Aligned_cols=36 Identities=28% Similarity=0.799 Sum_probs=27.6
Q ss_pred ccchhhccccc-----CCCccCcccccc--------------------cCcccccCccccc
Q psy11903 135 SCKICRQKVHQ-----VGSHYCQACAYK--------------------KGICAMCGKKLLD 170 (179)
Q Consensus 135 ~c~~ck~~~~~-----~~~~yc~~cay~--------------------~g~c~mcgk~~~d 170 (179)
.|.||...+.. =||.||..|.++ ...|.+|...|..
T Consensus 20 ~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~ 80 (193)
T PLN03208 20 DCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE 80 (193)
T ss_pred CCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh
Confidence 79999764433 389999999963 3579999998864
No 42
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=44.09 E-value=9.4 Score=30.05 Aligned_cols=22 Identities=32% Similarity=0.881 Sum_probs=15.6
Q ss_pred CcccchhhcccccCC--CccCccc
Q psy11903 133 FESCKICRQKVHQVG--SHYCQAC 154 (179)
Q Consensus 133 ~~~c~~ck~~~~~~~--~~yc~~c 154 (179)
-..|..|+.+|.+.+ ..+|..|
T Consensus 34 Y~aC~~C~kkv~~~~~~~~~C~~C 57 (166)
T cd04476 34 YPACPGCNKKVVEEGNGTYRCEKC 57 (166)
T ss_pred EccccccCcccEeCCCCcEECCCC
Confidence 459999999998753 4445444
No 43
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=43.79 E-value=11 Score=24.77 Aligned_cols=16 Identities=50% Similarity=0.939 Sum_probs=11.5
Q ss_pred cccccCcccccccccc
Q psy11903 160 ICAMCGKKLLDVKNYK 175 (179)
Q Consensus 160 ~c~mcgk~~~d~~~~~ 175 (179)
+|+.||+++--.+..+
T Consensus 1 ~C~iCg~kigl~~~~k 16 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFK 16 (51)
T ss_pred CCCcccccccccccee
Confidence 5899999887555443
No 44
>cd09020 D-hex-6-P-epi_like D-hexose-6-phosphate epimerase-like. D-Hexose-6-phosphate epimerase Ymr099c from Saccharomyces cerevisiae belongs to the large superfamily of aldose-1-epimerases. Its active site is very similar to the catalytic site of galactose mutarotase, the best studied member of the superfamily. It also contains the conserved glutamate and histidine residues that have been shown in galactose mutarotase to be critical for catalysis, the glutamate serving as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen. In addition Ymr099c contains 2 conserved arginine residues which are involved in phosphate binding, and exhibits hexose-6-phosphate mutarotase activity on glucose-6-P, galactose-6-P and mannose-6-P.
Probab=42.05 E-value=47 Score=28.22 Aligned_cols=32 Identities=22% Similarity=0.335 Sum_probs=25.1
Q ss_pred EEEEcCCCeEEEEecCCcEEEEEEeeCCCCcccceEe
Q psy11903 31 FTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVL 67 (179)
Q Consensus 31 ~tL~n~~gl~v~vlnyGAtI~sl~vpdr~G~~~dVVL 67 (179)
++|+++ +.+++|..+||.|.++.... | .+++-
T Consensus 2 i~i~~~-~~~a~i~~~Ga~l~s~~~~~--~--~~~L~ 33 (269)
T cd09020 2 IVLDHP-GASAEIALQGAQVLSWKPKG--G--QDLLW 33 (269)
T ss_pred EEEeCC-CceEEEECCCcEEEEEeCCC--C--ceeEE
Confidence 568885 89999999999999998752 2 45653
No 45
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=37.47 E-value=15 Score=24.74 Aligned_cols=14 Identities=43% Similarity=0.990 Sum_probs=10.4
Q ss_pred cccCcccccCcccc
Q psy11903 156 YKKGICAMCGKKLL 169 (179)
Q Consensus 156 y~~g~c~mcgk~~~ 169 (179)
|...+|..||+++.
T Consensus 3 ~~~~~C~~Cg~~~~ 16 (54)
T PF14446_consen 3 YEGCKCPVCGKKFK 16 (54)
T ss_pred ccCccChhhCCccc
Confidence 56677888888774
No 46
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=37.05 E-value=14 Score=33.77 Aligned_cols=38 Identities=16% Similarity=0.477 Sum_probs=23.7
Q ss_pred ccCCCc-cc-CcccchhhcccccCCCccCcccccccCcccccCcccc
Q psy11903 125 RFNPYT-QK-FESCKICRQKVHQVGSHYCQACAYKKGICAMCGKKLL 169 (179)
Q Consensus 125 ~~~p~~-~~-~~~c~~ck~~~~~~~~~yc~~cay~~g~c~mcgk~~~ 169 (179)
-|+|-- .| ...|+.|...+....+. ++ .++|+ ||++|.
T Consensus 230 g~~P~~GKYh~~~c~~C~~~~~~~~~~-----~~-~~~Cp-CG~~i~ 269 (374)
T TIGR00375 230 GLDPLLGKYHQTACEACGEPAVSEDAE-----TA-CANCP-CGGRIK 269 (374)
T ss_pred eECcCCCccchhhhcccCCcCCchhhh-----hc-CCCCC-CCCcce
Confidence 455643 22 56788887776542211 23 58999 999964
No 47
>KOG1594|consensus
Probab=36.13 E-value=89 Score=27.86 Aligned_cols=30 Identities=20% Similarity=0.357 Sum_probs=26.3
Q ss_pred cEEEEEEEcCCCeEEEEecCCcEEEEEEee
Q psy11903 27 PVRRFTLTNSQRMSVQVIDYGATITTIKVP 56 (179)
Q Consensus 27 ~v~~~tL~n~~gl~v~vlnyGAtI~sl~vp 56 (179)
....+.|++.+|-+++|.=|||.+.|+++.
T Consensus 22 g~~~ivL~~p~g~taev~L~Gg~V~SWK~~ 51 (305)
T KOG1594|consen 22 GLDKIVLTDPRGSTAEVYLYGGQVVSWKNE 51 (305)
T ss_pred CCceEEEeCCCCCeEEEEEeccEEEEeecC
Confidence 456777888889999999999999999986
No 48
>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=36.00 E-value=5.9 Score=23.89 Aligned_cols=10 Identities=30% Similarity=1.075 Sum_probs=7.1
Q ss_pred CCccCccccc
Q psy11903 147 GSHYCQACAY 156 (179)
Q Consensus 147 ~~~yc~~cay 156 (179)
||.||..|+.
T Consensus 18 GH~fC~~C~~ 27 (39)
T PF13923_consen 18 GHSFCKECIE 27 (39)
T ss_dssp SEEEEHHHHH
T ss_pred CCchhHHHHH
Confidence 6777777764
No 49
>KOG1701|consensus
Probab=36.00 E-value=6.9 Score=36.60 Aligned_cols=36 Identities=31% Similarity=0.929 Sum_probs=0.0
Q ss_pred ccchhhccc------ccCCCccCcccc-cccCcccccCccccc
Q psy11903 135 SCKICRQKV------HQVGSHYCQACA-YKKGICAMCGKKLLD 170 (179)
Q Consensus 135 ~c~~ck~~~------~~~~~~yc~~ca-y~~g~c~mcgk~~~d 170 (179)
+|.+|..+| ..++.-||..|- -..-.|.-||..|+|
T Consensus 304 tC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I~d 346 (468)
T KOG1701|consen 304 TCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPIMD 346 (468)
T ss_pred ehHhhhhhhccccccccCCcccchHHHHHHHHHHhhhhhHHHH
No 50
>PF14486 DUF4432: Domain of unknown function (DUF4432); PDB: 3TY1_A.
Probab=35.75 E-value=1.1e+02 Score=26.94 Aligned_cols=41 Identities=24% Similarity=0.332 Sum_probs=27.4
Q ss_pred cEEEEEEEcCCCeEEEEecC-CcEEEEEEeeCCCCcccceEeCcCCchh
Q psy11903 27 PVRRFTLTNSQRMSVQVIDY-GATITTIKVPDKRGNVDDVVLGFDDMRE 74 (179)
Q Consensus 27 ~v~~~tL~n~~gl~v~vlny-GAtI~sl~vpdr~G~~~dVVLGfd~~e~ 74 (179)
.++.++|+|+.||+++|+.. |.-|-++.+. | +-|++.++.+
T Consensus 3 Gv~~l~i~N~~gl~~~vlp~rg~dI~~~~~~---G----~~l~w~s~~~ 44 (302)
T PF14486_consen 3 GVRALEIRNGGGLRFTVLPDRGMDIWDAEFD---G----VNLGWHSPFG 44 (302)
T ss_dssp T-EEEEEEETTS-EEEEETTTTTEEEEEEET---T----EEE----S--
T ss_pred CcEEEEEECCCCcEEEEecccCCceEEEEEC---C----EEecccCCCc
Confidence 48899999988999999987 9999999883 4 4467766654
No 51
>KOG0153|consensus
Probab=34.58 E-value=10 Score=34.57 Aligned_cols=47 Identities=34% Similarity=0.798 Sum_probs=33.1
Q ss_pred ecccceeeeecccccCCCcccCcccchhhcccc----cCC-------CccCcccccccCccccc
Q psy11903 112 RIGENKALTASKARFNPYTQKFESCKICRQKVH----QVG-------SHYCQACAYKKGICAMC 164 (179)
Q Consensus 112 gi~~nk~l~~~k~~~~p~~~~~~~c~~ck~~~~----~~~-------~~yc~~cay~~g~c~mc 164 (179)
=+|+|-++.- -..||+ +-|+||-.... ++| -.-||.||=.|.+|.-|
T Consensus 26 CLGdnpyvRM---tK~~~g---kECKICtrPfT~Frw~pgr~~r~kKTeICqtCaklKNvCQ~C 83 (377)
T KOG0153|consen 26 CLGDNPYVRM---TKEPYG---KECKICTRPFTIFRWCPGRGARFKKTEICQTCAKLKNVCQTC 83 (377)
T ss_pred hcCCCceeee---eccccC---CccceecCcceEEEeccccccccccchHHHHHHHHHhHHHHh
Confidence 4678888854 336775 48999976431 111 23699999999999988
No 52
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=34.18 E-value=10 Score=24.55 Aligned_cols=32 Identities=34% Similarity=0.817 Sum_probs=25.0
Q ss_pred ccchhhcccccCCCccCcccccccCcccccCccccccc
Q psy11903 135 SCKICRQKVHQVGSHYCQACAYKKGICAMCGKKLLDVK 172 (179)
Q Consensus 135 ~c~~ck~~~~~~~~~yc~~cay~~g~c~mcgk~~~d~~ 172 (179)
+|-+|.+.... |-+ -|.+.||.-|-+.|..|.
T Consensus 1 ~CiiC~~~~~~-GI~-----I~~~fIC~~CE~~iv~~~ 32 (46)
T PF10764_consen 1 KCIICGKEKEE-GIH-----IYGKFICSDCEKEIVNTE 32 (46)
T ss_pred CeEeCCCcCCC-CEE-----EECeEehHHHHHHhccCC
Confidence 48888888776 655 467789999999998664
No 53
>PF14315 DUF4380: Domain of unknown function (DUF4380)
Probab=33.30 E-value=1.1e+02 Score=26.30 Aligned_cols=29 Identities=21% Similarity=0.312 Sum_probs=24.5
Q ss_pred EEEEEEEcCCCeEEEEe-cCCcEEEEEEeeC
Q psy11903 28 VRRFTLTNSQRMSVQVI-DYGATITTIKVPD 57 (179)
Q Consensus 28 v~~~tL~n~~gl~v~vl-nyGAtI~sl~vpd 57 (179)
...++|+|+ .+++.|+ .+|.+|.++.+.+
T Consensus 4 ~~~~~l~N~-~i~l~Vtp~~GgRIl~~~~~g 33 (274)
T PF14315_consen 4 GNCLRLSNG-DIELIVTPDVGGRILSFGLNG 33 (274)
T ss_pred ceEEEEECC-CEEEEEecCCCCEEEEEEeCC
Confidence 356889995 7999998 7899999999964
No 54
>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=33.14 E-value=17 Score=21.07 Aligned_cols=21 Identities=29% Similarity=0.920 Sum_probs=14.7
Q ss_pred CCccCccccc-----ccCcccccCcc
Q psy11903 147 GSHYCQACAY-----KKGICAMCGKK 167 (179)
Q Consensus 147 ~~~yc~~cay-----~~g~c~mcgk~ 167 (179)
||.||..|.. ....|.+|.+.
T Consensus 19 ~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 19 GHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 6778888764 25568888764
No 55
>PRK05580 primosome assembly protein PriA; Validated
Probab=33.08 E-value=34 Score=33.36 Aligned_cols=22 Identities=32% Similarity=0.851 Sum_probs=17.3
Q ss_pred CccCcccccccC---cccccCcccc
Q psy11903 148 SHYCQACAYKKG---ICAMCGKKLL 169 (179)
Q Consensus 148 ~~yc~~cay~~g---~c~mcgk~~~ 169 (179)
.-.|+.|-|... .|.-||...+
T Consensus 408 ~l~Ch~Cg~~~~~~~~Cp~Cg~~~l 432 (679)
T PRK05580 408 RLRCHHCGYQEPIPKACPECGSTDL 432 (679)
T ss_pred eEECCCCcCCCCCCCCCCCCcCCee
Confidence 346999999865 7999988754
No 56
>PHA02929 N1R/p28-like protein; Provisional
Probab=32.69 E-value=20 Score=30.90 Aligned_cols=41 Identities=27% Similarity=0.692 Sum_probs=30.5
Q ss_pred Ccccchhhcccc-------------cCCCccCcccc----cccCcccccCcccccccc
Q psy11903 133 FESCKICRQKVH-------------QVGSHYCQACA----YKKGICAMCGKKLLDVKN 173 (179)
Q Consensus 133 ~~~c~~ck~~~~-------------~~~~~yc~~ca----y~~g~c~mcgk~~~d~~~ 173 (179)
...|.||-..+. .=+|.||..|- =.+..|+||-..+.-+..
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~~v~~ 231 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFISVIK 231 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEeeEEee
Confidence 358999987643 23788999997 256799999988875443
No 57
>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=32.55 E-value=19 Score=21.51 Aligned_cols=12 Identities=42% Similarity=1.137 Sum_probs=9.0
Q ss_pred CcccccCccccc
Q psy11903 159 GICAMCGKKLLD 170 (179)
Q Consensus 159 g~c~mcgk~~~d 170 (179)
|+|..||..|.+
T Consensus 4 g~C~~CGe~I~~ 15 (36)
T PF01258_consen 4 GICEDCGEPIPE 15 (36)
T ss_dssp SB-TTTSSBEEH
T ss_pred CCccccCChHHH
Confidence 679999998874
No 58
>KOG4458|consensus
Probab=32.49 E-value=19 Score=25.41 Aligned_cols=33 Identities=30% Similarity=0.634 Sum_probs=22.5
Q ss_pred ccccCCCcccCcccchhhcccccCCCccCcccccccCccc
Q psy11903 123 KARFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKGICA 162 (179)
Q Consensus 123 k~~~~p~~~~~~~c~~ck~~~~~~~~~yc~~cay~~g~c~ 162 (179)
|.+++||.-..--=-.|+-.+|... ||+.|||-
T Consensus 4 k~k~~pydii~dd~~d~riplhne~-------a~qhgi~f 36 (78)
T KOG4458|consen 4 KKKHGPYDIIADDGHDCRIPLHNED-------AFQHGICF 36 (78)
T ss_pred ccccCCcceeecccccceeeccchh-------hhhccceE
Confidence 4578898743333345667888754 89999994
No 59
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=32.05 E-value=11 Score=19.23 Aligned_cols=15 Identities=27% Similarity=0.742 Sum_probs=8.0
Q ss_pred cccccCccccccccc
Q psy11903 160 ICAMCGKKLLDVKNY 174 (179)
Q Consensus 160 ~c~mcgk~~~d~~~~ 174 (179)
.|.+||+...+-..+
T Consensus 2 ~C~~C~~~~~~~~~l 16 (24)
T PF13894_consen 2 QCPICGKSFRSKSEL 16 (24)
T ss_dssp E-SSTS-EESSHHHH
T ss_pred CCcCCCCcCCcHHHH
Confidence 477888776654443
No 60
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=31.82 E-value=20 Score=23.65 Aligned_cols=28 Identities=25% Similarity=0.624 Sum_probs=19.1
Q ss_pred ccchhhcccccCCCccCcccccccCcccccCcccc
Q psy11903 135 SCKICRQKVHQVGSHYCQACAYKKGICAMCGKKLL 169 (179)
Q Consensus 135 ~c~~ck~~~~~~~~~yc~~cay~~g~c~mcgk~~~ 169 (179)
+|..|...+.+.. ++.--.|.-||-+|+
T Consensus 8 ~C~~Cg~~~~~~~-------~~~~irCp~Cg~rIl 35 (49)
T COG1996 8 KCARCGREVELDQ-------ETRGIRCPYCGSRIL 35 (49)
T ss_pred EhhhcCCeeehhh-------ccCceeCCCCCcEEE
Confidence 7888988887533 345556777776665
No 61
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=31.78 E-value=20 Score=31.53 Aligned_cols=32 Identities=22% Similarity=0.617 Sum_probs=24.7
Q ss_pred cccCCCcccCcccchhhcc-----cccCCCccCcccc
Q psy11903 124 ARFNPYTQKFESCKICRQK-----VHQVGSHYCQACA 155 (179)
Q Consensus 124 ~~~~p~~~~~~~c~~ck~~-----~~~~~~~yc~~ca 155 (179)
.++.-|+.....|+.|.+. +.+-+.+||..|-
T Consensus 236 ~~l~VYgR~GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 236 QELKVYGRAGEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred eeEEEecCCCCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 4566787778899999764 4566889999993
No 62
>KOG3896|consensus
Probab=31.76 E-value=20 Score=32.86 Aligned_cols=41 Identities=37% Similarity=0.865 Sum_probs=27.8
Q ss_pred cccCCCcccCcccchhhc------ccccCCCccCccc---------ccccCcccccC
Q psy11903 124 ARFNPYTQKFESCKICRQ------KVHQVGSHYCQAC---------AYKKGICAMCG 165 (179)
Q Consensus 124 ~~~~p~~~~~~~c~~ck~------~~~~~~~~yc~~c---------ay~~g~c~mcg 165 (179)
..|+|....+ -||-|-. .+|...+|||..| ..||..||-|-
T Consensus 16 g~~~pl~~L~-FCRyC~klrc~~Cv~hEvdshfCp~CLEn~ps~EArlKKn~CAnCf 71 (449)
T KOG3896|consen 16 GKFRPLPDLV-FCRYCFKLRCDDCVLHEVDSHFCPRCLENSPSPEARLKKNKCANCF 71 (449)
T ss_pred ccccccccee-eeecccccccccccccccccccchhhccCCCchHHHhhhccccccc
Confidence 3566665422 4554432 4677789999999 47999999883
No 63
>PRK00420 hypothetical protein; Validated
Probab=31.61 E-value=24 Score=27.09 Aligned_cols=22 Identities=18% Similarity=0.528 Sum_probs=15.5
Q ss_pred Ccccchhhccccc--CCCccCccc
Q psy11903 133 FESCKICRQKVHQ--VGSHYCQAC 154 (179)
Q Consensus 133 ~~~c~~ck~~~~~--~~~~yc~~c 154 (179)
...|..|...+-. .|..||+.|
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~C 46 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVH 46 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCC
Confidence 4689999997753 476666654
No 64
>PF10621 FpoO: F420H2 dehydrogenase subunit FpoO ; InterPro: IPR018288 This entry represents the FpoO subunit of membrane-bound multi-subunit F420H2 dehydrogenase, which oxidises the reduced coenzyme F420H2 to coenzyme F420 and feeds the electrons via an FeS cluster into an energy-conserving electron transport chain [, ]. This enzyme plays a role in the methanogenic pathway in methanogenic archaea. Reduced coenzyme F420H2 is the major cytoplasmic electron carrier of methanogens and a reversible hydride donor, much like NADH []. F420H2 + COB-S-S-CoM = F420 + CoM-SH + CoB-SH Where CoB-S-S-CoM (the heterosulphide of 2-mercaptoethanesulphonate and 7-mercaptoheptanoylthreonine phosphate) is the terminal electron acceptor of the methanogenic pathway, and is reduced with the concomitant generation of a transmembrane proton potential and ATP synthesis. The FpoO subunit of F420H2 dehydrogenase probably participates in the reduction of methanophenazine, where it acts as a special mechanism for the reduction of the methanogenic cofactor [].
Probab=30.72 E-value=22 Score=27.53 Aligned_cols=36 Identities=28% Similarity=0.563 Sum_probs=22.4
Q ss_pred CCcccCcccchhhc-------ccccCCCccCcccccccCcccccCcccc
Q psy11903 128 PYTQKFESCKICRQ-------KVHQVGSHYCQACAYKKGICAMCGKKLL 169 (179)
Q Consensus 128 p~~~~~~~c~~ck~-------~~~~~~~~yc~~cay~~g~c~mcgk~~~ 169 (179)
|-+.+..-|.+|-. .+.++ ..- -+.|.|.|||++-.
T Consensus 29 PeGvwKGLC~~CL~sa~~ty~e~~~~-~~s-----~~~gKC~LCG~kt~ 71 (119)
T PF10621_consen 29 PEGVWKGLCETCLDSAEKTYQEVNEN-ESS-----CRSGKCDLCGKKTQ 71 (119)
T ss_pred cchHHHhhHHHHHHHHHHHHHHHhcc-ccc-----ccccceeccCCcce
Confidence 55555667777743 33332 222 27899999999743
No 65
>cd09025 Aldose_epim_Slr1438 Aldose 1-epimerase, similar to Synechocystis Slr1438. Proteins similar to Synechocystis Slr1438 are uncharacterized members of aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen.
Probab=30.66 E-value=2.2e+02 Score=24.04 Aligned_cols=55 Identities=20% Similarity=0.253 Sum_probs=32.5
Q ss_pred EEEEEcC-CCeEEEEe-cCCcEEEEEEeeCCCCcccceEeCcCCchhhh------hhhhccccccceec
Q psy11903 30 RFTLTNS-QRMSVQVI-DYGATITTIKVPDKRGNVDDVVLGFDDMREEI------YFIMVCSKCEKKLG 90 (179)
Q Consensus 30 ~~tL~n~-~gl~v~vl-nyGAtI~sl~vpdr~G~~~dVVLGfd~~e~Y~------~~gmvc~kc~~klg 90 (179)
.++|+++ .++++.|+ .+||.|.++.. +| .+|+- ..+.+.+. .-..+|.+..+|++
T Consensus 3 ~~~l~~~~~~~~~~v~p~~Ga~l~s~~~---~g--~~~l~-~~~~~~~~~~~~~~gG~p~l~P~~gri~ 65 (271)
T cd09025 3 TYELSDEEAGSRLRVVPERGGLITRWTV---QG--RELLY-LDEERFADPAKSVRGGIPILFPICGNLP 65 (271)
T ss_pred EEEEEcCCCceEEEEecccCCEEEEEec---CC--EEEEe-cCChHHhccccccCCCCcEEECccCCCC
Confidence 3566764 24999998 67999999975 35 46653 22222221 11246666666664
No 66
>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=29.76 E-value=31 Score=21.81 Aligned_cols=11 Identities=18% Similarity=0.754 Sum_probs=6.2
Q ss_pred ccchhhccccc
Q psy11903 135 SCKICRQKVHQ 145 (179)
Q Consensus 135 ~c~~ck~~~~~ 145 (179)
+|..|++.+..
T Consensus 28 ~C~~C~~~l~~ 38 (58)
T PF00412_consen 28 KCSKCGKPLND 38 (58)
T ss_dssp BETTTTCBTTT
T ss_pred ccCCCCCccCC
Confidence 56666655543
No 67
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=29.44 E-value=16 Score=20.91 Aligned_cols=21 Identities=19% Similarity=0.654 Sum_probs=8.5
Q ss_pred ccchhhccccc-----CCCccCcccc
Q psy11903 135 SCKICRQKVHQ-----VGSHYCQACA 155 (179)
Q Consensus 135 ~c~~ck~~~~~-----~~~~yc~~ca 155 (179)
+|..|...+.. ....||..|.
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred cCccCCCcceEeEecCCCCeECcCCc
Confidence 56666655432 2335666653
No 68
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=27.74 E-value=30 Score=28.69 Aligned_cols=25 Identities=28% Similarity=0.693 Sum_probs=17.7
Q ss_pred cccchhhcccccCCCccCcccccccCcccccCcccc
Q psy11903 134 ESCKICRQKVHQVGSHYCQACAYKKGICAMCGKKLL 169 (179)
Q Consensus 134 ~~c~~ck~~~~~~~~~yc~~cay~~g~c~mcgk~~~ 169 (179)
-.|.-|+...+ +.+++|+.||-++.
T Consensus 140 ~rC~GC~~~f~-----------~~~~~Cp~CG~~~~ 164 (177)
T COG1439 140 LRCHGCKRIFP-----------EPKDFCPICGSPLK 164 (177)
T ss_pred EEEecCceecC-----------CCCCcCCCCCCceE
Confidence 46777777665 34678889997755
No 69
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.85 E-value=34 Score=36.21 Aligned_cols=31 Identities=23% Similarity=0.717 Sum_probs=16.0
Q ss_pred cccchhhcccccCCCccCcccccc---cCcccccCcc
Q psy11903 134 ESCKICRQKVHQVGSHYCQACAYK---KGICAMCGKK 167 (179)
Q Consensus 134 ~~c~~ck~~~~~~~~~yc~~cay~---~g~c~mcgk~ 167 (179)
.+|..|...+.+ .+|+.|-.+ ...|.-||.+
T Consensus 668 rkCPkCG~~t~~---~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 668 RRCPSCGTETYE---NRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred EECCCCCCcccc---ccCcccCCcCCCceeCccCCCc
Confidence 466666665544 366666544 2234444443
No 70
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=26.11 E-value=31 Score=29.71 Aligned_cols=31 Identities=19% Similarity=0.645 Sum_probs=21.0
Q ss_pred ccCCCcccCcccchhhcccc-----cCCCccCcccc
Q psy11903 125 RFNPYTQKFESCKICRQKVH-----QVGSHYCQACA 155 (179)
Q Consensus 125 ~~~p~~~~~~~c~~ck~~~~-----~~~~~yc~~ca 155 (179)
++.-|+.....|..|.+.+. .-+..||..|-
T Consensus 237 ~l~Vy~R~g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 237 SLQVYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred eeEEcCCCCCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 34456555678999988764 23678898884
No 71
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.82 E-value=32 Score=29.70 Aligned_cols=30 Identities=30% Similarity=0.730 Sum_probs=21.7
Q ss_pred ccCCCcccCcccchhhcccc-----cCCCccCccc
Q psy11903 125 RFNPYTQKFESCKICRQKVH-----QVGSHYCQAC 154 (179)
Q Consensus 125 ~~~p~~~~~~~c~~ck~~~~-----~~~~~yc~~c 154 (179)
++.-|+.....|..|.+.|. +-...||..|
T Consensus 236 ~~~Vy~R~g~pCprCG~~I~~~~~~gR~t~~CP~C 270 (272)
T PRK14810 236 SHRVYQRTGEPCLNCKTPIRRVVVAGRSSHYCPHC 270 (272)
T ss_pred hEeecCCCCCcCCCCCCeeEEEEECCCccEECcCC
Confidence 45567666779999988664 3466888887
No 72
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=24.88 E-value=32 Score=27.18 Aligned_cols=24 Identities=25% Similarity=0.885 Sum_probs=16.8
Q ss_pred cccchhhcccc-cCCCccCcccccc
Q psy11903 134 ESCKICRQKVH-QVGSHYCQACAYK 157 (179)
Q Consensus 134 ~~c~~ck~~~~-~~~~~yc~~cay~ 157 (179)
..|..|++.+- -+|.-||+.|-|+
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~~~ 53 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCGYR 53 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCCce
Confidence 48999999773 3476777666553
No 73
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=24.63 E-value=17 Score=21.94 Aligned_cols=29 Identities=21% Similarity=0.601 Sum_probs=19.1
Q ss_pred cccchhhcccccCCCccCcccccccCcccccCcc
Q psy11903 134 ESCKICRQKVHQVGSHYCQACAYKKGICAMCGKK 167 (179)
Q Consensus 134 ~~c~~ck~~~~~~~~~yc~~cay~~g~c~mcgk~ 167 (179)
..|..|....- ..||..|.. -+|..|-..
T Consensus 4 ~~C~~H~~~~~---~~~C~~C~~--~~C~~C~~~ 32 (42)
T PF00643_consen 4 PKCPEHPEEPL---SLFCEDCNE--PLCSECTVS 32 (42)
T ss_dssp SB-SSTTTSBE---EEEETTTTE--EEEHHHHHT
T ss_pred ccCccCCccce---EEEecCCCC--ccCccCCCC
Confidence 46777776533 378998876 688877543
No 74
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=23.32 E-value=38 Score=29.26 Aligned_cols=33 Identities=21% Similarity=0.615 Sum_probs=22.8
Q ss_pred ccCCCcccCcccchhhcccc-----cCCCccCcccccc
Q psy11903 125 RFNPYTQKFESCKICRQKVH-----QVGSHYCQACAYK 157 (179)
Q Consensus 125 ~~~p~~~~~~~c~~ck~~~~-----~~~~~yc~~cay~ 157 (179)
++.-|+.....|..|.+.+. +-+..||..|--.
T Consensus 227 ~~~Vy~R~g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 227 QHAVYGREGQPCPRCGTPIEKIVVGGRGTHFCPQCQPL 264 (269)
T ss_pred eEEecCCCcCCCCcCCCeeEEEEECCCCcEECCCCcCC
Confidence 34456655678999988664 3467899988543
No 75
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=22.97 E-value=57 Score=22.80 Aligned_cols=42 Identities=21% Similarity=0.592 Sum_probs=18.1
Q ss_pred ccchhhcccccC------CCccCccccccc--CcccccCccc--cccccccc
Q psy11903 135 SCKICRQKVHQV------GSHYCQACAYKK--GICAMCGKKL--LDVKNYKQ 176 (179)
Q Consensus 135 ~c~~ck~~~~~~------~~~yc~~cay~~--g~c~mcgk~~--~d~~~~~~ 176 (179)
+|.+|..-++.| .|.||..|.=.. -.|+.|-.+- .|++-.+|
T Consensus 9 rCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD~~~Nrq 60 (65)
T PF14835_consen 9 RCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQDIQINRQ 60 (65)
T ss_dssp S-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS----HH
T ss_pred CCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHHHHhhhh
Confidence 677887777665 578999998443 4588887775 56665544
No 76
>PF09706 Cas_CXXC_CXXC: CRISPR-associated protein (Cas_CXXC_CXXC); InterPro: IPR019121 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved domain of about 65 amino acids found in otherwise highly divergent proteins encoded in CRISPR-associated regions. This domain features two CXXC motifs.
Probab=22.75 E-value=43 Score=23.21 Aligned_cols=11 Identities=45% Similarity=1.026 Sum_probs=8.4
Q ss_pred ccCcccccCcc
Q psy11903 157 KKGICAMCGKK 167 (179)
Q Consensus 157 ~~g~c~mcgk~ 167 (179)
+++.|..||.+
T Consensus 4 ~~~~C~~Cg~r 14 (69)
T PF09706_consen 4 KKYNCIFCGER 14 (69)
T ss_pred CCCcCcCCCCc
Confidence 46789999944
No 77
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=22.15 E-value=31 Score=19.70 Aligned_cols=22 Identities=18% Similarity=0.588 Sum_probs=6.8
Q ss_pred ccchhhcccccCCCccCccccc
Q psy11903 135 SCKICRQKVHQVGSHYCQACAY 156 (179)
Q Consensus 135 ~c~~ck~~~~~~~~~yc~~cay 156 (179)
.|..|+.++......+|..|-|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf 23 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDF 23 (30)
T ss_dssp --TTTS----S--EEE-TTT--
T ss_pred cCCcCCCcCCCCceEECccCCC
Confidence 4667777665423455666654
No 78
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=22.02 E-value=41 Score=23.44 Aligned_cols=22 Identities=23% Similarity=0.780 Sum_probs=16.2
Q ss_pred CcccchhhcccccCCCccCcccccccCcccccCcc
Q psy11903 133 FESCKICRQKVHQVGSHYCQACAYKKGICAMCGKK 167 (179)
Q Consensus 133 ~~~c~~ck~~~~~~~~~yc~~cay~~g~c~mcgk~ 167 (179)
+..|+.|+.-++.. .|..||-.
T Consensus 5 ~~AC~~C~~i~~~~-------------~Cp~Cgs~ 26 (64)
T PRK06393 5 YRACKKCKRLTPEK-------------TCPVHGDE 26 (64)
T ss_pred hhhHhhCCcccCCC-------------cCCCCCCC
Confidence 35899999877531 78888875
No 79
>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=21.95 E-value=37 Score=25.31 Aligned_cols=11 Identities=36% Similarity=1.038 Sum_probs=8.9
Q ss_pred CcccccCcccc
Q psy11903 159 GICAMCGKKLL 169 (179)
Q Consensus 159 g~c~mcgk~~~ 169 (179)
|+|-.||+.|-
T Consensus 81 G~C~~Cge~I~ 91 (110)
T TIGR02420 81 GYCEECGEEIG 91 (110)
T ss_pred CchhccCCccc
Confidence 68889998874
No 80
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=21.92 E-value=38 Score=26.75 Aligned_cols=24 Identities=25% Similarity=0.667 Sum_probs=20.0
Q ss_pred ccCcccchhhcccccCCCccCccccc
Q psy11903 131 QKFESCKICRQKVHQVGSHYCQACAY 156 (179)
Q Consensus 131 ~~~~~c~~ck~~~~~~~~~yc~~cay 156 (179)
+..-.|..|-+.+.. | .||..|+-
T Consensus 79 nl~~~CE~CG~~I~~-G-r~C~~C~~ 102 (137)
T TIGR03826 79 NLGYPCERCGTSIRE-G-RLCDSCAG 102 (137)
T ss_pred CCcCcccccCCcCCC-C-CccHHHHH
Confidence 345699999999998 5 99999973
No 81
>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=21.67 E-value=87 Score=29.47 Aligned_cols=37 Identities=30% Similarity=0.789 Sum_probs=24.8
Q ss_pred Ccccchhhccc--cc-CCCccCcccccccC---cccccCcccc
Q psy11903 133 FESCKICRQKV--HQ-VGSHYCQACAYKKG---ICAMCGKKLL 169 (179)
Q Consensus 133 ~~~c~~ck~~~--~~-~~~~yc~~cay~~g---~c~mcgk~~~ 169 (179)
..+|..|-..+ |+ .+.-.|+.|.|... .|.-||-.-+
T Consensus 222 ~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s~~l 264 (505)
T TIGR00595 222 ILCCPNCDVSLTYHKKEGKLRCHYCGYQEPIPKTCPQCGSEDL 264 (505)
T ss_pred ccCCCCCCCceEEecCCCeEEcCCCcCcCCCCCCCCCCCCCee
Confidence 34566666544 32 23456999999876 8999998654
No 82
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=21.14 E-value=50 Score=22.79 Aligned_cols=29 Identities=24% Similarity=0.562 Sum_probs=19.4
Q ss_pred cccchhhcccccCCCccCcccccccCcccccCcccc
Q psy11903 134 ESCKICRQKVHQVGSHYCQACAYKKGICAMCGKKLL 169 (179)
Q Consensus 134 ~~c~~ck~~~~~~~~~yc~~cay~~g~c~mcgk~~~ 169 (179)
..|..|..-++. +.+ |-+-.|.+||+.++
T Consensus 10 ~~CtSCg~~i~p-~e~------~v~F~CPnCGe~~I 38 (61)
T COG2888 10 PVCTSCGREIAP-GET------AVKFPCPNCGEVEI 38 (61)
T ss_pred ceeccCCCEecc-CCc------eeEeeCCCCCceee
Confidence 489999999866 433 45556777774443
No 83
>KOG1734|consensus
Probab=20.87 E-value=32 Score=30.65 Aligned_cols=15 Identities=27% Similarity=0.751 Sum_probs=12.0
Q ss_pred cCcccccCccccccc
Q psy11903 158 KGICAMCGKKLLDVK 172 (179)
Q Consensus 158 ~g~c~mcgk~~~d~~ 172 (179)
.++||.||+++.++-
T Consensus 224 d~vCaVCg~~~~~s~ 238 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSV 238 (328)
T ss_pred cchhHhhcchheeec
Confidence 359999999998653
No 84
>PF06045 Rhamnogal_lyase: Rhamnogalacturonate lyase family; InterPro: IPR010325 Rhamnogalacturonate lyase degrades the rhamnogalacturonan I (RG-I) backbone of pectin []. This family contains mainly members from plants, but also contains the plant pathogen Erwinia chrysanthemi.
Probab=20.80 E-value=1.5e+02 Score=25.00 Aligned_cols=34 Identities=29% Similarity=0.364 Sum_probs=26.7
Q ss_pred EEEEcCCCeEEEEecCCcEEEEEEeeCCCCcccceEeCcC
Q psy11903 31 FTLTNSQRMSVQVIDYGATITTIKVPDKRGNVDDVVLGFD 70 (179)
Q Consensus 31 ~tL~n~~gl~v~vlnyGAtI~sl~vpdr~G~~~dVVLGfd 70 (179)
.+|.|+ =++|+|.+=|+.|++|+. +|. +.+|.+.
T Consensus 18 VvldNG-iVqVtls~p~G~VtgIkY---nGi--~NLle~~ 51 (203)
T PF06045_consen 18 VVLDNG-IVQVTLSKPGGIVTGIKY---NGI--DNLLEVA 51 (203)
T ss_pred EEEECC-EEEEEEcCCCceEEEEEE---CCE--ehhhccc
Confidence 678884 699999999999999998 573 4555543
No 85
>KOG1705|consensus
Probab=20.38 E-value=31 Score=25.97 Aligned_cols=33 Identities=27% Similarity=0.651 Sum_probs=22.8
Q ss_pred CcccCcccchhhcccccCCCccCcccc---cccCccc
Q psy11903 129 YTQKFESCKICRQKVHQVGSHYCQACA---YKKGICA 162 (179)
Q Consensus 129 ~~~~~~~c~~ck~~~~~~~~~yc~~ca---y~~g~c~ 162 (179)
|+.+...|.||.- +....+.||..|- |-+.-|+
T Consensus 51 ~Gs~q~~ciic~~-~gV~d~~yc~ectr~ekdrdgCp 86 (110)
T KOG1705|consen 51 YGSYQGRCVICGG-VGVSDAYYCKECTRQEKDRDGCP 86 (110)
T ss_pred CccccCceEEecC-CcccchHHHHHHHhhccccccCh
Confidence 4445679999998 5444789999986 4444454
No 86
>smart00746 TRASH metallochaperone-like domain.
Probab=20.18 E-value=47 Score=17.64 Aligned_cols=9 Identities=44% Similarity=1.435 Sum_probs=7.6
Q ss_pred ccccCcccc
Q psy11903 161 CAMCGKKLL 169 (179)
Q Consensus 161 c~mcgk~~~ 169 (179)
|+.||..|.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 788999886
No 87
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=20.16 E-value=56 Score=25.55 Aligned_cols=20 Identities=30% Similarity=0.815 Sum_probs=13.9
Q ss_pred cccchhhcccccCCCccCccc
Q psy11903 134 ESCKICRQKVHQVGSHYCQAC 154 (179)
Q Consensus 134 ~~c~~ck~~~~~~~~~yc~~c 154 (179)
++|..|-.-.+.+ ..+|..|
T Consensus 30 ~kC~~CG~v~~PP-r~~Cp~C 49 (140)
T COG1545 30 TKCKKCGRVYFPP-RAYCPKC 49 (140)
T ss_pred EEcCCCCeEEcCC-cccCCCC
Confidence 4899998877774 4555544
Done!