Query psy2231
Match_columns 201
No_of_seqs 174 out of 1529
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 19:32:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2231.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2231hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2272|consensus 99.9 3.3E-23 7.1E-28 171.4 0.8 166 21-195 81-305 (332)
2 KOG1701|consensus 99.8 3.7E-22 8E-27 175.2 2.1 108 43-158 276-407 (468)
3 KOG2272|consensus 99.8 2.4E-22 5.3E-27 166.2 -7.0 151 11-173 16-230 (332)
4 KOG1044|consensus 99.7 4.3E-19 9.3E-24 160.7 1.5 139 20-177 72-253 (670)
5 KOG1044|consensus 99.7 1.9E-17 4.1E-22 150.1 3.9 143 21-170 24-221 (670)
6 KOG1701|consensus 99.6 1.8E-17 3.8E-22 145.9 0.4 113 16-135 279-428 (468)
7 KOG1703|consensus 99.6 3.2E-16 7E-21 143.5 2.7 115 12-130 304-473 (479)
8 KOG1703|consensus 99.5 7.4E-15 1.6E-19 134.6 3.5 129 40-174 302-454 (479)
9 PF00412 LIM: LIM domain; Int 99.4 5.7E-14 1.2E-18 92.5 3.2 57 44-101 1-58 (58)
10 KOG4577|consensus 99.4 2.4E-14 5.3E-19 120.8 -3.9 101 42-149 34-159 (383)
11 KOG1700|consensus 98.6 1.7E-08 3.8E-13 82.8 1.0 62 44-106 10-71 (200)
12 smart00132 LIM Zinc-binding do 98.5 6.7E-08 1.4E-12 57.8 2.9 36 44-79 2-38 (39)
13 PF00412 LIM: LIM domain; Int 98.5 3.6E-07 7.8E-12 59.7 6.3 57 71-144 1-58 (58)
14 KOG4577|consensus 98.2 6.1E-08 1.3E-12 82.4 -3.2 94 10-105 32-158 (383)
15 KOG1702|consensus 98.0 5.1E-07 1.1E-11 73.6 -2.4 61 41-102 4-64 (264)
16 KOG1700|consensus 97.6 1.2E-05 2.7E-10 66.0 0.3 57 44-101 111-167 (200)
17 smart00132 LIM Zinc-binding do 96.0 0.0075 1.6E-07 35.3 2.7 36 110-156 2-38 (39)
18 KOG0490|consensus 93.5 0.016 3.4E-07 47.6 -0.7 58 47-106 2-63 (235)
19 PF08394 Arc_trans_TRASH: Arch 70.9 5.1 0.00011 24.0 2.5 23 110-132 1-24 (37)
20 PF06827 zf-FPG_IleRS: Zinc fi 69.3 2.6 5.6E-05 23.6 1.0 27 146-172 2-29 (30)
21 smart00504 Ubox Modified RING 62.4 11 0.00025 24.0 3.2 47 108-160 2-50 (63)
22 PF11781 RRN7: RNA polymerase 58.8 7.2 0.00016 23.0 1.6 25 69-98 9-33 (36)
23 COG2191 Formylmethanofuran deh 58.3 5.2 0.00011 33.0 1.2 31 69-100 173-203 (206)
24 KOG2462|consensus 56.4 7.7 0.00017 33.4 1.9 40 38-78 127-171 (279)
25 PRK14890 putative Zn-ribbon RN 55.6 17 0.00037 24.0 3.0 11 70-80 9-19 (59)
26 COG1645 Uncharacterized Zn-fin 53.2 10 0.00022 29.2 1.9 22 70-97 30-51 (131)
27 PF06677 Auto_anti-p27: Sjogre 53.1 11 0.00025 22.9 1.8 22 70-96 19-40 (41)
28 PF14835 zf-RING_6: zf-RING of 48.4 17 0.00037 24.5 2.2 26 136-161 31-56 (65)
29 KOG1702|consensus 48.3 3.2 6.8E-05 34.4 -1.6 44 95-145 21-64 (264)
30 PF14446 Prok-RING_1: Prokaryo 46.8 12 0.00027 24.2 1.3 27 43-69 7-36 (54)
31 PF13920 zf-C3HC4_3: Zinc fing 41.7 44 0.00095 20.5 3.3 43 109-157 4-49 (50)
32 PF09943 DUF2175: Uncharacteri 41.2 9.4 0.0002 28.0 0.1 29 44-72 5-34 (101)
33 PF02069 Metallothio_Pro: Prok 41.2 18 0.00039 23.3 1.4 30 109-143 9-38 (52)
34 PF06906 DUF1272: Protein of u 39.5 48 0.001 21.7 3.2 47 109-160 7-56 (57)
35 cd00162 RING RING-finger (Real 37.3 31 0.00068 19.6 2.0 41 110-155 2-45 (45)
36 PF10367 Vps39_2: Vacuolar sor 36.9 38 0.00081 23.9 2.8 15 70-84 80-94 (109)
37 PF01258 zf-dskA_traR: Prokary 36.5 5.6 0.00012 23.2 -1.4 28 110-142 6-33 (36)
38 PF10122 Mu-like_Com: Mu-like 35.6 14 0.0003 23.7 0.2 25 146-170 5-30 (51)
39 KOG3816|consensus 34.2 8.8 0.00019 34.8 -1.1 76 125-200 419-511 (526)
40 PF04570 DUF581: Protein of un 33.5 26 0.00056 23.1 1.2 23 70-92 18-42 (58)
41 PF14634 zf-RING_5: zinc-RING 32.3 49 0.0011 19.8 2.4 39 110-153 2-44 (44)
42 KOG0490|consensus 32.0 24 0.00053 28.5 1.2 42 108-155 24-69 (235)
43 PRK00807 50S ribosomal protein 29.1 69 0.0015 20.4 2.7 24 109-132 3-29 (52)
44 PF01286 XPA_N: XPA protein N- 28.7 26 0.00057 20.5 0.6 23 70-92 5-27 (34)
45 PF10235 Cript: Microtubule-as 28.3 36 0.00078 24.4 1.4 37 109-158 46-82 (90)
46 PRK00420 hypothetical protein; 28.2 44 0.00095 25.0 1.9 24 69-97 24-47 (112)
47 COG4357 Zinc finger domain con 27.1 7 0.00015 28.4 -2.4 46 47-92 41-86 (105)
48 COG2075 RPL24A Ribosomal prote 26.1 87 0.0019 21.2 2.8 33 109-144 5-40 (66)
49 COG4847 Uncharacterized protei 25.9 24 0.00051 25.7 0.1 35 44-78 9-44 (103)
50 PF14149 YhfH: YhfH-like prote 25.7 9.5 0.00021 22.8 -1.6 21 140-160 8-28 (37)
51 COG2888 Predicted Zn-ribbon RN 25.6 81 0.0018 20.9 2.5 6 147-152 52-57 (61)
52 COG2191 Formylmethanofuran deh 25.0 30 0.00065 28.6 0.6 31 108-143 173-203 (206)
53 PF13248 zf-ribbon_3: zinc-rib 24.9 56 0.0012 17.5 1.5 10 147-156 4-13 (26)
54 PF07191 zinc-ribbons_6: zinc- 24.8 40 0.00088 23.0 1.1 38 70-117 3-40 (70)
55 PF06750 DiS_P_DiS: Bacterial 24.7 20 0.00043 25.6 -0.5 38 109-159 35-72 (92)
56 smart00291 ZnF_ZZ Zinc-binding 24.3 57 0.0012 19.7 1.6 15 108-122 5-19 (44)
57 PRK14873 primosome assembly pr 24.1 66 0.0014 31.3 2.8 39 108-154 393-431 (665)
58 PF12674 Zn_ribbon_2: Putative 23.8 24 0.00052 24.7 -0.2 29 70-99 2-35 (81)
59 KOG0320|consensus 22.6 18 0.00038 29.3 -1.2 55 64-122 127-182 (187)
60 KOG1813|consensus 22.2 48 0.001 29.0 1.3 47 108-160 242-290 (313)
61 KOG0320|consensus 21.8 43 0.00093 27.2 0.9 48 108-160 132-182 (187)
62 PF04810 zf-Sec23_Sec24: Sec23 21.6 66 0.0014 19.1 1.5 22 109-130 4-25 (40)
63 TIGR00375 conserved hypothetic 21.5 39 0.00084 30.5 0.6 44 120-166 229-279 (374)
64 PRK11595 DNA utilization prote 20.6 70 0.0015 26.4 1.9 47 110-172 8-56 (227)
65 PF13834 DUF4193: Domain of un 20.4 38 0.00081 24.8 0.2 30 66-96 68-98 (99)
66 PF10886 DUF2685: Protein of u 20.3 72 0.0016 20.7 1.5 33 109-142 3-35 (54)
No 1
>KOG2272|consensus
Probab=99.86 E-value=3.3e-23 Score=171.36 Aligned_cols=166 Identities=14% Similarity=0.242 Sum_probs=135.7
Q ss_pred eeeeceeeccCCCcccCCCcccccC------------------------------------CCCCeeeecceEEeCCCcc
Q psy2231 21 AMILDLLLSSSGRRYVLQHHTSNAI------------------------------------NLPNSMYLAERKTSLGKDW 64 (201)
Q Consensus 21 ~~~~~~~~~a~g~~~h~~cf~C~cc------------------------------------~C~~~i~~~~~v~a~g~~w 64 (201)
|+|.|++|.||+.+|||+||+|+-| +|... |+.+.++..|..|
T Consensus 81 EFiiGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~-iD~~~l~fr~d~y 159 (332)
T KOG2272|consen 81 EFIIGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAH-IDEQPLTFRGDPY 159 (332)
T ss_pred cchhhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhh-cccccccccCCCC
Confidence 5889999999999999999999887 24444 4667899999999
Q ss_pred cCCCcccCCCCCcCCCCceeeeCCeeeecCCccccccCCccCc---------------------eeeCCCCccccCCcEE
Q psy2231 65 HGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSERSKF---------------------LGCLSSVCSILSQTFY 123 (201)
Q Consensus 65 H~~CF~C~~C~~~L~~~~f~~~~g~~yCe~~cy~~~~~p~C~~---------------------F~C~~C~~~l~~~~f~ 123 (201)
|+.+|+|..|++.|... -.+..|++|| ..|+.++--|.|.. |+|+.|.+|+.|..-+
T Consensus 160 H~yHFkCt~C~keL~sd-aRevk~eLyC-lrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPFlGHrHY 237 (332)
T KOG2272|consen 160 HPYHFKCTTCGKELTSD-AREVKGELYC-LRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGHRHY 237 (332)
T ss_pred Cccceecccccccccch-hhhhccceec-cccccccCCcccccccCchHHHHHHHhccccchhheeehhcCCcccchhhh
Confidence 99999999999999764 3467889999 79999988888763 9999999999999999
Q ss_pred EeCCeeeeccCCchhhhhhhcCCCCCCCCCcccCcceeecce-eeccccCcceeeeeeeCCcc-eEEEeecCcc
Q psy2231 124 SLSVDLYHASMHLRSDCLSMYGGKGNTSHTMIPDTYITQVTI-VIARCLSSVYSIQLVKPSIR-YRLTYIMPPC 195 (201)
Q Consensus 124 ~~~g~~yH~~~~C~~~y~~~~~~~C~~C~~~I~~~~i~a~~~-~~~~c~~~~~~~~~~~~~~~-~~~~~~~~~~ 195 (201)
++.|+.| |+.||.++|+..|..|+++|.+++++|+++ ++-.|.+ +....++.-.+. |--+-.||-|
T Consensus 238 EkkGlaY-----Ce~h~~qLfG~~CF~C~~~i~G~vv~al~KawCv~cf~-Cs~Cdkkl~~K~Kf~E~DmkP~C 305 (332)
T KOG2272|consen 238 EKKGLAY-----CETHYHQLFGNLCFICNRVIGGDVVSALNKAWCVECFS-CSTCDKKLTQKNKFYEFDMKPVC 305 (332)
T ss_pred hhcCchh-----HHHHHHHHhhhhheecCCccCccHHHHhhhhhcccccc-ccccccccccccceeeeccchHH
Confidence 9999999 999999999999999999999999999996 5666643 223333333333 2224445555
No 2
>KOG1701|consensus
Probab=99.84 E-value=3.7e-22 Score=175.21 Aligned_cols=108 Identities=18% Similarity=0.367 Sum_probs=97.7
Q ss_pred ccCCCCCeeeecc-eEEeCCCcccCCCcccCCCCCcCCCCceeeeCCeeeecCCccccc---------------------
Q psy2231 43 NAINLPNSMYLAE-RKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSAL--------------------- 100 (201)
Q Consensus 43 ~cc~C~~~i~~~~-~v~a~g~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yCe~~cy~~~--------------------- 100 (201)
.|.+|+|.|...+ .+.||++.||.+||+|..|++.|.++.||..|+++||| .||++.
T Consensus 276 iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE-~cyq~tlekC~~Cg~~I~d~iLrA~Gk 354 (468)
T KOG1701|consen 276 ICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCE-GCYQDTLEKCNKCGEPIMDRILRALGK 354 (468)
T ss_pred hhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccch-HHHHHHHHHHhhhhhHHHHHHHHhccc
Confidence 7999999986554 38999999999999999999999999999999999997 999753
Q ss_pred -cCCccCceeeCCCCccccCCcEEE-eCCeeeeccCCchhhhhhhcCCCCCCCCCcccCc
Q psy2231 101 -FSERSKFLGCLSSVCSILSQTFYS-LSVDLYHASMHLRSDCLSMYGGKGNTSHTMIPDT 158 (201)
Q Consensus 101 -~~p~C~~F~C~~C~~~l~~~~f~~-~~g~~yH~~~~C~~~y~~~~~~~C~~C~~~I~~~ 158 (201)
|+|.| |+|..|++.|+|..|.. .++++| |.+||+++||++|+.|++||+++
T Consensus 355 ayHp~C--F~Cv~C~r~ldgipFtvd~~n~v~-----Cv~dfh~kfAPrCs~C~~PI~P~ 407 (468)
T KOG1701|consen 355 AYHPGC--FTCVVCARCLDGIPFTVDSQNNVY-----CVPDFHKKFAPRCSVCGNPILPR 407 (468)
T ss_pred ccCCCc--eEEEEeccccCCccccccCCCcee-----eehhhhhhcCcchhhccCCccCC
Confidence 67778 99999999999999874 667777 99999999999999999999864
No 3
>KOG2272|consensus
Probab=99.80 E-value=2.4e-22 Score=166.22 Aligned_cols=151 Identities=17% Similarity=0.315 Sum_probs=125.4
Q ss_pred CcccCcccceeeeeceeeccCCCcccCCCcccccC-------------------------------CCCCeeeecceEEe
Q psy2231 11 NSRGAGLQQYAMILDLLLSSSGRRYVLQHHTSNAI-------------------------------NLPNSMYLAERKTS 59 (201)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~a~g~~~h~~cf~C~cc-------------------------------~C~~~i~~~~~v~a 59 (201)
.+.+.|... .+++++++|..||.+||+|+.| +|++.| .|++|.|
T Consensus 16 ~RC~~gF~~----~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFi-iGrVika 90 (332)
T KOG2272|consen 16 ERCRDGFEP----AEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFI-IGRVIKA 90 (332)
T ss_pred HHHhccCCc----hhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccch-hhHHHHh
Confidence 344445543 6788999999999999999888 588874 6899999
Q ss_pred CCCcccCCCcccCCCCCcCCCCceeeeCCeeeecCCccccccC--------CccCc------------------eeeCCC
Q psy2231 60 LGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFS--------ERSKF------------------LGCLSS 113 (201)
Q Consensus 60 ~g~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yCe~~cy~~~~~--------p~C~~------------------F~C~~C 113 (201)
++.+||+.||+|..|++.|.+..|+...|+.+| .+|.++.-+ .+|.+ |.|.+|
T Consensus 91 mnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC-~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C 169 (332)
T KOG2272|consen 91 MNNSWHPACFRCDLCNKHLADQGFYRNQGRALC-RECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTC 169 (332)
T ss_pred hccccCcccchhHHHHHHHhhhhhHhhcchHHh-hhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecccc
Confidence 999999999999999999999999999999999 599877321 12221 889999
Q ss_pred CccccCCcEEEeCCeeeeccCCchhhhhhhcCCCCCCCCCcccCcceeecc-------eeeccccCc
Q psy2231 114 VCSILSQTFYSLSVDLYHASMHLRSDCLSMYGGKGNTSHTMIPDTYITQVT-------IVIARCLSS 173 (201)
Q Consensus 114 ~~~l~~~~f~~~~g~~yH~~~~C~~~y~~~~~~~C~~C~~~I~~~~i~a~~-------~~~~~c~~~ 173 (201)
++.|... -.+..|.+| |..|++++--++|..|.+||.+++|.|++ +++|.|.+-
T Consensus 170 ~keL~sd-aRevk~eLy-----ClrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekP 230 (332)
T KOG2272|consen 170 GKELTSD-AREVKGELY-----CLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKP 230 (332)
T ss_pred cccccch-hhhhcccee-----ccccccccCCcccccccCchHHHHHHHhccccchhheeehhcCCc
Confidence 9888764 355677788 99999999999999999999999999998 577888543
No 4
>KOG1044|consensus
Probab=99.74 E-value=4.3e-19 Score=160.69 Aligned_cols=139 Identities=19% Similarity=0.369 Sum_probs=114.7
Q ss_pred eeeeeceeeccCCCcccCCCcccccC----------------------------------------CCCCeeeecceEEe
Q psy2231 20 YAMILDLLLSSSGRRYVLQHHTSNAI----------------------------------------NLPNSMYLAERKTS 59 (201)
Q Consensus 20 ~~~~~~~~~~a~g~~~h~~cf~C~cc----------------------------------------~C~~~i~~~~~v~a 59 (201)
-++++|++|+++|+.||+.||+|.-| +|++.|..|+.+.|
T Consensus 72 ~~~~~gevvsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~lla 151 (670)
T KOG1044|consen 72 RAFVEGEVVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLA 151 (670)
T ss_pred hhhccceeEecccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeee
Confidence 34778999999999999999999877 58888888999999
Q ss_pred CCCcccCCCcccCCCCCcCCCCceeeeCCeeeecCCccccccCCccCceeeCCCCccccCCcEEEeCCeeeeccCCchhh
Q psy2231 60 LGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSERSKFLGCLSSVCSILSQTFYSLSVDLYHASMHLRSD 139 (201)
Q Consensus 60 ~g~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yCe~~cy~~~~~p~C~~F~C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~ 139 (201)
+++.||..||+|..|+..|.+ .|+.++|.|||| .||++.|+-+| ..|.+.|.|.... ..|+.||+. |
T Consensus 152 ld~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce-~dy~~~fgvkc-----~~c~~fisgkvLq-ag~kh~HPt--C--- 218 (670)
T KOG1044|consen 152 LDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCE-KDYQAKFGVKC-----EECEKFISGKVLQ-AGDKHFHPT--C--- 218 (670)
T ss_pred eccceeeeeeehhhhcccccc-eeeccCCCcchh-hhhhhhcCeeh-----HHhhhhhhhhhhh-ccCcccCcc--h---
Confidence 999999999999999999965 799999999996 99999999665 7888899886544 455777665 3
Q ss_pred hhhhcCCCCCCCCCcccCc---ceeecceeeccccCcceee
Q psy2231 140 CLSMYGGKGNTSHTMIPDT---YITQVTIVIARCLSSVYSI 177 (201)
Q Consensus 140 y~~~~~~~C~~C~~~I~~~---~i~a~~~~~~~c~~~~~~~ 177 (201)
.+|..|+++++++ +++--.+||.+|--+-...
T Consensus 219 ------ARCsRCgqmF~eGEEMYlQGs~iWHP~C~qa~~tE 253 (670)
T KOG1044|consen 219 ------ARCSRCGQMFGEGEEMYLQGSEIWHPDCKQATKTE 253 (670)
T ss_pred ------hhhhhhccccccchheeeccccccCCccccccchh
Confidence 3789999999864 4555568899995443333
No 5
>KOG1044|consensus
Probab=99.68 E-value=1.9e-17 Score=150.08 Aligned_cols=143 Identities=17% Similarity=0.342 Sum_probs=116.6
Q ss_pred eeeeceeeccCCCcccCCCcccccCCCCCe--------------------eeecceEEeCCCcccCCCcccCCCCCcCCC
Q psy2231 21 AMILDLLLSSSGRRYVLQHHTSNAINLPNS--------------------MYLAERKTSLGKDWHGSCLRCENCNKTLVP 80 (201)
Q Consensus 21 ~~~~~~~~~a~g~~~h~~cf~C~cc~C~~~--------------------i~~~~~v~a~g~~wH~~CF~C~~C~~~L~~ 80 (201)
+...|+++++.++.||+.||+|.-|+|+.. ++.+++|.++|++||+.||.|+.|+.++..
T Consensus 24 ~kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~cs~ck~pf~~ 103 (670)
T KOG1044|consen 24 KKCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCSTCKSPFKS 103 (670)
T ss_pred CccccceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceeccccceecccCCCCCC
Confidence 346799999999999999999988865432 235678999999999999999999999987
Q ss_pred CceeeeCC-eeeecCCccccc-------cC-CccCc----------------------eeeCCCCccccCCcEEEeCCee
Q psy2231 81 GSHSEHDG-KPYCNYPCYSAL-------FS-ERSKF----------------------LGCLSSVCSILSQTFYSLSVDL 129 (201)
Q Consensus 81 ~~f~~~~g-~~yCe~~cy~~~-------~~-p~C~~----------------------F~C~~C~~~l~~~~f~~~~g~~ 129 (201)
+.-....| ...|+ .|-+-. ++ ..|++ |.|..|...|.| +++.+||.+
T Consensus 104 g~~vt~~gk~~~c~-~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey~skdg~p 181 (670)
T KOG1044|consen 104 GDKVTFSGKECLCQ-TCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVP 181 (670)
T ss_pred CCeeeecchhhhhh-hhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-eeeccCCCc
Confidence 76555555 46784 775422 11 12332 999999998877 588999999
Q ss_pred eeccCCchhhhhhhcCCCCCCCCCcccCcceeecce----eeccc
Q psy2231 130 YHASMHLRSDCLSMYGGKGNTSHTMIPDTYITQVTI----VIARC 170 (201)
Q Consensus 130 yH~~~~C~~~y~~~~~~~C~~C~~~I~~~~i~a~~~----~~~~c 170 (201)
| |+.||.+.|+.+|..|.+.|.+++++|.|. -||||
T Consensus 182 y-----ce~dy~~~fgvkc~~c~~fisgkvLqag~kh~HPtCARC 221 (670)
T KOG1044|consen 182 Y-----CEKDYQAKFGVKCEECEKFISGKVLQAGDKHFHPTCARC 221 (670)
T ss_pred c-----hhhhhhhhcCeehHHhhhhhhhhhhhccCcccCcchhhh
Confidence 9 999999999999999999999999999994 36666
No 6
>KOG1701|consensus
Probab=99.65 E-value=1.8e-17 Score=145.93 Aligned_cols=113 Identities=17% Similarity=0.253 Sum_probs=89.8
Q ss_pred cccceeeeeceeeccCCCcccCCCcccccC------------------------------CCCCeeeecceEEeCCCccc
Q psy2231 16 GLQQYAMILDLLLSSSGRRYVLQHHTSNAI------------------------------NLPNSMYLAERKTSLGKDWH 65 (201)
Q Consensus 16 ~~~~~~~~~~~~~~a~g~~~h~~cf~C~cc------------------------------~C~~~i~~~~~v~a~g~~wH 65 (201)
+..+...-.+..++||++.||..||+|.-| .|++.| .+..|.|+|+.||
T Consensus 279 ~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I-~d~iLrA~GkayH 357 (468)
T KOG1701|consen 279 FCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPI-MDRILRALGKAYH 357 (468)
T ss_pred hcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHHHHhhhhhHH-HHHHHHhcccccC
Confidence 333433445678899999999999999887 477774 5667999999999
Q ss_pred CCCcccCCCCCcCCCCceee-eCCeeeecCCccccccCCccCceeeCCCCccccCCc------EEEeCCeeeeccCC
Q psy2231 66 GSCLRCENCNKTLVPGSHSE-HDGKPYCNYPCYSALFSERSKFLGCLSSVCSILSQT------FYSLSVDLYHASMH 135 (201)
Q Consensus 66 ~~CF~C~~C~~~L~~~~f~~-~~g~~yCe~~cy~~~~~p~C~~F~C~~C~~~l~~~~------f~~~~g~~yH~~~~ 135 (201)
+.||+|..|.+.|++..|.. .++++|| .+||+++|+|+| +.|.++|..++ -+..-++-||..+|
T Consensus 358 p~CF~Cv~C~r~ldgipFtvd~~n~v~C-v~dfh~kfAPrC-----s~C~~PI~P~~G~~etvRvvamdr~fHv~CY 428 (468)
T KOG1701|consen 358 PGCFTCVVCARCLDGIPFTVDSQNNVYC-VPDFHKKFAPRC-----SVCGNPILPRDGKDETVRVVAMDRDFHVNCY 428 (468)
T ss_pred CCceEEEEeccccCCccccccCCCceee-ehhhhhhcCcch-----hhccCCccCCCCCcceEEEEEccccccccce
Confidence 99999999999999998885 5779999 799999999987 77888886542 12333466887655
No 7
>KOG1703|consensus
Probab=99.59 E-value=3.2e-16 Score=143.53 Aligned_cols=115 Identities=24% Similarity=0.522 Sum_probs=94.5
Q ss_pred cccCcccceeeeec-eeeccCCCcccCCCcccccC-------------------------------CCCCeeeecceEEe
Q psy2231 12 SRGAGLQQYAMILD-LLLSSSGRRYVLQHHTSNAI-------------------------------NLPNSMYLAERKTS 59 (201)
Q Consensus 12 ~~~~~~~~~~~~~~-~~~~a~g~~~h~~cf~C~cc-------------------------------~C~~~i~~~~~v~a 59 (201)
+++++... .|.+ +++.++++.||+++|.|.-+ +|+++| .++.|.|
T Consensus 304 p~c~~c~~--~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i-~~~~v~a 380 (479)
T KOG1703|consen 304 PLCLSCNQ--KIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPI-LEEGVCA 380 (479)
T ss_pred cccccccc--CcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCch-HHhHhhh
Confidence 33444333 5667 99999999999999998877 588884 6788999
Q ss_pred CCCcccCCCcccCCCCCcCCCCceeeeCCeeeecCCccccccCCccCc-----------------------eeeCCCCcc
Q psy2231 60 LGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSERSKF-----------------------LGCLSSVCS 116 (201)
Q Consensus 60 ~g~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yCe~~cy~~~~~p~C~~-----------------------F~C~~C~~~ 116 (201)
+++.||++||.|..|+++|....|+..+|.|||| .||.+++.++|.. |+|+.|.+.
T Consensus 381 ~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce-~~~~~~~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~ 459 (479)
T KOG1703|consen 381 LGRLWHPECFVCADCGKPLKNSSFFESDGEPYCE-DHYKKLFTTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKK 459 (479)
T ss_pred ccCeechhceeeecccCCCCCCcccccCCccchh-hhHhhhccccchhccchhHhhhhHhhccCccccccceehhhhhcc
Confidence 9999999999999999999999999999999996 9999999877632 667777777
Q ss_pred ccCCcEEEeCCeee
Q psy2231 117 ILSQTFYSLSVDLY 130 (201)
Q Consensus 117 l~~~~f~~~~g~~y 130 (201)
|.++.|++..++++
T Consensus 460 l~~~~~~~~~~~p~ 473 (479)
T KOG1703|consen 460 LTKKTFFETLDKPL 473 (479)
T ss_pred ccCCceeecCCccc
Confidence 76666666666666
No 8
>KOG1703|consensus
Probab=99.51 E-value=7.4e-15 Score=134.61 Aligned_cols=129 Identities=19% Similarity=0.378 Sum_probs=113.6
Q ss_pred cccccCCCCCeeeecceEEeCCCcccCCCcccCCCCCcCCCCceeeeCCeeeecCCccccccCCccCc------------
Q psy2231 40 HTSNAINLPNSMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSERSKF------------ 107 (201)
Q Consensus 40 f~C~cc~C~~~i~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yCe~~cy~~~~~p~C~~------------ 107 (201)
++-.|..|++.|...+.+.++++.||+.+|.|+.|+..+....|...+|++|| ..||.+.+.|.|.+
T Consensus 302 ~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c-~~~~~~~~~p~C~~C~~~i~~~~v~a 380 (479)
T KOG1703|consen 302 TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILC-HECFHAPFRPNCKRCLLPILEEGVCA 380 (479)
T ss_pred ccccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccH-HHHHHHhhCccccccCCchHHhHhhh
Confidence 44556678888644388999999999999999999999999889999999999 59999999999885
Q ss_pred ---------eeeCCCCccccCCcEEEeCCeeeeccCCchhhhhhhcCCCCCCCCCccc--Ccceeecce-eeccccCcc
Q psy2231 108 ---------LGCLSSVCSILSQTFYSLSVDLYHASMHLRSDCLSMYGGKGNTSHTMIP--DTYITQVTI-VIARCLSSV 174 (201)
Q Consensus 108 ---------F~C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~y~~~~~~~C~~C~~~I~--~~~i~a~~~-~~~~c~~~~ 174 (201)
|.|..|+++|....|++.+|.+| |+.||.+++.++|..|.+||+ +..|++++. ++..|++-.
T Consensus 381 ~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~py-----ce~~~~~~~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~ 454 (479)
T KOG1703|consen 381 LGRLWHPECFVCADCGKPLKNSSFFESDGEPY-----CEDHYKKLFTTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCA 454 (479)
T ss_pred ccCeechhceeeecccCCCCCCcccccCCccc-----hhhhHhhhccccchhccchhHhhhhHhhccCccccccceehh
Confidence 99999999999999999999999 999999999999999999988 888999983 566555443
No 9
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.44 E-value=5.7e-14 Score=92.45 Aligned_cols=57 Identities=39% Similarity=0.871 Sum_probs=51.5
Q ss_pred cCCCCCeeeecceE-EeCCCcccCCCcccCCCCCcCCCCceeeeCCeeeecCCcccccc
Q psy2231 44 AINLPNSMYLAERK-TSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALF 101 (201)
Q Consensus 44 cc~C~~~i~~~~~v-~a~g~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yCe~~cy~~~~ 101 (201)
|.+|+++|.+++.+ .++|+.||++||+|..|+++|.+..|+..+|++|| .+||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C-~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYC-KDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEE-HHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEEC-HHHHhhhC
Confidence 56899998777765 69999999999999999999999999999999999 59998875
No 10
>KOG4577|consensus
Probab=99.35 E-value=2.4e-14 Score=120.79 Aligned_cols=101 Identities=19% Similarity=0.394 Sum_probs=87.9
Q ss_pred cccCCCCCeeeecceEEeCCCcccCCCcccCCCCCcCCCCceeeeCCeeeecCCccccccCCccCc--------------
Q psy2231 42 SNAINLPNSMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSERSKF-------------- 107 (201)
Q Consensus 42 C~cc~C~~~i~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yCe~~cy~~~~~p~C~~-------------- 107 (201)
-.|++|.+.|.+.-.+.++++.||..|++|++|..+|.+ ..+.++|..|| +++|.++|+.+|..
T Consensus 34 p~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yC-kedFfKrfGTKCsaC~~GIpPtqVVRkA 111 (383)
T KOG4577|consen 34 PICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYC-KEDFFKRFGTKCSACQEGIPPTQVVRKA 111 (383)
T ss_pred ccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceee-hHHHHHHhCCcchhhcCCCChHHHHHHh
Confidence 358999999877777889999999999999999999976 56789999999 89999999999974
Q ss_pred ---------eeeCCCCccccC-CcEE-EeCCeeeeccCCchhhhhhhcCCCCC
Q psy2231 108 ---------LGCLSSVCSILS-QTFY-SLSVDLYHASMHLRSDCLSMYGGKGN 149 (201)
Q Consensus 108 ---------F~C~~C~~~l~~-~~f~-~~~g~~yH~~~~C~~~y~~~~~~~C~ 149 (201)
|.|..|+++|.. .+|+ +.|+++. |+.||+..-+..|.
T Consensus 112 qd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLv-----CK~DYE~Ak~k~~~ 159 (383)
T KOG4577|consen 112 QDFVYHLHCFACFICKRQLATGDEFYLMEDARLV-----CKDDYETAKQKHCN 159 (383)
T ss_pred hcceeehhhhhhHhhhcccccCCeeEEeccceee-----hhhhHHHHHhcccc
Confidence 999999999964 4565 6788999 99999988777664
No 11
>KOG1700|consensus
Probab=98.56 E-value=1.7e-08 Score=82.79 Aligned_cols=62 Identities=35% Similarity=0.746 Sum_probs=55.6
Q ss_pred cCCCCCeeeecceEEeCCCcccCCCcccCCCCCcCCCCceeeeCCeeeecCCccccccCCccC
Q psy2231 44 AINLPNSMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSERSK 106 (201)
Q Consensus 44 cc~C~~~i~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yCe~~cy~~~~~p~C~ 106 (201)
|-.|++.|+..+.+...|..||+.||.|..|.+.|....+..+++.+|| +.+|...++|+..
T Consensus 10 c~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc-~~~~~~~~~~~~~ 71 (200)
T KOG1700|consen 10 CNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYC-KNCHVAQFGPKGG 71 (200)
T ss_pred hhhccCcchHHHHHhccCcchhhhHHhcccccccccccccccccccccc-ccchHhhhCcccc
Confidence 7789999999999999999999999999999999999999999999999 5877777766543
No 12
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.53 E-value=6.7e-08 Score=57.78 Aligned_cols=36 Identities=28% Similarity=0.587 Sum_probs=32.0
Q ss_pred cCCCCCeeeec-ceEEeCCCcccCCCcccCCCCCcCC
Q psy2231 44 AINLPNSMYLA-ERKTSLGKDWHGSCLRCENCNKTLV 79 (201)
Q Consensus 44 cc~C~~~i~~~-~~v~a~g~~wH~~CF~C~~C~~~L~ 79 (201)
|.+|++.|.++ ..+.++++.||++||+|..|+++|.
T Consensus 2 C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 67899998766 6688999999999999999999985
No 13
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=98.52 E-value=3.6e-07 Score=59.71 Aligned_cols=57 Identities=18% Similarity=0.336 Sum_probs=48.2
Q ss_pred cCCCCCcCCCCcee-eeCCeeeecCCccccccCCccCceeeCCCCccccCCcEEEeCCeeeeccCCchhhhhhhc
Q psy2231 71 CENCNKTLVPGSHS-EHDGKPYCNYPCYSALFSERSKFLGCLSSVCSILSQTFYSLSVDLYHASMHLRSDCLSMY 144 (201)
Q Consensus 71 C~~C~~~L~~~~f~-~~~g~~yCe~~cy~~~~~p~C~~F~C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~y~~~~ 144 (201)
|..|++++.+.... ...|+.|. .+| |.|..|+++|.++.|++.+|++| |..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H-~~C-----------f~C~~C~~~l~~~~~~~~~~~~~-----C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWH-PEC-----------FKCSKCGKPLNDGDFYEKDGKPY-----CKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEE-TTT-----------SBETTTTCBTTTSSEEEETTEEE-----EHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEE-ccc-----------cccCCCCCccCCCeeEeECCEEE-----CHHHHhhhC
Confidence 77899999876544 46777777 355 99999999999988999999999 999999876
No 14
>KOG4577|consensus
Probab=98.24 E-value=6.1e-08 Score=82.41 Aligned_cols=94 Identities=15% Similarity=0.197 Sum_probs=72.5
Q ss_pred cCcccCcccceeeeeceeeccCCCcccCCCcccccC------------------------------CCCCeeeecceEE-
Q psy2231 10 VNSRGAGLQQYAMILDLLLSSSGRRYVLQHHTSNAI------------------------------NLPNSMYLAERKT- 58 (201)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~a~g~~~h~~cf~C~cc------------------------------~C~~~i~~~~~v~- 58 (201)
..+.++|+++.. ...-++.++++.||..|..|.-| .|.+.|.+.++|.
T Consensus 32 eip~CagC~q~I-lDrFilKvl~R~wHs~CLkCs~C~~qL~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRk 110 (383)
T KOG4577|consen 32 EIPICAGCDQHI-LDRFILKVLDRHWHSSCLKCSDCHDQLADRCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRK 110 (383)
T ss_pred ccccccchHHHH-HHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHH
Confidence 455667777643 23456679999999999998877 4777776667654
Q ss_pred eCCCcccCCCcccCCCCCcCCCC-ceee-eCCeeeecCCccccccCCcc
Q psy2231 59 SLGKDWHGSCLRCENCNKTLVPG-SHSE-HDGKPYCNYPCYSALFSERS 105 (201)
Q Consensus 59 a~g~~wH~~CF~C~~C~~~L~~~-~f~~-~~g~~yCe~~cy~~~~~p~C 105 (201)
|.+..||..||.|..|++.|..+ .||. .|+++.| +++|+..-...|
T Consensus 111 Aqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvC-K~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 111 AQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVC-KDDYETAKQKHC 158 (383)
T ss_pred hhcceeehhhhhhHhhhcccccCCeeEEeccceeeh-hhhHHHHHhccc
Confidence 78999999999999999999866 5664 5779999 899987655444
No 15
>KOG1702|consensus
Probab=97.99 E-value=5.1e-07 Score=73.59 Aligned_cols=61 Identities=34% Similarity=0.672 Sum_probs=55.2
Q ss_pred ccccCCCCCeeeecceEEeCCCcccCCCcccCCCCCcCCCCceeeeCCeeeecCCccccccC
Q psy2231 41 TSNAINLPNSMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALFS 102 (201)
Q Consensus 41 ~C~cc~C~~~i~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yCe~~cy~~~~~ 102 (201)
.|++..|++.+++.|.+..+++.||..||+|..|+.+|..+.|...+.+|||+ .+|.+..+
T Consensus 4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn-~hYpkq~a 64 (264)
T KOG1702|consen 4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCN-PHYPKQVA 64 (264)
T ss_pred cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcC-ccccccee
Confidence 46788999999999999999999999999999999999998988889999996 99977643
No 16
>KOG1700|consensus
Probab=97.64 E-value=1.2e-05 Score=65.97 Aligned_cols=57 Identities=32% Similarity=0.698 Sum_probs=51.6
Q ss_pred cCCCCCeeeecceEEeCCCcccCCCcccCCCCCcCCCCceeeeCCeeeecCCcccccc
Q psy2231 44 AINLPNSMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYCNYPCYSALF 101 (201)
Q Consensus 44 cc~C~~~i~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yCe~~cy~~~~ 101 (201)
|.+|.+.+++.+.+...+..||..||+|..|+..|+.+.+...+|.+|| ...+..++
T Consensus 111 c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~-~~~~~~~~ 167 (200)
T KOG1700|consen 111 CARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYC-KHHFAQLF 167 (200)
T ss_pred cccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCcccc-chhhheee
Confidence 7789999999999999999999999999999999999999999999999 46665543
No 17
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=95.97 E-value=0.0075 Score=35.31 Aligned_cols=36 Identities=11% Similarity=0.067 Sum_probs=21.0
Q ss_pred eCCCCccccCC-cEEEeCCeeeeccCCchhhhhhhcCCCCCCCCCccc
Q psy2231 110 CLSSVCSILSQ-TFYSLSVDLYHASMHLRSDCLSMYGGKGNTSHTMIP 156 (201)
Q Consensus 110 C~~C~~~l~~~-~f~~~~g~~yH~~~~C~~~y~~~~~~~C~~C~~~I~ 156 (201)
|..|+++|.+. ..+...++.||.. || +|..|+++|.
T Consensus 2 C~~C~~~i~~~~~~~~~~~~~~H~~-----Cf------~C~~C~~~L~ 38 (39)
T smart00132 2 CAGCGKPIRGGELVLRALGKVWHPE-----CF------KCSKCGKPLG 38 (39)
T ss_pred ccccCCcccCCcEEEEeCCcccccc-----CC------CCcccCCcCc
Confidence 56667777665 4555566667543 22 5666666653
No 18
>KOG0490|consensus
Probab=93.50 E-value=0.016 Score=47.64 Aligned_cols=58 Identities=31% Similarity=0.595 Sum_probs=45.4
Q ss_pred CCCeeeecceEEeCCCcccCCCcccCCCCCcCC--CCceeeeCCeeeecCCcccc--ccCCccC
Q psy2231 47 LPNSMYLAERKTSLGKDWHGSCLRCENCNKTLV--PGSHSEHDGKPYCNYPCYSA--LFSERSK 106 (201)
Q Consensus 47 C~~~i~~~~~v~a~g~~wH~~CF~C~~C~~~L~--~~~f~~~~g~~yCe~~cy~~--~~~p~C~ 106 (201)
|+..|.+...+.+.+..||..|..|..|...|. ...|.. +|..|| ..+|.+ .+..+|.
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~-~~d~~~~~~~~~rr~ 63 (235)
T KOG0490|consen 2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYC-KRDYQREFKFSKRCA 63 (235)
T ss_pred CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccc-cccchhhhhcccccc
Confidence 566665555567779999999999999999997 445555 999999 699998 5555554
No 19
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=70.93 E-value=5.1 Score=23.96 Aligned_cols=23 Identities=13% Similarity=0.177 Sum_probs=15.9
Q ss_pred eCCCCccccCCcEE-EeCCeeeec
Q psy2231 110 CLSSVCSILSQTFY-SLSVDLYHA 132 (201)
Q Consensus 110 C~~C~~~l~~~~f~-~~~g~~yH~ 132 (201)
|.-|+.+|.+++.. -.+|++||.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~f 24 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYF 24 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEE
Confidence 56677788877643 457777776
No 20
>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=69.34 E-value=2.6 Score=23.55 Aligned_cols=27 Identities=26% Similarity=0.310 Sum_probs=15.7
Q ss_pred CCCCCCCCcccCccee-ecceeeccccC
Q psy2231 146 GKGNTSHTMIPDTYIT-QVTIVIARCLS 172 (201)
Q Consensus 146 ~~C~~C~~~I~~~~i~-a~~~~~~~c~~ 172 (201)
.+|..|+..|.+..+. ..+.++++|..
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCcC
Confidence 5788899988776663 44567888753
No 21
>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=62.35 E-value=11 Score=24.03 Aligned_cols=47 Identities=13% Similarity=0.068 Sum_probs=33.6
Q ss_pred eeeCCCCccccCCcEEEeCCeeeeccCCchhhhhhhc--CCCCCCCCCcccCcce
Q psy2231 108 LGCLSSVCSILSQTFYSLSVDLYHASMHLRSDCLSMY--GGKGNTSHTMIPDTYI 160 (201)
Q Consensus 108 F~C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~y~~~~--~~~C~~C~~~I~~~~i 160 (201)
|.|..|...+.. ......|..| |+.+..+.+ ...|..|++++..+.+
T Consensus 2 ~~Cpi~~~~~~~-Pv~~~~G~v~-----~~~~i~~~~~~~~~cP~~~~~~~~~~l 50 (63)
T smart00504 2 FLCPISLEVMKD-PVILPSGQTY-----ERRAIEKWLLSHGTDPVTGQPLTHEDL 50 (63)
T ss_pred cCCcCCCCcCCC-CEECCCCCEE-----eHHHHHHHHHHCCCCCCCcCCCChhhc
Confidence 457777777654 5666778889 999887654 4679889888865433
No 22
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=58.76 E-value=7.2 Score=23.02 Aligned_cols=25 Identities=28% Similarity=0.534 Sum_probs=18.3
Q ss_pred cccCCCCCcCCCCceeeeCCeeeecCCccc
Q psy2231 69 LRCENCNKTLVPGSHSEHDGKPYCNYPCYS 98 (201)
Q Consensus 69 F~C~~C~~~L~~~~f~~~~g~~yCe~~cy~ 98 (201)
+.|..|+.. .|...||..|| ..|..
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC-~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYC-DRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEh-hhCce
Confidence 347888764 57788999999 46654
No 23
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=58.34 E-value=5.2 Score=32.95 Aligned_cols=31 Identities=29% Similarity=0.742 Sum_probs=26.7
Q ss_pred cccCCCCCcCCCCceeeeCCeeeecCCccccc
Q psy2231 69 LRCENCNKTLVPGSHSEHDGKPYCNYPCYSAL 100 (201)
Q Consensus 69 F~C~~C~~~L~~~~f~~~~g~~yCe~~cy~~~ 100 (201)
-+|+.|+..+....-...+|++.| +.|+.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~vC-~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPVC-KPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCceec-ccccccc
Confidence 589999999887777788999999 7998764
No 24
>KOG2462|consensus
Probab=56.38 E-value=7.7 Score=33.42 Aligned_cols=40 Identities=20% Similarity=0.289 Sum_probs=19.6
Q ss_pred CCcccccCCCCCeeeecceEEeCCCccc-----CCCcccCCCCCcC
Q psy2231 38 QHHTSNAINLPNSMYLAERKTSLGKDWH-----GSCLRCENCNKTL 78 (201)
Q Consensus 38 ~cf~C~cc~C~~~i~~~~~v~a~g~~wH-----~~CF~C~~C~~~L 78 (201)
..-...|..|++.. ....=.+.-+++| +.=|.|..|++..
T Consensus 127 ~~~r~~c~eCgk~y-sT~snLsrHkQ~H~~~~s~ka~~C~~C~K~Y 171 (279)
T KOG2462|consen 127 KHPRYKCPECGKSY-STSSNLSRHKQTHRSLDSKKAFSCKYCGKVY 171 (279)
T ss_pred cCCceecccccccc-ccccccchhhcccccccccccccCCCCCcee
Confidence 33344477788763 2211112234444 3456777776643
No 25
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=55.60 E-value=17 Score=24.02 Aligned_cols=11 Identities=27% Similarity=1.065 Sum_probs=5.9
Q ss_pred ccCCCCCcCCC
Q psy2231 70 RCENCNKTLVP 80 (201)
Q Consensus 70 ~C~~C~~~L~~ 80 (201)
+|..|+..|.+
T Consensus 9 ~CtSCg~~i~~ 19 (59)
T PRK14890 9 KCTSCGIEIAP 19 (59)
T ss_pred cccCCCCcccC
Confidence 45555555543
No 26
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=53.16 E-value=10 Score=29.15 Aligned_cols=22 Identities=32% Similarity=0.857 Sum_probs=17.4
Q ss_pred ccCCCCCcCCCCceeeeCCeeeecCCcc
Q psy2231 70 RCENCNKTLVPGSHSEHDGKPYCNYPCY 97 (201)
Q Consensus 70 ~C~~C~~~L~~~~f~~~~g~~yCe~~cy 97 (201)
.|..|+.|| |.++|..|| ..|-
T Consensus 30 hCp~Cg~PL-----F~KdG~v~C-PvC~ 51 (131)
T COG1645 30 HCPKCGTPL-----FRKDGEVFC-PVCG 51 (131)
T ss_pred hCcccCCcc-----eeeCCeEEC-CCCC
Confidence 588998888 349999999 5664
No 27
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=53.12 E-value=11 Score=22.89 Aligned_cols=22 Identities=41% Similarity=1.149 Sum_probs=15.9
Q ss_pred ccCCCCCcCCCCceeeeCCeeeecCCc
Q psy2231 70 RCENCNKTLVPGSHSEHDGKPYCNYPC 96 (201)
Q Consensus 70 ~C~~C~~~L~~~~f~~~~g~~yCe~~c 96 (201)
.|..|+.||.. .++|+.|| ..|
T Consensus 19 ~Cp~C~~PL~~----~k~g~~~C-v~C 40 (41)
T PF06677_consen 19 HCPDCGTPLMR----DKDGKIYC-VSC 40 (41)
T ss_pred ccCCCCCeeEE----ecCCCEEC-CCC
Confidence 57788877743 57888999 455
No 28
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=48.43 E-value=17 Score=24.51 Aligned_cols=26 Identities=19% Similarity=-0.049 Sum_probs=15.6
Q ss_pred chhhhhhhcCCCCCCCCCcccCccee
Q psy2231 136 LRSDCLSMYGGKGNTSHTMIPDTYIT 161 (201)
Q Consensus 136 C~~~y~~~~~~~C~~C~~~I~~~~i~ 161 (201)
|..|-...++..|..|+.|-..+.++
T Consensus 31 Cs~Ci~~~~~~~CPvC~~Paw~qD~~ 56 (65)
T PF14835_consen 31 CSSCIRDCIGSECPVCHTPAWIQDIQ 56 (65)
T ss_dssp -TTTGGGGTTTB-SSS--B-S-SS--
T ss_pred HHHHhHHhcCCCCCCcCChHHHHHHH
Confidence 99998888999999999997655443
No 29
>KOG1702|consensus
Probab=48.27 E-value=3.2 Score=34.44 Aligned_cols=44 Identities=7% Similarity=0.221 Sum_probs=35.2
Q ss_pred CccccccCCccCceeeCCCCccccCCcEEEeCCeeeeccCCchhhhhhhcC
Q psy2231 95 PCYSALFSERSKFLGCLSSVCSILSQTFYSLSVDLYHASMHLRSDCLSMYG 145 (201)
Q Consensus 95 ~cy~~~~~p~C~~F~C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~y~~~~~ 145 (201)
.|-++.++..| |.|..|+.+|.-..+-..|.++| |..+|.+..+
T Consensus 21 ~cldk~whk~c--fkce~c~mtlnmKnyKgy~kkpy-----cn~hYpkq~a 64 (264)
T KOG1702|consen 21 KCLDKVWHKQC--FKCEVCGMTLNMKNYKGYDKKPY-----CNPHYPKQVA 64 (264)
T ss_pred hhHHHHHHHHh--heeeeccCChhhhhccccccCCC-----cCccccccee
Confidence 45566677788 99999999987777766777888 9999987664
No 30
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=46.75 E-value=12 Score=24.22 Aligned_cols=27 Identities=11% Similarity=0.190 Sum_probs=16.3
Q ss_pred ccCCCCCeeeecceEE---eCCCcccCCCc
Q psy2231 43 NAINLPNSMYLAERKT---SLGKDWHGSCL 69 (201)
Q Consensus 43 ~cc~C~~~i~~~~~v~---a~g~~wH~~CF 69 (201)
.|..|+++|.+++-+. .-+..||.+|.
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 4677888875343322 34667777775
No 31
>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=41.68 E-value=44 Score=20.50 Aligned_cols=43 Identities=9% Similarity=-0.024 Sum_probs=27.0
Q ss_pred eeCCCCccccCCcEEEeCCee-eeccCCchhhhhhh--cCCCCCCCCCcccC
Q psy2231 109 GCLSSVCSILSQTFYSLSVDL-YHASMHLRSDCLSM--YGGKGNTSHTMIPD 157 (201)
Q Consensus 109 ~C~~C~~~l~~~~f~~~~g~~-yH~~~~C~~~y~~~--~~~~C~~C~~~I~~ 157 (201)
.|..|...... .....=|.. + |..|..+. -..+|..|.++|.+
T Consensus 4 ~C~iC~~~~~~-~~~~pCgH~~~-----C~~C~~~~~~~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 4 ECPICFENPRD-VVLLPCGHLCF-----CEECAERLLKRKKKCPICRQPIES 49 (50)
T ss_dssp B-TTTSSSBSS-EEEETTCEEEE-----EHHHHHHHHHTTSBBTTTTBB-SE
T ss_pred CCccCCccCCc-eEEeCCCChHH-----HHHHhHHhcccCCCCCcCChhhcC
Confidence 35555554332 223334566 7 99999887 46889999999863
No 32
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=41.23 E-value=9.4 Score=27.99 Aligned_cols=29 Identities=17% Similarity=0.126 Sum_probs=21.9
Q ss_pred cCCCCCeeeecceEEeC-CCcccCCCcccC
Q psy2231 44 AINLPNSMYLAERKTSL-GKDWHGSCLRCE 72 (201)
Q Consensus 44 cc~C~~~i~~~~~v~a~-g~~wH~~CF~C~ 72 (201)
|--||++|+.|+..++. +..-|-.||.=.
T Consensus 5 C~iCg~~I~~gqlFTF~~kG~VH~~C~~~~ 34 (101)
T PF09943_consen 5 CYICGKPIYEGQLFTFTKKGPVHYECFREK 34 (101)
T ss_pred EEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence 77899999999987764 456787887543
No 33
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=41.18 E-value=18 Score=23.29 Aligned_cols=30 Identities=17% Similarity=0.344 Sum_probs=18.3
Q ss_pred eeCCCCccccCCcEEEeCCeeeeccCCchhhhhhh
Q psy2231 109 GCLSSVCSILSQTFYSLSVDLYHASMHLRSDCLSM 143 (201)
Q Consensus 109 ~C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~y~~~ 143 (201)
.|..|...+..++-+.+||+.| |.+.....
T Consensus 9 aC~~C~C~V~~~~Ai~~dGk~Y-----CS~aCA~g 38 (52)
T PF02069_consen 9 ACPSCSCVVSEEEAIQKDGKYY-----CSEACANG 38 (52)
T ss_dssp SSTT----B-TTTSEESSS-EE-----SSHHHHHT
T ss_pred cCCCCEeEECchHhHHhCCEee-----ecHHHhcc
Confidence 4778888888777789999999 87766543
No 34
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=39.50 E-value=48 Score=21.70 Aligned_cols=47 Identities=6% Similarity=0.012 Sum_probs=32.1
Q ss_pred eeCCCCccccCCc---EEEeCCeeeeccCCchhhhhhhcCCCCCCCCCcccCcce
Q psy2231 109 GCLSSVCSILSQT---FYSLSVDLYHASMHLRSDCLSMYGGKGNTSHTMIPDTYI 160 (201)
Q Consensus 109 ~C~~C~~~l~~~~---f~~~~g~~yH~~~~C~~~y~~~~~~~C~~C~~~I~~~~i 160 (201)
.|..|++.|.+.. ++-. ++.-+|.+|-+.++..+|..|+..+..+.+
T Consensus 7 nCE~C~~dLp~~s~~A~ICS-----fECTFC~~C~e~~l~~~CPNCgGelv~RP~ 56 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICS-----FECTFCADCAETMLNGVCPNCGGELVRRPR 56 (57)
T ss_pred CccccCCCCCCCCCcceEEe-----EeCcccHHHHHHHhcCcCcCCCCccccCCC
Confidence 3566777775543 3221 234459999999999999999987766543
No 35
>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=37.34 E-value=31 Score=19.55 Aligned_cols=41 Identities=12% Similarity=0.013 Sum_probs=22.1
Q ss_pred eCCCCccccCCcEEEeCCeeeeccCCchhhhhhhc---CCCCCCCCCcc
Q psy2231 110 CLSSVCSILSQTFYSLSVDLYHASMHLRSDCLSMY---GGKGNTSHTMI 155 (201)
Q Consensus 110 C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~y~~~~---~~~C~~C~~~I 155 (201)
|..|...+........=|..| |..|....+ ..+|..|++.+
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~-----c~~C~~~~~~~~~~~Cp~C~~~~ 45 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVF-----CRSCIDKWLKSGKNTCPLCRTPI 45 (45)
T ss_pred CCcCchhhhCceEecCCCChh-----cHHHHHHHHHhCcCCCCCCCCcC
Confidence 455555552211222245556 777776544 45788887653
No 36
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=36.92 E-value=38 Score=23.88 Aligned_cols=15 Identities=27% Similarity=0.567 Sum_probs=7.4
Q ss_pred ccCCCCCcCCCCcee
Q psy2231 70 RCENCNKTLVPGSHS 84 (201)
Q Consensus 70 ~C~~C~~~L~~~~f~ 84 (201)
.|..|+++|..+.|.
T Consensus 80 ~C~vC~k~l~~~~f~ 94 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFV 94 (109)
T ss_pred CccCcCCcCCCceEE
Confidence 355555555544433
No 37
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=36.51 E-value=5.6 Score=23.17 Aligned_cols=28 Identities=7% Similarity=-0.066 Sum_probs=19.6
Q ss_pred eCCCCccccCCcEEEeCCeeeeccCCchhhhhh
Q psy2231 110 CLSSVCSILSQTFYSLSVDLYHASMHLRSDCLS 142 (201)
Q Consensus 110 C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~y~~ 142 (201)
|..|+.+|..+.....++..+ |.+|..+
T Consensus 6 C~~CGe~I~~~Rl~~~p~~~~-----C~~C~~~ 33 (36)
T PF01258_consen 6 CEDCGEPIPEERLVAVPGATL-----CVECQER 33 (36)
T ss_dssp -TTTSSBEEHHHHHHCTTECS------HHHHHH
T ss_pred ccccCChHHHHHHHhCCCcEE-----CHHHhCc
Confidence 788888887776666677777 8888754
No 38
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=35.57 E-value=14 Score=23.72 Aligned_cols=25 Identities=12% Similarity=0.320 Sum_probs=16.0
Q ss_pred CCCCCCCCcccC-cceeecceeeccc
Q psy2231 146 GKGNTSHTMIPD-TYITQVTIVIARC 170 (201)
Q Consensus 146 ~~C~~C~~~I~~-~~i~a~~~~~~~c 170 (201)
.+|..|++.+.. +.+..+.+.|.||
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC 30 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRC 30 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCC
Confidence 367777776655 4555666677777
No 39
>KOG3816|consensus
Probab=34.17 E-value=8.8 Score=34.79 Aligned_cols=76 Identities=12% Similarity=0.068 Sum_probs=44.5
Q ss_pred eCCeeeeccCCchhhhhhhcCCCCCCCCCcccCcceeec-----c-----------eeeccccCcceeeeeeeCC-cceE
Q psy2231 125 LSVDLYHASMHLRSDCLSMYGGKGNTSHTMIPDTYITQV-----T-----------IVIARCLSSVYSIQLVKPS-IRYR 187 (201)
Q Consensus 125 ~~g~~yH~~~~C~~~y~~~~~~~C~~C~~~I~~~~i~a~-----~-----------~~~~~c~~~~~~~~~~~~~-~~~~ 187 (201)
.+|+.+|-...|..|-..-....|..|+++-++....-- | .+|-.|.+++++.+...-. -.|.
T Consensus 419 l~GR~~yL~~vC~~CL~g~~sI~C~~Ck~~wDGss~vLGTmY~YDI~aa~pCC~~R~~C~~C~k~l~~~~q~~t~~s~ys 498 (526)
T KOG3816|consen 419 LDGRRFYLQQVCARCLWGDWSIICKNCKKDWDGSSFVLGTMYYYDIVAAGPCCPVRLVCQSCRKSLGVRDQLATQLSNYS 498 (526)
T ss_pred ecceehhHHHHHHHHhcccchHHHhhcCCCCCCcceeechhhhhhhhhcCCcchhhhhhhhhccccccHHHHHHHHhhhh
Confidence 567766666667777766666778888888766433211 2 2445555555443322211 2456
Q ss_pred EEeecCccccccc
Q psy2231 188 LTYIMPPCTYAQT 200 (201)
Q Consensus 188 ~~~~~~~~~~~~~ 200 (201)
.+-|-|+|.++++
T Consensus 499 ~~~~cP~c~~~d~ 511 (526)
T KOG3816|consen 499 ALRICPSCKLADR 511 (526)
T ss_pred cccccCCcCcccc
Confidence 6677777777664
No 40
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=33.48 E-value=26 Score=23.07 Aligned_cols=23 Identities=30% Similarity=0.560 Sum_probs=17.7
Q ss_pred ccCCCCCcCCC-C-ceeeeCCeeee
Q psy2231 70 RCENCNKTLVP-G-SHSEHDGKPYC 92 (201)
Q Consensus 70 ~C~~C~~~L~~-~-~f~~~~g~~yC 92 (201)
.|..|++.|.. + .|..+..+++|
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFC 42 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFC 42 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccc
Confidence 46778889984 3 67788889999
No 41
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=32.26 E-value=49 Score=19.79 Aligned_cols=39 Identities=5% Similarity=-0.042 Sum_probs=24.2
Q ss_pred eCCCCccccCC-c-EEEeCCeeeeccCCchhhhhhhc--CCCCCCCCC
Q psy2231 110 CLSSVCSILSQ-T-FYSLSVDLYHASMHLRSDCLSMY--GGKGNTSHT 153 (201)
Q Consensus 110 C~~C~~~l~~~-~-f~~~~g~~yH~~~~C~~~y~~~~--~~~C~~C~~ 153 (201)
|..|...+.++ . +...=|..+ |..|..++. ..+|..|++
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~-----C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIF-----CEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHH-----HHHHHHhhcCCCCCCcCCCC
Confidence 45555555221 2 233336667 999998887 677888864
No 42
>KOG0490|consensus
Probab=32.02 E-value=24 Score=28.53 Aligned_cols=42 Identities=14% Similarity=0.237 Sum_probs=34.3
Q ss_pred eeeCCCCcccc--CCcEEEeCCeeeeccCCchhhhhh--hcCCCCCCCCCcc
Q psy2231 108 LGCLSSVCSIL--SQTFYSLSVDLYHASMHLRSDCLS--MYGGKGNTSHTMI 155 (201)
Q Consensus 108 F~C~~C~~~l~--~~~f~~~~g~~yH~~~~C~~~y~~--~~~~~C~~C~~~I 155 (201)
..|..|..++. ...|.. +|..| |..+|.. .+..+|.+|...|
T Consensus 24 ~~~~~~~~~~~~~~~~~~~-~g~~~-----~~~d~~~~~~~~~rr~rt~~~~ 69 (235)
T KOG0490|consen 24 LKCAECDNPLGVGDTCFSK-DGSIY-----CKRDYQREFKFSKRCARCKFTI 69 (235)
T ss_pred HhhhhhcchhccCCCcccC-CCccc-----ccccchhhhhccccccCCCCCc
Confidence 55677777876 444555 99999 9999998 8899999999987
No 43
>PRK00807 50S ribosomal protein L24e; Validated
Probab=29.08 E-value=69 Score=20.39 Aligned_cols=24 Identities=8% Similarity=-0.036 Sum_probs=16.9
Q ss_pred eeCCCCccccCC---cEEEeCCeeeec
Q psy2231 109 GCLSSVCSILSQ---TFYSLSVDLYHA 132 (201)
Q Consensus 109 ~C~~C~~~l~~~---~f~~~~g~~yH~ 132 (201)
.|+-|+..|.++ .|+..||++|..
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~Dgkv~~F 29 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKDGTILYF 29 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeCCcEEEE
Confidence 367777787633 367789998855
No 44
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=28.66 E-value=26 Score=20.49 Aligned_cols=23 Identities=22% Similarity=0.638 Sum_probs=7.1
Q ss_pred ccCCCCCcCCCCceeeeCCeeee
Q psy2231 70 RCENCNKTLVPGSHSEHDGKPYC 92 (201)
Q Consensus 70 ~C~~C~~~L~~~~f~~~~g~~yC 92 (201)
.|.+|++++.++.....=+-+.|
T Consensus 5 ~C~eC~~~f~dSyL~~~F~~~VC 27 (34)
T PF01286_consen 5 KCDECGKPFMDSYLLNNFDLPVC 27 (34)
T ss_dssp E-TTT--EES-SSCCCCTS-S--
T ss_pred hHhHhCCHHHHHHHHHhCCcccc
Confidence 35555565554433333333444
No 45
>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=28.27 E-value=36 Score=24.43 Aligned_cols=37 Identities=16% Similarity=0.113 Sum_probs=26.2
Q ss_pred eeCCCCccccCCcEEEeCCeeeeccCCchhhhhhhcCCCCCCCCCcccCc
Q psy2231 109 GCLSSVCSILSQTFYSLSVDLYHASMHLRSDCLSMYGGKGNTSHTMIPDT 158 (201)
Q Consensus 109 ~C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~y~~~~~~~C~~C~~~I~~~ 158 (201)
.|..|+..+. +.|..| |..|-.+ ..+|+.|++.|++.
T Consensus 46 ~C~~CK~~v~------q~g~~Y-----Cq~CAYk--kGiCamCGKki~dt 82 (90)
T PF10235_consen 46 KCKICKTKVH------QPGAKY-----CQTCAYK--KGICAMCGKKILDT 82 (90)
T ss_pred cccccccccc------cCCCcc-----Chhhhcc--cCcccccCCeeccc
Confidence 4677777653 335557 9999543 35899999999764
No 46
>PRK00420 hypothetical protein; Validated
Probab=28.22 E-value=44 Score=24.96 Aligned_cols=24 Identities=25% Similarity=0.420 Sum_probs=16.2
Q ss_pred cccCCCCCcCCCCceeeeCCeeeecCCcc
Q psy2231 69 LRCENCNKTLVPGSHSEHDGKPYCNYPCY 97 (201)
Q Consensus 69 F~C~~C~~~L~~~~f~~~~g~~yCe~~cy 97 (201)
-.|..|+.+|- -.++|+.|| ..|-
T Consensus 24 ~~CP~Cg~pLf----~lk~g~~~C-p~Cg 47 (112)
T PRK00420 24 KHCPVCGLPLF----ELKDGEVVC-PVHG 47 (112)
T ss_pred CCCCCCCCcce----ecCCCceEC-CCCC
Confidence 36788887762 237888888 4553
No 47
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=27.06 E-value=7 Score=28.45 Aligned_cols=46 Identities=15% Similarity=0.252 Sum_probs=26.1
Q ss_pred CCCeeeecceEEeCCCcccCCCcccCCCCCcCCCCceeeeCCeeee
Q psy2231 47 LPNSMYLAERKTSLGKDWHGSCLRCENCNKTLVPGSHSEHDGKPYC 92 (201)
Q Consensus 47 C~~~i~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC 92 (201)
|...+..--...+.-..+++.+..|-.|++.|.-..|..-+.-|||
T Consensus 41 CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C 86 (105)
T COG4357 41 CHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYC 86 (105)
T ss_pred HHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCc
Confidence 5554422222334445677777777777777765555555555555
No 48
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=26.07 E-value=87 Score=21.15 Aligned_cols=33 Identities=15% Similarity=0.172 Sum_probs=21.3
Q ss_pred eeCCCCccccCCc---EEEeCCeeeeccCCchhhhhhhc
Q psy2231 109 GCLSSVCSILSQT---FYSLSVDLYHASMHLRSDCLSMY 144 (201)
Q Consensus 109 ~C~~C~~~l~~~~---f~~~~g~~yH~~~~C~~~y~~~~ 144 (201)
+|.=|+..|.++. |+..||++++. |..-.++++
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v~~F---cssKc~k~~ 40 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKVLRF---CSSKCEKLF 40 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeEEEE---echhHHHHH
Confidence 5677788886654 77788888755 544443343
No 49
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.86 E-value=24 Score=25.66 Aligned_cols=35 Identities=14% Similarity=0.038 Sum_probs=25.3
Q ss_pred cCCCCCeeeecceEEeC-CCcccCCCcccCCCCCcC
Q psy2231 44 AINLPNSMYLAERKTSL-GKDWHGSCLRCENCNKTL 78 (201)
Q Consensus 44 cc~C~~~i~~~~~v~a~-g~~wH~~CF~C~~C~~~L 78 (201)
|..|+++|+.|+..++- -..-|-+||.=+.-+++-
T Consensus 9 C~VCg~~iieGqkFTF~~kGsVH~eCl~~s~~~k~~ 44 (103)
T COG4847 9 CYVCGGTIIEGQKFTFTKKGSVHYECLAESKRKKPG 44 (103)
T ss_pred EeeeCCEeeeccEEEEeeCCcchHHHHHHHHhcCcC
Confidence 77899999999986653 446888888766555443
No 50
>PF14149 YhfH: YhfH-like protein
Probab=25.70 E-value=9.5 Score=22.81 Aligned_cols=21 Identities=10% Similarity=-0.083 Sum_probs=16.0
Q ss_pred hhhhcCCCCCCCCCcccCcce
Q psy2231 140 CLSMYGGKGNTSHTMIPDTYI 160 (201)
Q Consensus 140 y~~~~~~~C~~C~~~I~~~~i 160 (201)
|..+..+.|..|++.|.++.-
T Consensus 8 frnLp~K~C~~CG~~i~EQ~E 28 (37)
T PF14149_consen 8 FRNLPPKKCTECGKEIEEQAE 28 (37)
T ss_pred HHhCCCcccHHHHHHHHHHHH
Confidence 455667889999999987643
No 51
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=25.56 E-value=81 Score=20.91 Aligned_cols=6 Identities=0% Similarity=-0.075 Sum_probs=3.3
Q ss_pred CCCCCC
Q psy2231 147 KGNTSH 152 (201)
Q Consensus 147 ~C~~C~ 152 (201)
+|..|+
T Consensus 52 ~Cp~CG 57 (61)
T COG2888 52 RCPKCG 57 (61)
T ss_pred ECCCcC
Confidence 555554
No 52
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=25.03 E-value=30 Score=28.56 Aligned_cols=31 Identities=6% Similarity=-0.054 Sum_probs=25.5
Q ss_pred eeeCCCCccccCCcEEEeCCeeeeccCCchhhhhhh
Q psy2231 108 LGCLSSVCSILSQTFYSLSVDLYHASMHLRSDCLSM 143 (201)
Q Consensus 108 F~C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~y~~~ 143 (201)
-.|..|+..+....-...+|++. |..||.+.
T Consensus 173 v~C~kCGE~~~e~~~~~~ng~~v-----C~~C~~~~ 203 (206)
T COG2191 173 VRCSKCGELFMEPRAVVLNGKPV-----CKPCAEKK 203 (206)
T ss_pred eeccccCcccccchhhhcCCcee-----cccccccc
Confidence 47899998887777778899999 99998753
No 53
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=24.93 E-value=56 Score=17.48 Aligned_cols=10 Identities=10% Similarity=-0.167 Sum_probs=5.6
Q ss_pred CCCCCCCccc
Q psy2231 147 KGNTSHTMIP 156 (201)
Q Consensus 147 ~C~~C~~~I~ 156 (201)
.|..|+.+|.
T Consensus 4 ~Cp~Cg~~~~ 13 (26)
T PF13248_consen 4 FCPNCGAEID 13 (26)
T ss_pred CCcccCCcCC
Confidence 4666666544
No 54
>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=24.75 E-value=40 Score=23.03 Aligned_cols=38 Identities=18% Similarity=0.443 Sum_probs=14.9
Q ss_pred ccCCCCCcCCCCceeeeCCeeeecCCccccccCCccCceeeCCCCccc
Q psy2231 70 RCENCNKTLVPGSHSEHDGKPYCNYPCYSALFSERSKFLGCLSSVCSI 117 (201)
Q Consensus 70 ~C~~C~~~L~~~~f~~~~g~~yCe~~cy~~~~~p~C~~F~C~~C~~~l 117 (201)
.|..|+.+|.. .++..+|+ .|.... ... -.|..|+.+|
T Consensus 3 ~CP~C~~~L~~-----~~~~~~C~-~C~~~~-~~~---a~CPdC~~~L 40 (70)
T PF07191_consen 3 TCPKCQQELEW-----QGGHYHCE-ACQKDY-KKE---AFCPDCGQPL 40 (70)
T ss_dssp B-SSS-SBEEE-----ETTEEEET-TT--EE-EEE---EE-TTT-SB-
T ss_pred cCCCCCCccEE-----eCCEEECc-cccccc-eec---ccCCCcccHH
Confidence 45666666543 33566663 554321 111 3456666665
No 55
>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=24.72 E-value=20 Score=25.64 Aligned_cols=38 Identities=16% Similarity=0.210 Sum_probs=22.7
Q ss_pred eeCCCCccccCCcEEEeCCeeeeccCCchhhhhhhcCCCCCCCCCcccCcc
Q psy2231 109 GCLSSVCSILSQTFYSLSVDLYHASMHLRSDCLSMYGGKGNTSHTMIPDTY 159 (201)
Q Consensus 109 ~C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~y~~~~~~~C~~C~~~I~~~~ 159 (201)
.|..|+++|.--+-+..-+.. ....||..|+++|...+
T Consensus 35 ~C~~C~~~L~~~~lIPi~S~l-------------~lrGrCr~C~~~I~~~y 72 (92)
T PF06750_consen 35 HCPHCGHPLSWWDLIPILSYL-------------LLRGRCRYCGAPIPPRY 72 (92)
T ss_pred cCcCCCCcCcccccchHHHHH-------------HhCCCCcccCCCCChHH
Confidence 467777787543322222221 23568999999997654
No 56
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=24.32 E-value=57 Score=19.69 Aligned_cols=15 Identities=13% Similarity=0.299 Sum_probs=8.8
Q ss_pred eeeCCCCccccCCcE
Q psy2231 108 LGCLSSVCSILSQTF 122 (201)
Q Consensus 108 F~C~~C~~~l~~~~f 122 (201)
+.|..|+++|.+..|
T Consensus 5 ~~C~~C~~~i~g~ry 19 (44)
T smart00291 5 YSCDTCGKPIVGVRY 19 (44)
T ss_pred cCCCCCCCCCcCCEE
Confidence 446666666655544
No 57
>PRK14873 primosome assembly protein PriA; Provisional
Probab=24.15 E-value=66 Score=31.26 Aligned_cols=39 Identities=8% Similarity=-0.173 Sum_probs=20.4
Q ss_pred eeeCCCCccccCCcEEEeCCeeeeccCCchhhhhhhcCCCCCCCCCc
Q psy2231 108 LGCLSSVCSILSQTFYSLSVDLYHASMHLRSDCLSMYGGKGNTSHTM 154 (201)
Q Consensus 108 F~C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~y~~~~~~~C~~C~~~ 154 (201)
+.|..|.-+|. +...++.+. |.-|-......+|..|+..
T Consensus 393 ~~C~~C~~~L~---~h~~~~~l~-----Ch~CG~~~~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLG---LPSAGGTPR-----CRWCGRAAPDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCcee---EecCCCeeE-----CCCCcCCCcCccCCCCcCC
Confidence 45666666653 333334444 5555433345667777653
No 58
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=23.82 E-value=24 Score=24.66 Aligned_cols=29 Identities=31% Similarity=0.753 Sum_probs=19.8
Q ss_pred ccCCCCCcCCCCceee--eCC---eeeecCCcccc
Q psy2231 70 RCENCNKTLVPGSHSE--HDG---KPYCNYPCYSA 99 (201)
Q Consensus 70 ~C~~C~~~L~~~~f~~--~~g---~~yCe~~cy~~ 99 (201)
.|+.|+-||.....+. .|| .-|| ..||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC-~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYC-SYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHH-HHHhcC
Confidence 4899999998776332 244 3588 688764
No 59
>KOG0320|consensus
Probab=22.56 E-value=18 Score=29.34 Aligned_cols=55 Identities=16% Similarity=0.375 Sum_probs=37.6
Q ss_pred ccCCCcccCCCCCcCCCC-ceeeeCCeeeecCCccccccCCccCceeeCCCCccccCCcE
Q psy2231 64 WHGSCLRCENCNKTLVPG-SHSEHDGKPYCNYPCYSALFSERSKFLGCLSSVCSILSQTF 122 (201)
Q Consensus 64 wH~~CF~C~~C~~~L~~~-~f~~~~g~~yCe~~cy~~~~~p~C~~F~C~~C~~~l~~~~f 122 (201)
--..+|+|-.|-.....+ .+..+-|..|| +.|-....... -.|-.|++.|.-..|
T Consensus 127 ~~~~~~~CPiCl~~~sek~~vsTkCGHvFC-~~Cik~alk~~---~~CP~C~kkIt~k~~ 182 (187)
T KOG0320|consen 127 RKEGTYKCPICLDSVSEKVPVSTKCGHVFC-SQCIKDALKNT---NKCPTCRKKITHKQF 182 (187)
T ss_pred ccccccCCCceecchhhccccccccchhHH-HHHHHHHHHhC---CCCCCcccccchhhh
Confidence 334678898887777666 46678899999 78876654322 456778777765444
No 60
>KOG1813|consensus
Probab=22.22 E-value=48 Score=28.97 Aligned_cols=47 Identities=9% Similarity=0.081 Sum_probs=34.9
Q ss_pred eeeCCCCccccCCcEEEeCCeeeeccCCchhhhhhhcC--CCCCCCCCcccCcce
Q psy2231 108 LGCLSSVCSILSQTFYSLSVDLYHASMHLRSDCLSMYG--GKGNTSHTMIPDTYI 160 (201)
Q Consensus 108 F~C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~y~~~~~--~~C~~C~~~I~~~~i 160 (201)
|.|..|+++.... .+..=|..+ |..|..+.+. ++|..|++.|.+.+-
T Consensus 242 f~c~icr~~f~~p-Vvt~c~h~f-----c~~ca~~~~qk~~~c~vC~~~t~g~~~ 290 (313)
T KOG1813|consen 242 FKCFICRKYFYRP-VVTKCGHYF-----CEVCALKPYQKGEKCYVCSQQTHGSFN 290 (313)
T ss_pred ccccccccccccc-hhhcCCcee-----ehhhhccccccCCcceecccccccccc
Confidence 8899998887543 333445556 9999987764 799999999887543
No 61
>KOG0320|consensus
Probab=21.76 E-value=43 Score=27.16 Aligned_cols=48 Identities=10% Similarity=0.054 Sum_probs=34.1
Q ss_pred eeeCCCCccccCCc-EEEeCCeeeeccCCchhhhhhh--cCCCCCCCCCcccCcce
Q psy2231 108 LGCLSSVCSILSQT-FYSLSVDLYHASMHLRSDCLSM--YGGKGNTSHTMIPDTYI 160 (201)
Q Consensus 108 F~C~~C~~~l~~~~-f~~~~g~~yH~~~~C~~~y~~~--~~~~C~~C~~~I~~~~i 160 (201)
|.|..|-.+..-.. +-.+=|.+| |..|-+.. -+.+|..|++.|+.+.+
T Consensus 132 ~~CPiCl~~~sek~~vsTkCGHvF-----C~~Cik~alk~~~~CP~C~kkIt~k~~ 182 (187)
T KOG0320|consen 132 YKCPICLDSVSEKVPVSTKCGHVF-----CSQCIKDALKNTNKCPTCRKKITHKQF 182 (187)
T ss_pred cCCCceecchhhccccccccchhH-----HHHHHHHHHHhCCCCCCcccccchhhh
Confidence 66777655543333 335668888 99999865 46899999999987643
No 62
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=21.62 E-value=66 Score=19.08 Aligned_cols=22 Identities=5% Similarity=0.022 Sum_probs=10.2
Q ss_pred eeCCCCccccCCcEEEeCCeee
Q psy2231 109 GCLSSVCSILSQTFYSLSVDLY 130 (201)
Q Consensus 109 ~C~~C~~~l~~~~f~~~~g~~y 130 (201)
+|..|+.-|.+-.-+..+|+.|
T Consensus 4 rC~~C~aylNp~~~~~~~~~~w 25 (40)
T PF04810_consen 4 RCRRCRAYLNPFCQFDDGGKTW 25 (40)
T ss_dssp B-TTT--BS-TTSEEETTTTEE
T ss_pred ccCCCCCEECCcceEcCCCCEE
Confidence 4566666665554455555556
No 63
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=21.52 E-value=39 Score=30.51 Aligned_cols=44 Identities=9% Similarity=-0.058 Sum_probs=28.3
Q ss_pred CcEEEeCCeeeeccCCchhhhhhh-------cCCCCCCCCCcccCcceeeccee
Q psy2231 120 QTFYSLSVDLYHASMHLRSDCLSM-------YGGKGNTSHTMIPDTYITQVTIV 166 (201)
Q Consensus 120 ~~f~~~~g~~yH~~~~C~~~y~~~-------~~~~C~~C~~~I~~~~i~a~~~~ 166 (201)
-.|....|| ||. -+|+.|+..+ ...+|. |+++|+-++..-+...
T Consensus 229 ~g~~P~~GK-Yh~-~~c~~C~~~~~~~~~~~~~~~Cp-CG~~i~~GV~~Rv~eL 279 (374)
T TIGR00375 229 YGLDPLLGK-YHQ-TACEACGEPAVSEDAETACANCP-CGGRIKKGVSDRLREL 279 (374)
T ss_pred eeECcCCCc-cch-hhhcccCCcCCchhhhhcCCCCC-CCCcceechHHHHHHH
Confidence 347778888 775 2366666322 247799 9999987765544433
No 64
>PRK11595 DNA utilization protein GntX; Provisional
Probab=20.59 E-value=70 Score=26.38 Aligned_cols=47 Identities=9% Similarity=-0.031 Sum_probs=29.9
Q ss_pred eCCCCccccCCcEEEeCCeeeeccCCchhhhhhhc--CCCCCCCCCcccCcceeecceeeccccC
Q psy2231 110 CLSSVCSILSQTFYSLSVDLYHASMHLRSDCLSMY--GGKGNTSHTMIPDTYITQVTIVIARCLS 172 (201)
Q Consensus 110 C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~y~~~~--~~~C~~C~~~I~~~~i~a~~~~~~~c~~ 172 (201)
|..|+.++... .... |..|...+. .+.|..|++++... +.+|.+|..
T Consensus 8 C~~C~~~~~~~------~~~l-----C~~C~~~l~~~~~~C~~Cg~~~~~~-----~~~C~~C~~ 56 (227)
T PRK11595 8 CWLCRMPLALS------HWGI-----CSVCSRALRTLKTCCPQCGLPATHP-----HLPCGRCLQ 56 (227)
T ss_pred CccCCCccCCC------CCcc-----cHHHHhhCCcccCcCccCCCcCCCC-----CCCcHHHHc
Confidence 57777776432 1124 888876643 46799999986532 235888855
No 65
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=20.38 E-value=38 Score=24.76 Aligned_cols=30 Identities=27% Similarity=0.644 Sum_probs=19.0
Q ss_pred CCCcccCCCCCcCCCCc-eeeeCCeeeecCCc
Q psy2231 66 GSCLRCENCNKTLVPGS-HSEHDGKPYCNYPC 96 (201)
Q Consensus 66 ~~CF~C~~C~~~L~~~~-f~~~~g~~yCe~~c 96 (201)
.+=|+|+.|=..-.... -...+|.++| .+|
T Consensus 68 ~DEFTCssCFLV~HRSqLa~~~~g~~iC-~DC 98 (99)
T PF13834_consen 68 ADEFTCSSCFLVHHRSQLAREKDGQPIC-RDC 98 (99)
T ss_pred CCceeeeeeeeEechhhhccccCCCEec-ccc
Confidence 46689999844332221 2256889999 677
No 66
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=20.29 E-value=72 Score=20.69 Aligned_cols=33 Identities=9% Similarity=-0.033 Sum_probs=19.4
Q ss_pred eeCCCCccccCCcEEEeCCeeeeccCCchhhhhh
Q psy2231 109 GCLSSVCSILSQTFYSLSVDLYHASMHLRSDCLS 142 (201)
Q Consensus 109 ~C~~C~~~l~~~~f~~~~g~~yH~~~~C~~~y~~ 142 (201)
.|..|++||.....++-++.+.|+.. |-....+
T Consensus 3 ~CvVCKqpi~~a~~v~T~~G~VH~g~-C~~y~~e 35 (54)
T PF10886_consen 3 ICVVCKQPIDDALVVETESGPVHPGV-CAQYLEE 35 (54)
T ss_pred eeeeeCCccCcceEEEcCCCccCcHH-HHHHHHh
Confidence 47888888877554444444566532 5444443
Done!