Query psy11904
Match_columns 199
No_of_seqs 109 out of 127
Neff 2.9
Searched_HMMs 46136
Date Fri Aug 16 21:56:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11904.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11904hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3476|consensus 100.0 2.8E-46 6.1E-51 287.4 0.7 91 55-145 1-91 (100)
2 PF10235 Cript: Microtubule-as 100.0 1.3E-38 2.9E-43 242.2 3.8 79 65-145 1-81 (90)
3 PF00595 PDZ: PDZ domain (Also 95.7 0.013 2.9E-07 40.8 3.5 44 2-47 36-80 (81)
4 PF10217 DUF2039: Uncharacteri 94.7 0.0044 9.5E-08 48.1 -1.6 35 108-142 55-90 (92)
5 cd00992 PDZ_signaling PDZ doma 92.3 0.25 5.3E-06 33.6 3.9 43 2-46 37-80 (82)
6 smart00228 PDZ Domain present 90.9 0.54 1.2E-05 31.6 4.5 44 2-49 37-83 (85)
7 KOG3241|consensus 90.0 0.021 4.6E-07 50.1 -3.8 57 100-157 60-119 (227)
8 PF13180 PDZ_2: PDZ domain; PD 89.9 0.38 8.3E-06 33.8 3.1 45 2-49 25-71 (82)
9 cd00988 PDZ_CTP_protease PDZ d 89.6 0.66 1.4E-05 32.0 4.1 46 2-50 24-72 (85)
10 cd00986 PDZ_LON_protease PDZ d 89.1 0.87 1.9E-05 31.6 4.4 44 2-49 19-64 (79)
11 cd00990 PDZ_glycyl_aminopeptid 88.7 0.91 2E-05 31.0 4.2 43 2-49 23-66 (80)
12 COG5152 Uncharacterized conser 87.9 0.14 3E-06 45.8 -0.4 34 110-143 198-240 (259)
13 PF12773 DZR: Double zinc ribb 87.7 0.38 8.2E-06 31.5 1.7 34 111-145 1-41 (50)
14 cd00136 PDZ PDZ domain, also c 85.9 1.4 3E-05 29.3 3.7 35 2-39 24-61 (70)
15 KOG3580|consensus 85.7 0.56 1.2E-05 47.8 2.5 57 2-59 440-500 (1027)
16 KOG3571|consensus 84.4 0.69 1.5E-05 45.9 2.4 45 4-48 290-337 (626)
17 PRK14559 putative protein seri 84.2 0.73 1.6E-05 45.7 2.5 37 109-146 2-40 (645)
18 cd00989 PDZ_metalloprotease PD 83.0 2.5 5.3E-05 28.6 4.1 45 2-49 23-68 (79)
19 TIGR00570 cdk7 CDK-activating 79.8 0.82 1.8E-05 42.1 1.0 38 110-147 5-57 (309)
20 cd00991 PDZ_archaeal_metallopr 79.2 4.3 9.2E-05 28.5 4.3 45 2-49 21-67 (79)
21 TIGR00225 prc C-terminal pepti 78.6 2.8 6E-05 37.1 3.9 46 2-50 73-121 (334)
22 cd00987 PDZ_serine_protease PD 74.9 6.2 0.00014 27.1 4.1 45 2-49 35-81 (90)
23 PF13248 zf-ribbon_3: zinc-rib 73.9 1.6 3.6E-05 26.0 0.9 21 109-130 3-23 (26)
24 PLN00049 carboxyl-terminal pro 73.4 4.9 0.00011 36.8 4.2 46 2-50 113-161 (389)
25 smart00504 Ubox Modified RING 72.2 1.7 3.8E-05 28.8 0.8 24 122-145 20-47 (63)
26 PRK11186 carboxy-terminal prot 71.3 5.3 0.00011 40.0 4.2 48 2-49 266-319 (667)
27 COG0793 Prc Periplasmic protea 69.6 7.4 0.00016 36.4 4.5 48 2-50 123-171 (406)
28 PF13240 zinc_ribbon_2: zinc-r 69.1 2.1 4.7E-05 25.3 0.6 20 110-130 1-20 (23)
29 PF14634 zf-RING_5: zinc-RING 68.4 1.4 3E-05 28.5 -0.3 20 122-141 21-44 (44)
30 COG4847 Uncharacterized protei 63.7 4.5 9.8E-05 32.4 1.6 22 132-162 5-26 (103)
31 PRK12496 hypothetical protein; 63.6 3 6.5E-05 34.5 0.7 26 123-148 127-158 (164)
32 TIGR02860 spore_IV_B stage IV 63.6 9.8 0.00021 36.2 4.1 46 2-50 124-170 (402)
33 TIGR00054 RIP metalloprotease 58.3 14 0.00029 34.3 4.0 46 2-50 214-260 (420)
34 PLN03208 E3 ubiquitin-protein 56.8 4.7 0.0001 35.0 0.7 49 109-158 19-93 (193)
35 TIGR02037 degP_htrA_DO peripla 52.5 22 0.00048 32.5 4.3 45 2-49 268-314 (428)
36 TIGR00599 rad18 DNA repair pro 52.4 6.8 0.00015 37.2 1.1 37 109-145 27-72 (397)
37 KOG3550|consensus 48.9 15 0.00032 32.2 2.5 44 4-48 128-172 (207)
38 PRK00762 hypA hydrogenase nick 47.6 15 0.00033 29.0 2.2 30 134-169 93-122 (124)
39 PRK11595 DNA utilization prote 46.5 12 0.00027 31.6 1.6 36 109-144 6-45 (227)
40 PF06689 zf-C4_ClpX: ClpX C4-t 44.0 13 0.00029 24.4 1.2 20 134-156 2-21 (41)
41 PF09943 DUF2175: Uncharacteri 43.7 16 0.00035 29.0 1.8 22 133-163 2-23 (101)
42 smart00132 LIM Zinc-binding do 42.7 20 0.00043 21.0 1.7 9 135-143 29-37 (39)
43 cd04476 RPA1_DBD_C RPA1_DBD_C: 42.6 9.7 0.00021 30.3 0.4 26 108-143 34-61 (166)
44 PRK08351 DNA-directed RNA poly 42.1 25 0.00054 25.6 2.4 38 109-168 4-42 (61)
45 PF06906 DUF1272: Protein of u 41.5 13 0.00027 27.2 0.8 36 109-144 6-52 (57)
46 PF06750 DiS_P_DiS: Bacterial 40.6 12 0.00027 28.3 0.7 38 108-145 33-70 (92)
47 PRK10779 zinc metallopeptidase 40.2 39 0.00085 31.5 4.0 46 2-50 232-278 (449)
48 PF07191 zinc-ribbons_6: zinc- 39.4 6.7 0.00015 29.4 -0.9 36 110-145 3-42 (70)
49 PRK10898 serine endoprotease; 39.3 45 0.00098 30.3 4.2 46 2-50 290-337 (353)
50 KOG1813|consensus 38.9 15 0.00033 34.3 1.1 34 110-143 243-285 (313)
51 TIGR02038 protease_degS peripl 38.7 47 0.001 30.0 4.2 45 2-49 289-335 (351)
52 smart00746 TRASH metallochaper 38.1 42 0.00091 18.1 2.5 23 136-158 1-24 (39)
53 KOG3799|consensus 38.0 17 0.00037 31.1 1.2 41 108-150 65-106 (169)
54 PF00412 LIM: LIM domain; Int 37.5 26 0.00057 22.7 1.8 13 135-147 28-40 (58)
55 PRK12380 hydrogenase nickel in 37.5 29 0.00063 27.0 2.3 40 109-163 71-110 (113)
56 PRK06393 rpoE DNA-directed RNA 36.5 30 0.00065 25.5 2.1 40 108-168 5-44 (64)
57 KOG3209|consensus 36.4 28 0.00061 36.5 2.6 38 2-39 789-827 (984)
58 PHA02565 49 recombination endo 36.4 21 0.00046 30.4 1.5 15 132-146 19-33 (157)
59 PF02945 Endonuclease_7: Recom 36.0 13 0.00027 28.0 0.1 22 131-153 20-41 (81)
60 TIGR01713 typeII_sec_gspC gene 35.9 56 0.0012 28.8 4.1 45 4-50 203-249 (259)
61 cd00162 RING RING-finger (Real 35.5 17 0.00037 21.3 0.6 21 122-142 19-44 (45)
62 PRK03681 hypA hydrogenase nick 35.3 42 0.00092 26.2 2.9 41 109-163 71-111 (114)
63 PF03660 PHF5: PHF5-like prote 35.2 10 0.00022 30.5 -0.5 25 105-129 52-76 (106)
64 PF10083 DUF2321: Uncharacteri 35.2 19 0.00042 30.7 1.1 37 109-147 40-82 (158)
65 PF10571 UPF0547: Uncharacteri 33.8 21 0.00045 21.8 0.8 21 110-131 2-22 (26)
66 PRK00564 hypA hydrogenase nick 33.5 54 0.0012 25.7 3.3 41 109-163 72-112 (117)
67 TIGR00100 hypA hydrogenase nic 33.1 39 0.00086 26.3 2.5 40 109-163 71-110 (115)
68 PF07660 STN: Secretin and Ton 32.7 58 0.0013 21.0 2.9 29 17-45 14-42 (52)
69 PF13923 zf-C3HC4_2: Zinc fing 32.4 7.8 0.00017 24.2 -1.3 10 122-131 18-27 (39)
70 KOG2272|consensus 31.7 26 0.00057 32.7 1.4 52 90-144 148-206 (332)
71 COG3814 Uncharacterized protei 31.5 32 0.00069 29.4 1.8 39 7-48 71-114 (157)
72 PF05715 zf-piccolo: Piccolo Z 31.4 19 0.00041 26.6 0.4 12 132-143 29-40 (61)
73 KOG3580|consensus 30.0 45 0.00098 34.7 2.9 45 3-48 231-276 (1027)
74 PF10764 Gin: Inhibitor of sig 27.6 19 0.0004 24.7 -0.2 22 51-72 15-36 (46)
75 KOG1892|consensus 26.5 63 0.0014 35.4 3.2 51 3-54 972-1025(1629)
76 PF07943 PBP5_C: Penicillin-bi 26.2 69 0.0015 22.5 2.5 20 8-27 58-77 (91)
77 PF13806 Rieske_2: Rieske-like 26.2 69 0.0015 24.4 2.7 54 143-198 11-68 (104)
78 PRK00415 rps27e 30S ribosomal 25.8 33 0.00072 25.0 0.8 44 109-158 12-55 (59)
79 PF13920 zf-C3HC4_3: Zinc fing 25.1 13 0.00029 24.2 -1.2 23 122-144 21-48 (50)
80 PRK00420 hypothetical protein; 25.0 34 0.00075 27.4 0.9 21 108-128 23-45 (112)
81 cd06462 Peptidase_S24_S26 The 24.7 89 0.0019 20.9 2.8 38 150-190 11-51 (84)
82 KOG2836|consensus 24.3 30 0.00065 29.8 0.5 30 25-54 123-165 (173)
83 COG0266 Nei Formamidopyrimidin 24.0 38 0.00081 30.9 1.0 32 99-130 236-272 (273)
84 PRK10139 serine endoprotease; 23.5 1.1E+02 0.0025 28.9 4.1 45 2-49 301-347 (455)
85 TIGR00686 phnA alkylphosphonat 23.1 1.4E+02 0.003 24.3 3.9 51 135-190 21-86 (109)
86 KOG4458|consensus 23.0 35 0.00076 26.0 0.6 33 98-137 4-36 (78)
87 PF14446 Prok-RING_1: Prokaryo 22.9 48 0.001 23.7 1.2 10 109-118 6-15 (54)
88 PF01155 HypA: Hydrogenase exp 22.7 29 0.00063 26.8 0.1 40 109-163 71-110 (113)
89 cd00730 rubredoxin Rubredoxin; 22.6 79 0.0017 21.9 2.2 19 162-184 10-28 (50)
90 PHA02929 N1R/p28-like protein; 22.5 39 0.00084 30.1 0.8 37 108-144 174-227 (238)
91 COG3684 LacD Tagatose-1,6-bisp 22.5 29 0.00062 32.4 -0.0 60 130-199 147-209 (306)
92 PRK05580 primosome assembly pr 22.0 55 0.0012 32.4 1.8 21 122-142 407-430 (679)
93 PRK01103 formamidopyrimidine/5 21.9 38 0.00083 29.7 0.6 29 102-130 239-272 (274)
94 PRK14810 formamidopyrimidine-D 21.5 42 0.00091 29.6 0.8 29 101-129 237-270 (272)
95 PHA02054 hypothetical protein 21.1 51 0.0011 26.0 1.1 14 158-171 15-28 (94)
96 cd03539 Rieske_RO_Alpha_S5H Th 21.0 2.4E+02 0.0051 22.1 4.9 45 143-188 10-54 (129)
97 PLN00209 ribosomal protein S27 20.9 62 0.0014 25.3 1.5 45 109-159 37-82 (86)
98 TIGR01044 rplV_bact ribosomal 20.6 53 0.0011 25.3 1.1 28 23-51 20-47 (103)
99 PTZ00083 40S ribosomal protein 20.5 57 0.0012 25.4 1.2 46 108-159 35-81 (85)
100 PF06827 zf-FPG_IleRS: Zinc fi 20.2 27 0.0006 20.9 -0.4 21 110-130 3-28 (30)
No 1
>KOG3476|consensus
Probab=100.00 E-value=2.8e-46 Score=287.38 Aligned_cols=91 Identities=58% Similarity=1.012 Sum_probs=87.5
Q ss_pred hhhhhhhcccCcccccCCCCCCCcccccCCCcccccccchhhhhhccCCCcccCcccchhhcccccCCCcCCcccccccC
Q psy11904 55 MVCSKCEKKLGKVITPDNWKSGSRNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKG 134 (199)
Q Consensus 55 MVC~KCEKKL~KLaTPD~wK~Gs~nt~~~ggRkIgeNKLLSs~K~R~nPY~~~~skCkiCK~kVhQ~G~kYCQ~CAYkKG 134 (199)
|||+||||||+++++|||||+|+||++++|+|+|+|||.|.+.++||+||+..+.+|+|||+.|||+|+||||.|||+||
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 99999999999999999999999999999999999999888889999999999999999999999999999999999999
Q ss_pred CcccCCCCCCC
Q psy11904 135 EHLVLVTADPE 145 (199)
Q Consensus 135 iCAMCGk~~~~ 145 (199)
|||||||..-.
T Consensus 81 iCAMCGKki~n 91 (100)
T KOG3476|consen 81 ICAMCGKKILN 91 (100)
T ss_pred HHHHhhhHhhc
Confidence 99999997543
No 2
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=100.00 E-value=1.3e-38 Score=242.25 Aligned_cols=79 Identities=53% Similarity=0.933 Sum_probs=74.0
Q ss_pred CcccccCCCCCCC--cccccCCCcccccccchhhhhhccCCCcccCcccchhhcccccCCCcCCcccccccCCcccCCCC
Q psy11904 65 GKVITPDNWKSGS--RNTIESGGRRIGENKALTASKARFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKGEHLVLVTA 142 (199)
Q Consensus 65 ~KLaTPD~wK~Gs--~nt~~~ggRkIgeNKLLSs~K~R~nPY~~~~skCkiCK~kVhQ~G~kYCQ~CAYkKGiCAMCGk~ 142 (199)
++||||||||+|+ +++.++|+|+||||||||++ ++ |||++++++|++||++|||+|+||||.|||++||||||||.
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 4899999999999 99999999999999999874 34 99999999999999999999999999999999999999999
Q ss_pred CCC
Q psy11904 143 DPE 145 (199)
Q Consensus 143 ~~~ 145 (199)
+..
T Consensus 79 i~d 81 (90)
T PF10235_consen 79 ILD 81 (90)
T ss_pred ecc
Confidence 844
No 3
>PF00595 PDZ: PDZ domain (Also known as DHR or GLGF) Coordinates are not yet available; InterPro: IPR001478 PDZ domains are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates [, ]. PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They bind either the carboxyl-terminal sequences of proteins or internal peptide sequences []. In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated. PDZ domains consist of 80 to 90 amino acids comprising six beta-strands (beta-A to beta-F) and two alpha-helices, A and B, compactly arranged in a globular structure. Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel beta-strand interacts with the beta-B strand and the B helix. The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands.; GO: 0005515 protein binding; PDB: 3AXA_A 1WF8_A 1QAV_B 1QAU_A 1B8Q_A 1MC7_A 2KAW_A 1I16_A 1VB7_A 1WI4_A ....
Probab=95.71 E-value=0.013 Score=40.77 Aligned_cols=44 Identities=30% Similarity=0.369 Sum_probs=35.6
Q ss_pred CccccccccCCCCeeeEE-EEeecccchhhHHhhhhccccceEEEEE
Q psy11904 2 SHCAETWALNNGDRITSV-RISFRHMVYEDALTILSYASPYEVQIET 47 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~-ti~F~n~~yEDAl~iL~~a~PYkv~~~l 47 (199)
|||++.+ |++||+|+++ -...+++..+++..+|+-+.. .|.+.+
T Consensus 36 ~~a~~~g-l~~GD~Il~INg~~v~~~~~~~~~~~l~~~~~-~v~L~V 80 (81)
T PF00595_consen 36 SPAERAG-LKVGDRILEINGQSVRGMSHDEVVQLLKSASN-PVTLTV 80 (81)
T ss_dssp SHHHHHT-SSTTEEEEEETTEESTTSBHHHHHHHHHHSTS-EEEEEE
T ss_pred ChHHhcc-cchhhhhheeCCEeCCCCCHHHHHHHHHCCCC-cEEEEE
Confidence 6788888 9999999995 245677889999999988887 666655
No 4
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=94.71 E-value=0.0044 Score=48.15 Aligned_cols=35 Identities=20% Similarity=0.324 Sum_probs=31.2
Q ss_pred Ccccchhhc-ccccCCCcCCcccccccCCcccCCCC
Q psy11904 108 FESCKICRQ-KVHQVGSHYCQACAYKKGEHLVLVTA 142 (199)
Q Consensus 108 ~skCkiCK~-kVhQ~G~kYCQ~CAYkKGiCAMCGk~ 142 (199)
.++|-.|.+ +|.+.=|..|+.||-..++||.||++
T Consensus 55 p~kC~~C~qktVk~AYh~iC~~Ca~~~~vCaKC~k~ 90 (92)
T PF10217_consen 55 PKKCNKCQQKTVKHAYHVICDPCAKELKVCAKCGKP 90 (92)
T ss_pred CccccccccchHHHHHHHHHHHHHHhhccCcccCCC
Confidence 469999997 67777788999999999999999986
No 5
>cd00992 PDZ_signaling PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
Probab=92.27 E-value=0.25 Score=33.57 Aligned_cols=43 Identities=28% Similarity=0.410 Sum_probs=29.5
Q ss_pred CccccccccCCCCeeeEEE-EeecccchhhHHhhhhccccceEEEE
Q psy11904 2 SHCAETWALNNGDRITSVR-ISFRHMVYEDALTILSYASPYEVQIE 46 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~t-i~F~n~~yEDAl~iL~~a~PYkv~~~ 46 (199)
|||++ ..|++||+|+++- ..+.++.++|++.+|+.+.+ .+.+.
T Consensus 37 s~a~~-~gl~~GD~I~~ing~~i~~~~~~~~~~~l~~~~~-~v~l~ 80 (82)
T cd00992 37 GPAER-GGLRVGDRILEVNGVSVEGLTHEEAVELLKNSGD-EVTLT 80 (82)
T ss_pred ChHHh-CCCCCCCEEEEECCEEcCccCHHHHHHHHHhCCC-eEEEE
Confidence 56555 6799999999932 22333468888999988765 55544
No 6
>smart00228 PDZ Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
Probab=90.92 E-value=0.54 Score=31.64 Aligned_cols=44 Identities=23% Similarity=0.242 Sum_probs=28.5
Q ss_pred CccccccccCCCCeeeEEEEeec---ccchhhHHhhhhccccceEEEEEee
Q psy11904 2 SHCAETWALNNGDRITSVRISFR---HMVYEDALTILSYASPYEVQIETEK 49 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~---n~~yEDAl~iL~~a~PYkv~~~l~r 49 (199)
|||++.+ |++||+|++ |.-. +...++.+.++..+.. .+.+.+.|
T Consensus 37 s~a~~~g-l~~GD~I~~--In~~~v~~~~~~~~~~~~~~~~~-~~~l~i~r 83 (85)
T smart00228 37 SPAAKAG-LKVGDVILE--VNGTSVEGLTHLEAVDLLKKAGG-KVTLTVLR 83 (85)
T ss_pred CHHHHcC-CCCCCEEEE--ECCEECCCCCHHHHHHHHHhCCC-eEEEEEEe
Confidence 6777878 999999988 4333 2334555666665533 66666655
No 7
>KOG3241|consensus
Probab=90.04 E-value=0.021 Score=50.11 Aligned_cols=57 Identities=18% Similarity=0.424 Sum_probs=42.6
Q ss_pred ccCCCcccCcccchhhc-ccccCCCcCCcccccccCCcccCCCCCCC--CCCcceeeecce
Q psy11904 100 RFNPYTQKFESCKICRQ-KVHQVGSHYCQACAYKKGEHLVLVTADPE--KGDKFALISGEH 157 (199)
Q Consensus 100 R~nPY~~~~skCkiCK~-kVhQ~G~kYCQ~CAYkKGiCAMCGk~~~~--~~~~~~~i~g~~ 157 (199)
+|.|.++ ..+|..|++ .|.|.-|+.|..||-...+||-|+|+..+ -.+-+|+-.-|+
T Consensus 60 KYKpLt~-akkC~kC~~r~Vk~aYH~~Cr~CA~e~~vCAKC~ks~~~i~i~d~~p~~~E~~ 119 (227)
T KOG3241|consen 60 KYKPLTE-AKKCQKCTKRNVKQAYHKLCRGCAKEQKVCAKCCKSVDQILIRDIYPVEAEQK 119 (227)
T ss_pred cccccch-hHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHhccHHHhhhcCCCCCcHHHH
Confidence 3445543 469999987 78888889999999999999999998766 334445544443
No 8
>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C ....
Probab=89.89 E-value=0.38 Score=33.78 Aligned_cols=45 Identities=31% Similarity=0.350 Sum_probs=29.4
Q ss_pred CccccccccCCCCeeeEEEEeeccc-chhhHHhhhhcccc-ceEEEEEee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHM-VYEDALTILSYASP-YEVQIETEK 49 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~-~yEDAl~iL~~a~P-Ykv~~~l~r 49 (199)
|||++.+ |++||.|++ |....+ ..+|...+|+..+| =.|.+.+.|
T Consensus 25 spA~~aG-l~~GD~I~~--ing~~v~~~~~~~~~l~~~~~g~~v~l~v~R 71 (82)
T PF13180_consen 25 SPAAKAG-LQPGDIILA--INGKPVNSSEDLVNILSKGKPGDTVTLTVLR 71 (82)
T ss_dssp SHHHHTT-S-TTEEEEE--ETTEESSSHHHHHHHHHCSSTTSEEEEEEEE
T ss_pred CcHHHCC-CCCCcEEEE--ECCEEcCCHHHHHHHHHhCCCCCEEEEEEEE
Confidence 7888888 999999998 544444 23555666654444 456777766
No 9
>cd00988 PDZ_CTP_protease PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=89.60 E-value=0.66 Score=31.99 Aligned_cols=46 Identities=22% Similarity=0.274 Sum_probs=31.5
Q ss_pred CccccccccCCCCeeeEEEEeecccch---hhHHhhhhccccceEEEEEeee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHMVY---EDALTILSYASPYEVQIETEKE 50 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~~y---EDAl~iL~~a~PYkv~~~l~re 50 (199)
|||++. -|++||+|++ |....+.. +|...+|+......+.+.+.|.
T Consensus 24 s~a~~~-gl~~GD~I~~--vng~~i~~~~~~~~~~~l~~~~~~~i~l~v~r~ 72 (85)
T cd00988 24 SPAAKA-GIKAGDIIVA--IDGEPVDGLSLEDVVKLLRGKAGTKVRLTLKRG 72 (85)
T ss_pred CCHHHc-CCCCCCEEEE--ECCEEcCCCCHHHHHHHhcCCCCCEEEEEEEcC
Confidence 566665 7999999999 55544443 5667777665556777777753
No 10
>cd00986 PDZ_LON_protease PDZ domain of ATP-dependent LON serine proteases. Most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this bacterial subfamily of protease-associated PDZ domains a C-terminal beta-strand is thought to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=89.09 E-value=0.87 Score=31.57 Aligned_cols=44 Identities=16% Similarity=0.237 Sum_probs=28.4
Q ss_pred CccccccccCCCCeeeEEEEeecccc-hhhHHhhhhccc-cceEEEEEee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHMV-YEDALTILSYAS-PYEVQIETEK 49 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~~-yEDAl~iL~~a~-PYkv~~~l~r 49 (199)
|||++ + |++||+|++ |....+. .+|...+|+... .-.+.+.+.|
T Consensus 19 s~A~~-g-L~~GD~I~~--Ing~~v~~~~~~~~~l~~~~~~~~v~l~v~r 64 (79)
T cd00986 19 MPAAG-K-LKAGDHIIA--VDGKPFKEAEELIDYIQSKKEGDTVKLKVKR 64 (79)
T ss_pred Cchhh-C-CCCCCEEEE--ECCEECCCHHHHHHHHHhCCCCCEEEEEEEE
Confidence 56665 5 999999999 6665555 355556666432 2356666655
No 11
>cd00990 PDZ_glycyl_aminopeptidase PDZ domain associated with archaeal and bacterial M61 glycyl-aminopeptidases. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand is presumed to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=88.67 E-value=0.91 Score=31.03 Aligned_cols=43 Identities=14% Similarity=0.105 Sum_probs=24.8
Q ss_pred CccccccccCCCCeeeEEEEeecccchhhHHhhhhcc-ccceEEEEEee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHMVYEDALTILSYA-SPYEVQIETEK 49 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~~yEDAl~iL~~a-~PYkv~~~l~r 49 (199)
|||++.+ |++||+|++ | ++....+...+|+.. ..-.+.+.+.|
T Consensus 23 s~a~~aG-l~~GD~I~~--I--ng~~v~~~~~~l~~~~~~~~v~l~v~r 66 (80)
T cd00990 23 SPADKAG-LVAGDELVA--V--NGWRVDALQDRLKEYQAGDPVELTVFR 66 (80)
T ss_pred ChHHHhC-CCCCCEEEE--E--CCEEhHHHHHHHHhcCCCCEEEEEEEE
Confidence 5666655 999999999 4 344433333344443 22356666654
No 12
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=87.91 E-value=0.14 Score=45.85 Aligned_cols=34 Identities=38% Similarity=0.810 Sum_probs=27.0
Q ss_pred ccchhhccc-----ccCCCcCCcccc---cccC-CcccCCCCC
Q psy11904 110 SCKICRQKV-----HQVGSHYCQACA---YKKG-EHLVLVTAD 143 (199)
Q Consensus 110 kCkiCK~kV-----hQ~G~kYCQ~CA---YkKG-iCAMCGk~~ 143 (199)
.|.|||..- ..-||++|..|| |++| .|-+||+.-
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 344999999998 5555 699999853
No 13
>PF12773 DZR: Double zinc ribbon
Probab=87.67 E-value=0.38 Score=31.54 Aligned_cols=34 Identities=15% Similarity=0.354 Sum_probs=22.3
Q ss_pred cchhhcccccCCCcCCcccccccC-------CcccCCCCCCC
Q psy11904 111 CKICRQKVHQVGSHYCQACAYKKG-------EHLVLVTADPE 145 (199)
Q Consensus 111 CkiCK~kVhQ~G~kYCQ~CAYkKG-------iCAMCGk~~~~ 145 (199)
|..|.+.+.. ++.||..|-..-. +|.-||..++.
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 5566666666 5677777755444 58888876554
No 14
>cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(pos
Probab=85.89 E-value=1.4 Score=29.31 Aligned_cols=35 Identities=23% Similarity=0.286 Sum_probs=24.9
Q ss_pred CccccccccCCCCeeeEEEEeec---ccchhhHHhhhhccc
Q psy11904 2 SHCAETWALNNGDRITSVRISFR---HMVYEDALTILSYAS 39 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~---n~~yEDAl~iL~~a~ 39 (199)
|||++ .-|++||+|++ |.-. ++.++|+..+|+...
T Consensus 24 s~a~~-~gl~~GD~I~~--Ing~~v~~~~~~~~~~~l~~~~ 61 (70)
T cd00136 24 SPAER-AGLQAGDVILA--VNGTDVKNLTLEDVAELLKKEV 61 (70)
T ss_pred CHHHH-cCCCCCCEEEE--ECCEECCCCCHHHHHHHHhhCC
Confidence 56655 56999999999 4444 344478888888764
No 15
>KOG3580|consensus
Probab=85.70 E-value=0.56 Score=47.79 Aligned_cols=57 Identities=32% Similarity=0.458 Sum_probs=39.9
Q ss_pred CccccccccCCCCeeeEE-EEeecccchhhHH-hhhhccccceEEEEE--eeehhhhhhhhh
Q psy11904 2 SHCAETWALNNGDRITSV-RISFRHMVYEDAL-TILSYASPYEVQIET--EKEIYFIMVCSK 59 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~-ti~F~n~~yEDAl-~iL~~a~PYkv~~~l--~reIyf~MVC~K 59 (199)
|||+ .--|.|||||+.| +|.|+|++-|+|+ =+|.-----.|.+-. +..||-+||-..
T Consensus 440 spA~-~eGlqEGDQIL~VN~vdF~nl~REeAVlfLL~lPkGEevtilaQ~k~Dvyr~iv~s~ 500 (1027)
T KOG3580|consen 440 SPAE-QEGLQEGDQILKVNTVDFRNLVREEAVLFLLELPKGEEVTILAQSKADVYRDIVASG 500 (1027)
T ss_pred Cchh-hccccccceeEEeccccchhhhHHHHHHHHhcCCCCcEEeehhhhhhHHHHHHHhcc
Confidence 4443 3458999999998 6999999999994 445443334455544 556888888653
No 16
>KOG3571|consensus
Probab=84.40 E-value=0.69 Score=45.92 Aligned_cols=45 Identities=24% Similarity=0.394 Sum_probs=35.9
Q ss_pred cccccccCCCCeeeEE-EEeecccchhhHHhhhhc--cccceEEEEEe
Q psy11904 4 CAETWALNNGDRITSV-RISFRHMVYEDALTILSY--ASPYEVQIETE 48 (199)
Q Consensus 4 a~~~~~l~~GD~i~s~-ti~F~n~~yEDAl~iL~~--a~PYkv~~~l~ 48 (199)
-|.-++|.+||+|+-| .|+|+||.+.||+..|.- +.|+-+++.+-
T Consensus 290 VA~DGRIe~GDMiLQVNevsFENmSNd~AVrvLREaV~~~gPi~ltvA 337 (626)
T KOG3571|consen 290 VALDGRIEPGDMILQVNEVSFENMSNDQAVRVLREAVSRPGPIKLTVA 337 (626)
T ss_pred eeccCccCccceEEEeeecchhhcCchHHHHHHHHHhccCCCeEEEEe
Confidence 3556899999999987 599999999999998864 35676665553
No 17
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=84.25 E-value=0.73 Score=45.72 Aligned_cols=37 Identities=19% Similarity=0.331 Sum_probs=30.5
Q ss_pred cccchhhcccccCCCcCCccccccc--CCcccCCCCCCCC
Q psy11904 109 ESCKICRQKVHQVGSHYCQACAYKK--GEHLVLVTADPEK 146 (199)
Q Consensus 109 skCkiCK~kVhQ~G~kYCQ~CAYkK--GiCAMCGk~~~~~ 146 (199)
..|..|...+.. +++||+.|-.+- ..|.-||..++..
T Consensus 2 ~~Cp~Cg~~n~~-~akFC~~CG~~l~~~~Cp~CG~~~~~~ 40 (645)
T PRK14559 2 LICPQCQFENPN-NNRFCQKCGTSLTHKPCPQCGTEVPVD 40 (645)
T ss_pred CcCCCCCCcCCC-CCccccccCCCCCCCcCCCCCCCCCcc
Confidence 479999999877 899999997763 4799999988764
No 18
>cd00989 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=83.04 E-value=2.5 Score=28.61 Aligned_cols=45 Identities=24% Similarity=0.382 Sum_probs=25.6
Q ss_pred CccccccccCCCCeeeEEEEeecccc-hhhHHhhhhccccceEEEEEee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHMV-YEDALTILSYASPYEVQIETEK 49 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~~-yEDAl~iL~~a~PYkv~~~l~r 49 (199)
|||++. -|++||+|.+ |....+. .+|...+|+....=.+.+.+.|
T Consensus 23 s~a~~~-gl~~GD~I~~--ing~~i~~~~~~~~~l~~~~~~~~~l~v~r 68 (79)
T cd00989 23 SPAAKA-GLKAGDRILA--INGQKIKSWEDLVDAVQENPGKPLTLTVER 68 (79)
T ss_pred CHHHHc-CCCCCCEEEE--ECCEECCCHHHHHHHHHHCCCceEEEEEEE
Confidence 566554 4899999998 4444332 3455555554322245555554
No 19
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=79.79 E-value=0.82 Score=42.12 Aligned_cols=38 Identities=21% Similarity=0.446 Sum_probs=28.4
Q ss_pred ccchhhcc----------cccCCCcCCcccccc-----cCCcccCCCCCCCCC
Q psy11904 110 SCKICRQK----------VHQVGSHYCQACAYK-----KGEHLVLVTADPEKG 147 (199)
Q Consensus 110 kCkiCK~k----------VhQ~G~kYCQ~CAYk-----KGiCAMCGk~~~~~~ 147 (199)
.|.+|++. |+.=||.+|.+|.-. .+.|..|++++.+..
T Consensus 5 ~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 5 GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN 57 (309)
T ss_pred CCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence 68888872 233489999999543 458999999988764
No 20
>cd00991 PDZ_archaeal_metalloprotease PDZ domain of archaeal zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=79.16 E-value=4.3 Score=28.52 Aligned_cols=45 Identities=22% Similarity=0.189 Sum_probs=26.9
Q ss_pred CccccccccCCCCeeeEEEEeecccc-hhhHHhhhhccc-cceEEEEEee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHMV-YEDALTILSYAS-PYEVQIETEK 49 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~~-yEDAl~iL~~a~-PYkv~~~l~r 49 (199)
|||++ .-|++||+|++ |....+. .+|...+|.... --.+.+.+.|
T Consensus 21 spa~~-aGL~~GDiI~~--Ing~~v~~~~d~~~~l~~~~~g~~v~l~v~r 67 (79)
T cd00991 21 SPAEN-AVLHTGDVIYS--INGTPITTLEDFMEALKPTKPGEVITVTVLP 67 (79)
T ss_pred ChHHh-cCCCCCCEEEE--ECCEEcCCHHHHHHHHhcCCCCCEEEEEEEE
Confidence 45544 35999999999 5444332 345566666543 2356666654
No 21
>TIGR00225 prc C-terminal peptidase (prc). A C-terminal peptidase with different substrates in different species including processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in E.coli E.coli and H influenza have the most distal branch of the tree and their proteins have an N-terminal 200 amino acids that show no homology to other proteins in the database.
Probab=78.59 E-value=2.8 Score=37.11 Aligned_cols=46 Identities=20% Similarity=0.319 Sum_probs=31.3
Q ss_pred CccccccccCCCCeeeEEEEeecccc---hhhHHhhhhccccceEEEEEeee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHMV---YEDALTILSYASPYEVQIETEKE 50 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~~---yEDAl~iL~~a~PYkv~~~l~re 50 (199)
|||++.+ |+.||+|++ |....+. .++...+|+...--.|.+.+.|.
T Consensus 73 spA~~aG-L~~GD~I~~--Ing~~v~~~~~~~~~~~l~~~~g~~v~l~v~R~ 121 (334)
T TIGR00225 73 SPAEKAG-IKPGDKIIK--INGKSVAGMSLDDAVALIRGKKGTKVSLEILRA 121 (334)
T ss_pred ChHHHcC-CCCCCEEEE--ECCEECCCCCHHHHHHhccCCCCCEEEEEEEeC
Confidence 6787777 999999999 5555443 24666777655555666666653
No 22
>cd00987 PDZ_serine_protease PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=74.86 E-value=6.2 Score=27.07 Aligned_cols=45 Identities=20% Similarity=0.195 Sum_probs=25.4
Q ss_pred CccccccccCCCCeeeEEEEeecccch-hhHHhhhhccc-cceEEEEEee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHMVY-EDALTILSYAS-PYEVQIETEK 49 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~~y-EDAl~iL~~a~-PYkv~~~l~r 49 (199)
|||++. -|++||+|.+ |....+.. +|...+|.... .-.+.+.+.|
T Consensus 35 s~a~~~-gl~~GD~I~~--Ing~~i~~~~~~~~~l~~~~~~~~i~l~v~r 81 (90)
T cd00987 35 SPAAKA-GLKPGDVILA--VNGKPVKSVADLRRALAELKPGDKVTLTVLR 81 (90)
T ss_pred CHHHHc-CCCcCCEEEE--ECCEECCCHHHHHHHHHhcCCCCEEEEEEEE
Confidence 555554 4899999998 55444432 34445554432 2345555544
No 23
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=73.89 E-value=1.6 Score=26.04 Aligned_cols=21 Identities=19% Similarity=0.762 Sum_probs=16.1
Q ss_pred cccchhhcccccCCCcCCcccc
Q psy11904 109 ESCKICRQKVHQVGSHYCQACA 130 (199)
Q Consensus 109 skCkiCK~kVhQ~G~kYCQ~CA 130 (199)
..|..|.+.+.. +++||..|-
T Consensus 3 ~~Cp~Cg~~~~~-~~~fC~~CG 23 (26)
T PF13248_consen 3 MFCPNCGAEIDP-DAKFCPNCG 23 (26)
T ss_pred CCCcccCCcCCc-ccccChhhC
Confidence 578999996555 788888764
No 24
>PLN00049 carboxyl-terminal processing protease; Provisional
Probab=73.37 E-value=4.9 Score=36.80 Aligned_cols=46 Identities=17% Similarity=0.124 Sum_probs=32.4
Q ss_pred CccccccccCCCCeeeEEEEeeccc---chhhHHhhhhccccceEEEEEeee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHM---VYEDALTILSYASPYEVQIETEKE 50 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~---~yEDAl~iL~~a~PYkv~~~l~re 50 (199)
|||++.+ |++||+|++ |....+ ..+++..+|+...--.|.+.++|.
T Consensus 113 SPA~~aG-l~~GD~Iv~--InG~~v~~~~~~~~~~~l~g~~g~~v~ltv~r~ 161 (389)
T PLN00049 113 GPAARAG-IRPGDVILA--IDGTSTEGLSLYEAADRLQGPEGSSVELTLRRG 161 (389)
T ss_pred ChHHHcC-CCCCCEEEE--ECCEECCCCCHHHHHHHHhcCCCCEEEEEEEEC
Confidence 7888887 899999999 655544 346777777654444677777663
No 25
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=72.25 E-value=1.7 Score=28.79 Aligned_cols=24 Identities=17% Similarity=0.142 Sum_probs=19.0
Q ss_pred CCcCCccccc----ccCCcccCCCCCCC
Q psy11904 122 GSHYCQACAY----KKGEHLVLVTADPE 145 (199)
Q Consensus 122 G~kYCQ~CAY----kKGiCAMCGk~~~~ 145 (199)
|+.||..|.- ..+.|.+||++++.
T Consensus 20 G~v~~~~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 20 GQTYERRAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred CCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence 7889988854 46789999988854
No 26
>PRK11186 carboxy-terminal protease; Provisional
Probab=71.33 E-value=5.3 Score=40.02 Aligned_cols=48 Identities=19% Similarity=0.268 Sum_probs=37.2
Q ss_pred CccccccccCCCCeeeEEE------EeecccchhhHHhhhhccccceEEEEEee
Q psy11904 2 SHCAETWALNNGDRITSVR------ISFRHMVYEDALTILSYASPYEVQIETEK 49 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~t------i~F~n~~yEDAl~iL~~a~PYkv~~~l~r 49 (199)
|||+++.-|++||+|++|- +.-.++..+|+..+|.-..=-.|.+.++|
T Consensus 266 sPA~ka~gLk~GD~IlaVn~~g~~~~dv~g~~~~~vv~lirG~~Gt~V~LtV~r 319 (667)
T PRK11186 266 GPAAKSKKLSVGDKIVGVGQDGKPIVDVIGWRLDDVVALIKGPKGSKVRLEILP 319 (667)
T ss_pred ChHHHhCCCCCCCEEEEECCCCCcccccccCCHHHHHHHhcCCCCCEEEEEEEe
Confidence 7899988999999999964 23345667888888876666678888776
No 27
>COG0793 Prc Periplasmic protease [Cell envelope biogenesis, outer membrane]
Probab=69.62 E-value=7.4 Score=36.37 Aligned_cols=48 Identities=17% Similarity=0.229 Sum_probs=39.1
Q ss_pred CccccccccCCCCeeeEEE-EeecccchhhHHhhhhccccceEEEEEeee
Q psy11904 2 SHCAETWALNNGDRITSVR-ISFRHMVYEDALTILSYASPYEVQIETEKE 50 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~t-i~F~n~~yEDAl~iL~~a~PYkv~~~l~re 50 (199)
|||++.+ |++||+|.++- ..+.+|..++|++.+.--.==+|.+++.|+
T Consensus 123 ~PA~kag-i~~GD~I~~IdG~~~~~~~~~~av~~irG~~Gt~V~L~i~r~ 171 (406)
T COG0793 123 SPAAKAG-IKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPGTKVTLTILRA 171 (406)
T ss_pred ChHHHcC-CCCCCEEEEECCEEccCCCHHHHHHHhCCCCCCeEEEEEEEc
Confidence 7999999 99999999953 456778888898887777666788888876
No 28
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=69.06 E-value=2.1 Score=25.31 Aligned_cols=20 Identities=20% Similarity=0.866 Sum_probs=15.1
Q ss_pred ccchhhcccccCCCcCCcccc
Q psy11904 110 SCKICRQKVHQVGSHYCQACA 130 (199)
Q Consensus 110 kCkiCK~kVhQ~G~kYCQ~CA 130 (199)
.|..|...+.. ++++|+.|-
T Consensus 1 ~Cp~CG~~~~~-~~~fC~~CG 20 (23)
T PF13240_consen 1 YCPNCGAEIED-DAKFCPNCG 20 (23)
T ss_pred CCcccCCCCCC-cCcchhhhC
Confidence 48889999976 778876653
No 29
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=68.43 E-value=1.4 Score=28.51 Aligned_cols=20 Identities=20% Similarity=0.461 Sum_probs=17.2
Q ss_pred CCcCCcccccccC----CcccCCC
Q psy11904 122 GSHYCQACAYKKG----EHLVLVT 141 (199)
Q Consensus 122 G~kYCQ~CAYkKG----iCAMCGk 141 (199)
||.+|+.|+.+.- .|.+|++
T Consensus 21 gH~~C~~C~~~~~~~~~~CP~C~k 44 (44)
T PF14634_consen 21 GHIFCEKCLKKLKGKSVKCPICRK 44 (44)
T ss_pred CCHHHHHHHHhhcCCCCCCcCCCC
Confidence 7899999998877 8988875
No 30
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=63.73 E-value=4.5 Score=32.38 Aligned_cols=22 Identities=18% Similarity=0.280 Sum_probs=18.1
Q ss_pred ccCCcccCCCCCCCCCCcceeeecceEEEEe
Q psy11904 132 KKGEHLVLVTADPEKGDKFALISGEHLVLVT 162 (199)
Q Consensus 132 kKGiCAMCGk~~~~~~~~~~~i~g~~~~~~~ 162 (199)
++-.|+.||+ |||.||+||...
T Consensus 5 kewkC~VCg~---------~iieGqkFTF~~ 26 (103)
T COG4847 5 KEWKCYVCGG---------TIIEGQKFTFTK 26 (103)
T ss_pred ceeeEeeeCC---------EeeeccEEEEee
Confidence 4457999995 689999999875
No 31
>PRK12496 hypothetical protein; Provisional
Probab=63.64 E-value=3 Score=34.47 Aligned_cols=26 Identities=15% Similarity=0.252 Sum_probs=18.4
Q ss_pred CcCCcccc--c----ccCCcccCCCCCCCCCC
Q psy11904 123 SHYCQACA--Y----KKGEHLVLVTADPEKGD 148 (199)
Q Consensus 123 ~kYCQ~CA--Y----kKGiCAMCGk~~~~~~~ 148 (199)
.++|++|- | ....|.+||.++..+..
T Consensus 127 ~~~C~gC~~~~~~~~~~~~C~~CG~~~~r~~~ 158 (164)
T PRK12496 127 RKVCKGCKKKYPEDYPDDVCEICGSPVKRKMV 158 (164)
T ss_pred eEECCCCCccccCCCCCCcCCCCCChhhhcch
Confidence 35688884 5 44679999988766544
No 32
>TIGR02860 spore_IV_B stage IV sporulation protein B. SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase, expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else.
Probab=63.60 E-value=9.8 Score=36.22 Aligned_cols=46 Identities=22% Similarity=0.317 Sum_probs=32.9
Q ss_pred CccccccccCCCCeeeEEEEeecccc-hhhHHhhhhccccceEEEEEeee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHMV-YEDALTILSYASPYEVQIETEKE 50 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~~-yEDAl~iL~~a~PYkv~~~l~re 50 (199)
|||++. -|++||+|++ |....+. .+|...+|+.+..-.+.+.++|.
T Consensus 124 SPAa~A-GLq~GDiIvs--ING~~V~s~~DL~~iL~~~~g~~V~LtV~R~ 170 (402)
T TIGR02860 124 SPGEEA-GIQIGDRILK--INGEKIKNMDDLANLINKAGGEKLTLTIERG 170 (402)
T ss_pred CHHHHc-CCCCCCEEEE--ECCEECCCHHHHHHHHHhCCCCeEEEEEEEC
Confidence 566554 4899999999 6665554 34557788887777788887664
No 33
>TIGR00054 RIP metalloprotease RseP. A model that detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain.
Probab=58.30 E-value=14 Score=34.30 Aligned_cols=46 Identities=22% Similarity=0.338 Sum_probs=30.4
Q ss_pred CccccccccCCCCeeeEEEEeecccc-hhhHHhhhhccccceEEEEEeee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHMV-YEDALTILSYASPYEVQIETEKE 50 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~~-yEDAl~iL~~a~PYkv~~~l~re 50 (199)
|||++. -|++||+|.+ |....+. .+|....|+......+.+.++|.
T Consensus 214 SpA~~a-GL~~GD~Iv~--Vng~~V~s~~dl~~~l~~~~~~~v~l~v~R~ 260 (420)
T TIGR00054 214 SPAEKA-GLKEGDYIQS--INGEKLRSWTDFVSAVKENPGKSMDIKVERN 260 (420)
T ss_pred CHHHHc-CCCCCCEEEE--ECCEECCCHHHHHHHHHhCCCCceEEEEEEC
Confidence 555543 4999999999 5555443 45666677665445577777764
No 34
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=56.76 E-value=4.7 Score=35.04 Aligned_cols=49 Identities=22% Similarity=0.434 Sum_probs=34.8
Q ss_pred cccchhhcccc-----cCCCcCCcccccc--------------------cCCcccCCCCCCCCCCcceee-ecceE
Q psy11904 109 ESCKICRQKVH-----QVGSHYCQACAYK--------------------KGEHLVLVTADPEKGDKFALI-SGEHL 158 (199)
Q Consensus 109 skCkiCK~kVh-----Q~G~kYCQ~CAYk--------------------KGiCAMCGk~~~~~~~~~~~i-~g~~~ 158 (199)
-.|.||...+. .=||.||..|.++ ...|.+|...++. ..-.||. .|++-
T Consensus 19 ~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~-~~LvPiygrg~~~ 93 (193)
T PLN03208 19 FDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSE-ATLVPIYGRGQKA 93 (193)
T ss_pred cCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCCh-hcEEEeeccCCCC
Confidence 37888866443 3489999999863 3579999999977 4445655 66643
No 35
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=52.52 E-value=22 Score=32.53 Aligned_cols=45 Identities=20% Similarity=0.224 Sum_probs=28.6
Q ss_pred CccccccccCCCCeeeEEEEeecccch-hhHHhhhhcccc-ceEEEEEee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHMVY-EDALTILSYASP-YEVQIETEK 49 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~~y-EDAl~iL~~a~P-Ykv~~~l~r 49 (199)
|||++.+ |++||+|++ |....+.. +|....|....| -.|.+.+.|
T Consensus 268 spA~~aG-L~~GDvI~~--Vng~~i~~~~~~~~~l~~~~~g~~v~l~v~R 314 (428)
T TIGR02037 268 SPAEKAG-LKAGDVILS--VNGKPISSFADLRRAIGTLKPGKKVTLGILR 314 (428)
T ss_pred CChHHcC-CCCCCEEEE--ECCEEcCCHHHHHHHHHhcCCCCEEEEEEEE
Confidence 6777776 999999998 55554432 233444444333 467787776
No 36
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=52.38 E-value=6.8 Score=37.15 Aligned_cols=37 Identities=19% Similarity=0.484 Sum_probs=28.5
Q ss_pred cccchhhccccc-----CCCcCCccccc----ccCCcccCCCCCCC
Q psy11904 109 ESCKICRQKVHQ-----VGSHYCQACAY----KKGEHLVLVTADPE 145 (199)
Q Consensus 109 skCkiCK~kVhQ-----~G~kYCQ~CAY----kKGiCAMCGk~~~~ 145 (199)
-.|.||..-+.. -||.||..|.. ..+.|.+|......
T Consensus 27 l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~~~~~CP~Cr~~~~~ 72 (397)
T TIGR00599 27 LRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQE 72 (397)
T ss_pred cCCCcCchhhhCccCCCCCCchhHHHHHHHHhCCCCCCCCCCcccc
Confidence 378888765543 39999999986 35689999988765
No 37
>KOG3550|consensus
Probab=48.87 E-value=15 Score=32.16 Aligned_cols=44 Identities=25% Similarity=0.300 Sum_probs=35.3
Q ss_pred cccccccCCCCeeeEEE-EeecccchhhHHhhhhccccceEEEEEe
Q psy11904 4 CAETWALNNGDRITSVR-ISFRHMVYEDALTILSYASPYEVQIETE 48 (199)
Q Consensus 4 a~~~~~l~~GD~i~s~t-i~F~n~~yEDAl~iL~~a~PYkv~~~l~ 48 (199)
|.+.+-|+-|||++|+. |+.+.---|.|+.+|+-|.- .|++.++
T Consensus 128 adrhgglkrgdqllsvngvsvege~hekavellkaa~g-svklvvr 172 (207)
T KOG3550|consen 128 ADRHGGLKRGDQLLSVNGVSVEGEHHEKAVELLKAAVG-SVKLVVR 172 (207)
T ss_pred ccccCcccccceeEeecceeecchhhHHHHHHHHHhcC-cEEEEEe
Confidence 67889999999999975 47777788999999987764 5666554
No 38
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=47.61 E-value=15 Score=29.01 Aligned_cols=30 Identities=20% Similarity=0.134 Sum_probs=21.7
Q ss_pred CCcccCCCCCCCCCCcceeeecceEEEEecCCCCCC
Q psy11904 134 GEHLVLVTADPEKGDKFALISGEHLVLVTADPEKGD 169 (199)
Q Consensus 134 GiCAMCGk~~~~~~~~~~~i~g~~~~~~~~~~~~~~ 169 (199)
..|+-||-. ..-|++|+-|.|....-+.+|
T Consensus 93 ~~CP~Cgs~------~~~i~~G~El~i~~Ieve~~~ 122 (124)
T PRK00762 93 IECPVCGNK------RAHILGGRECNVKNIKIEKED 122 (124)
T ss_pred CcCcCCCCC------CCEEecCCeEEEEEEEEecCC
Confidence 369999933 356899999999876555443
No 39
>PRK11595 DNA utilization protein GntX; Provisional
Probab=46.46 E-value=12 Score=31.59 Aligned_cols=36 Identities=17% Similarity=0.227 Sum_probs=20.9
Q ss_pred cccchhhcccccCCCcCCcccccc----cCCcccCCCCCC
Q psy11904 109 ESCKICRQKVHQVGSHYCQACAYK----KGEHLVLVTADP 144 (199)
Q Consensus 109 skCkiCK~kVhQ~G~kYCQ~CAYk----KGiCAMCGk~~~ 144 (199)
..|-.|.+.++......|..|.-+ ...|..||++..
T Consensus 6 ~~C~~C~~~~~~~~~~lC~~C~~~l~~~~~~C~~Cg~~~~ 45 (227)
T PRK11595 6 GLCWLCRMPLALSHWGICSVCSRALRTLKTCCPQCGLPAT 45 (227)
T ss_pred CcCccCCCccCCCCCcccHHHHhhCCcccCcCccCCCcCC
Confidence 357777776654333457777422 345777776543
No 40
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=44.03 E-value=13 Score=24.35 Aligned_cols=20 Identities=20% Similarity=0.101 Sum_probs=12.4
Q ss_pred CCcccCCCCCCCCCCcceeeecc
Q psy11904 134 GEHLVLVTADPEKGDKFALISGE 156 (199)
Q Consensus 134 GiCAMCGk~~~~~~~~~~~i~g~ 156 (199)
-.|+.||++-+ +..+||+|.
T Consensus 2 ~~CSFCgr~~~---~v~~li~g~ 21 (41)
T PF06689_consen 2 KRCSFCGRPES---EVGRLISGP 21 (41)
T ss_dssp -B-TTT--BTT---TSSSEEEES
T ss_pred CCccCCCCCHH---HHhceecCC
Confidence 37999998765 456889987
No 41
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=43.75 E-value=16 Score=29.04 Aligned_cols=22 Identities=9% Similarity=0.156 Sum_probs=17.5
Q ss_pred cCCcccCCCCCCCCCCcceeeecceEEEEec
Q psy11904 133 KGEHLVLVTADPEKGDKFALISGEHLVLVTA 163 (199)
Q Consensus 133 KGiCAMCGk~~~~~~~~~~~i~g~~~~~~~~ 163 (199)
+-.|..||+ ||+.||.||...-
T Consensus 2 kWkC~iCg~---------~I~~gqlFTF~~k 23 (101)
T PF09943_consen 2 KWKCYICGK---------PIYEGQLFTFTKK 23 (101)
T ss_pred ceEEEecCC---------eeeecceEEEecC
Confidence 447999995 6899999998643
No 42
>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=42.66 E-value=20 Score=20.97 Aligned_cols=9 Identities=0% Similarity=-0.451 Sum_probs=5.4
Q ss_pred CcccCCCCC
Q psy11904 135 EHLVLVTAD 143 (199)
Q Consensus 135 iCAMCGk~~ 143 (199)
.|+.|++++
T Consensus 29 ~C~~C~~~L 37 (39)
T smart00132 29 KCSKCGKPL 37 (39)
T ss_pred CCcccCCcC
Confidence 466666655
No 43
>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=42.64 E-value=9.7 Score=30.33 Aligned_cols=26 Identities=19% Similarity=0.321 Sum_probs=18.4
Q ss_pred CcccchhhcccccCC--CcCCcccccccCCcccCCCCC
Q psy11904 108 FESCKICRQKVHQVG--SHYCQACAYKKGEHLVLVTAD 143 (199)
Q Consensus 108 ~skCkiCK~kVhQ~G--~kYCQ~CAYkKGiCAMCGk~~ 143 (199)
-..|..|+.+|.+.+ .. .|.-|++..
T Consensus 34 Y~aC~~C~kkv~~~~~~~~----------~C~~C~~~~ 61 (166)
T cd04476 34 YPACPGCNKKVVEEGNGTY----------RCEKCNKSV 61 (166)
T ss_pred EccccccCcccEeCCCCcE----------ECCCCCCcC
Confidence 359999999998753 33 455567664
No 44
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=42.09 E-value=25 Score=25.64 Aligned_cols=38 Identities=16% Similarity=0.308 Sum_probs=25.0
Q ss_pred cccchhhcccccCCCcCCcccccccCCcccCCCCC-CCCCCcceeeecceEEEEecCCCCC
Q psy11904 109 ESCKICRQKVHQVGSHYCQACAYKKGEHLVLVTAD-PEKGDKFALISGEHLVLVTADPEKG 168 (199)
Q Consensus 109 skCkiCK~kVhQ~G~kYCQ~CAYkKGiCAMCGk~~-~~~~~~~~~i~g~~~~~~~~~~~~~ 168 (199)
..|+.|+.-+... .|..||-+. ++. .+| .|+-.|||+-
T Consensus 4 kAC~~C~~i~~~~-------------~CP~Cgs~~~T~~------W~G---~viI~dPe~S 42 (61)
T PRK08351 4 KACRHCHYITTED-------------RCPVCGSRDLSDE------WFD---LVIIIDVENS 42 (61)
T ss_pred hhhhhCCcccCCC-------------cCCCCcCCccccc------ccc---EEEEeCCcHh
Confidence 4799999888642 599999654 222 244 3446788864
No 45
>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=41.46 E-value=13 Score=27.15 Aligned_cols=36 Identities=17% Similarity=0.337 Sum_probs=27.8
Q ss_pred cccchhhcccccCC---------CcCCccccccc--CCcccCCCCCC
Q psy11904 109 ESCKICRQKVHQVG---------SHYCQACAYKK--GEHLVLVTADP 144 (199)
Q Consensus 109 skCkiCK~kVhQ~G---------~kYCQ~CAYkK--GiCAMCGk~~~ 144 (199)
..|..|.+.+.++. -.||..||-.. |+|.-||-.+.
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 46888888887754 26888898776 99999996654
No 46
>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=40.65 E-value=12 Score=28.30 Aligned_cols=38 Identities=11% Similarity=0.044 Sum_probs=24.6
Q ss_pred CcccchhhcccccCCCcCCcccccccCCcccCCCCCCC
Q psy11904 108 FESCKICRQKVHQVGSHYCQACAYKKGEHLVLVTADPE 145 (199)
Q Consensus 108 ~skCkiCK~kVhQ~G~kYCQ~CAYkKGiCAMCGk~~~~ 145 (199)
.|.|..|++++.--.--===+=-..+|.|.-|+.+.+-
T Consensus 33 rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred CCcCcCCCCcCcccccchHHHHHHhCCCCcccCCCCCh
Confidence 48999999988642111001123578999999988764
No 47
>PRK10779 zinc metallopeptidase RseP; Provisional
Probab=40.18 E-value=39 Score=31.47 Aligned_cols=46 Identities=20% Similarity=0.379 Sum_probs=27.8
Q ss_pred CccccccccCCCCeeeEEEEeecccc-hhhHHhhhhccccceEEEEEeee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHMV-YEDALTILSYASPYEVQIETEKE 50 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~~-yEDAl~iL~~a~PYkv~~~l~re 50 (199)
|||++. -|++||+|++ |....+. .+|.-.+++...--.+.+.+.|.
T Consensus 232 SpA~~A-GL~~GDvIl~--Ing~~V~s~~dl~~~l~~~~~~~v~l~v~R~ 278 (449)
T PRK10779 232 SAASKA-GLQAGDRIVK--VDGQPLTQWQTFVTLVRDNPGKPLALEIERQ 278 (449)
T ss_pred CHHHHc-CCCCCCEEEE--ECCEEcCCHHHHHHHHHhCCCCEEEEEEEEC
Confidence 455554 4999999999 5544443 24445555543334577777764
No 48
>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=39.44 E-value=6.7 Score=29.35 Aligned_cols=36 Identities=22% Similarity=0.331 Sum_probs=21.8
Q ss_pred ccchhhcccccCC-CcCCcccc---cccCCcccCCCCCCC
Q psy11904 110 SCKICRQKVHQVG-SHYCQACA---YKKGEHLVLVTADPE 145 (199)
Q Consensus 110 kCkiCK~kVhQ~G-~kYCQ~CA---YkKGiCAMCGk~~~~ 145 (199)
.|..|.+.+...+ ..+|..|. -+.+.|.-||.++..
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEV 42 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EE
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCcccHHHH
Confidence 6888999886655 66788873 356789999877653
No 49
>PRK10898 serine endoprotease; Provisional
Probab=39.35 E-value=45 Score=30.26 Aligned_cols=46 Identities=11% Similarity=0.213 Sum_probs=27.3
Q ss_pred CccccccccCCCCeeeEEEEeecccch-hhHHhhhhcccc-ceEEEEEeee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHMVY-EDALTILSYASP-YEVQIETEKE 50 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~~y-EDAl~iL~~a~P-Ykv~~~l~re 50 (199)
|||++. -|++||+|++ |....+.. +|-...|....| -.|.+.+.|.
T Consensus 290 spA~~a-GL~~GDvI~~--Ing~~V~s~~~l~~~l~~~~~g~~v~l~v~R~ 337 (353)
T PRK10898 290 GPAAKA-GIQVNDLIIS--VNNKPAISALETMDQVAEIRPGSVIPVVVMRD 337 (353)
T ss_pred ChHHHc-CCCCCCEEEE--ECCEEcCCHHHHHHHHHhcCCCCEEEEEEEEC
Confidence 455553 4999999999 55544422 344455544333 4677777763
No 50
>KOG1813|consensus
Probab=38.89 E-value=15 Score=34.32 Aligned_cols=34 Identities=32% Similarity=0.765 Sum_probs=27.1
Q ss_pred ccchhhccc-----ccCCCcCCcccc---ccc-CCcccCCCCC
Q psy11904 110 SCKICRQKV-----HQVGSHYCQACA---YKK-GEHLVLVTAD 143 (199)
Q Consensus 110 kCkiCK~kV-----hQ~G~kYCQ~CA---YkK-GiCAMCGk~~ 143 (199)
+|-||+..- ..-||++|-.|| |++ -.|-+|+++.
T Consensus 243 ~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t 285 (313)
T KOG1813|consen 243 KCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQT 285 (313)
T ss_pred cccccccccccchhhcCCceeehhhhccccccCCcceeccccc
Confidence 899999853 444899999998 666 6899999764
No 51
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=38.74 E-value=47 Score=30.03 Aligned_cols=45 Identities=11% Similarity=0.079 Sum_probs=26.7
Q ss_pred CccccccccCCCCeeeEEEEeecccch-hhHHhhhhcc-ccceEEEEEee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHMVY-EDALTILSYA-SPYEVQIETEK 49 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~~y-EDAl~iL~~a-~PYkv~~~l~r 49 (199)
|||++.+ |++||.|++ |....+.. +|....|+.. .--.|.+.+.|
T Consensus 289 spA~~aG-L~~GDvI~~--Ing~~V~s~~dl~~~l~~~~~g~~v~l~v~R 335 (351)
T TIGR02038 289 GPAARAG-ILVRDVILK--YDGKDVIGAEELMDRIAETRPGSKVMVTVLR 335 (351)
T ss_pred ChHHHCC-CCCCCEEEE--ECCEEcCCHHHHHHHHHhcCCCCEEEEEEEE
Confidence 5666554 999999999 54444432 3334555542 22356777665
No 52
>smart00746 TRASH metallochaperone-like domain.
Probab=38.07 E-value=42 Score=18.09 Aligned_cols=23 Identities=4% Similarity=-0.135 Sum_probs=12.5
Q ss_pred cccCCCCCCC-CCCcceeeecceE
Q psy11904 136 HLVLVTADPE-KGDKFALISGEHL 158 (199)
Q Consensus 136 CAMCGk~~~~-~~~~~~~i~g~~~ 158 (199)
|+.||..... .....-.+.|+.+
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g~~~ 24 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVF 24 (39)
T ss_pred CCCCCCCccCCCCceEEEECCEEE
Confidence 7788887763 3233223555444
No 53
>KOG3799|consensus
Probab=37.99 E-value=17 Score=31.11 Aligned_cols=41 Identities=20% Similarity=0.311 Sum_probs=27.1
Q ss_pred Ccccchhhc-ccccCCCcCCcccccccCCcccCCCCCCCCCCcc
Q psy11904 108 FESCKICRQ-KVHQVGSHYCQACAYKKGEHLVLVTADPEKGDKF 150 (199)
Q Consensus 108 ~skCkiCK~-kVhQ~G~kYCQ~CAYkKGiCAMCGk~~~~~~~~~ 150 (199)
-..|-||-. +...--+|-|..|-.+ .||.||-..+-++.|.
T Consensus 65 datC~IC~KTKFADG~GH~C~YCq~r--~CARCGGrv~lrsNKv 106 (169)
T KOG3799|consen 65 DATCGICHKTKFADGCGHNCSYCQTR--FCARCGGRVSLRSNKV 106 (169)
T ss_pred CcchhhhhhcccccccCcccchhhhh--HHHhcCCeeeeccCce
Confidence 458999955 5544334666666544 7999997776665554
No 54
>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=37.52 E-value=26 Score=22.67 Aligned_cols=13 Identities=0% Similarity=-0.291 Sum_probs=7.4
Q ss_pred CcccCCCCCCCCC
Q psy11904 135 EHLVLVTADPEKG 147 (199)
Q Consensus 135 iCAMCGk~~~~~~ 147 (199)
.|+.|++++....
T Consensus 28 ~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 28 KCSKCGKPLNDGD 40 (58)
T ss_dssp BETTTTCBTTTSS
T ss_pred ccCCCCCccCCCe
Confidence 4666666665443
No 55
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=37.47 E-value=29 Score=27.04 Aligned_cols=40 Identities=15% Similarity=0.217 Sum_probs=26.8
Q ss_pred cccchhhcccccCCCcCCcccccccCCcccCCCCCCCCCCcceeeecceEEEEec
Q psy11904 109 ESCKICRQKVHQVGSHYCQACAYKKGEHLVLVTADPEKGDKFALISGEHLVLVTA 163 (199)
Q Consensus 109 skCkiCK~kVhQ~G~kYCQ~CAYkKGiCAMCGk~~~~~~~~~~~i~g~~~~~~~~ 163 (199)
..|+.|.+...... ....|+-||.. ..-|++|+-|.|...
T Consensus 71 ~~C~~Cg~~~~~~~---------~~~~CP~Cgs~------~~~i~~G~El~i~~i 110 (113)
T PRK12380 71 AWCWDCSQVVEIHQ---------HDAQCPHCHGE------RLRVDTGDSLIVKSI 110 (113)
T ss_pred EEcccCCCEEecCC---------cCccCcCCCCC------CcEEccCCeEEEEEE
Confidence 47888886554422 12259999943 456899999988753
No 56
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=36.55 E-value=30 Score=25.55 Aligned_cols=40 Identities=20% Similarity=0.341 Sum_probs=25.0
Q ss_pred CcccchhhcccccCCCcCCcccccccCCcccCCCCCCCCCCcceeeecceEEEEecCCCCC
Q psy11904 108 FESCKICRQKVHQVGSHYCQACAYKKGEHLVLVTADPEKGDKFALISGEHLVLVTADPEKG 168 (199)
Q Consensus 108 ~skCkiCK~kVhQ~G~kYCQ~CAYkKGiCAMCGk~~~~~~~~~~~i~g~~~~~~~~~~~~~ 168 (199)
+..|+.|+.-++-. .|.+||-+. .-+-.+|- ++-.|||+-
T Consensus 5 ~~AC~~C~~i~~~~-------------~Cp~Cgs~~-----~S~~w~G~---v~i~dPe~S 44 (64)
T PRK06393 5 YRACKKCKRLTPEK-------------TCPVHGDEK-----TTTEWFGF---LIITEPEGS 44 (64)
T ss_pred hhhHhhCCcccCCC-------------cCCCCCCCc-----CCcCcceE---EEEECCchh
Confidence 35899999888542 899999642 22334452 333488853
No 57
>KOG3209|consensus
Probab=36.37 E-value=28 Score=36.48 Aligned_cols=38 Identities=26% Similarity=0.315 Sum_probs=31.2
Q ss_pred CccccccccCCCCeeeEEE-EeecccchhhHHhhhhccc
Q psy11904 2 SHCAETWALNNGDRITSVR-ISFRHMVYEDALTILSYAS 39 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~t-i~F~n~~yEDAl~iL~~a~ 39 (199)
|||+|-++|++||+|+-|. ++.-|+.-.|-+.+++-|-
T Consensus 789 SPAdRCgkLkVGDrilAVNG~sI~~lsHadiv~LIKdaG 827 (984)
T KOG3209|consen 789 SPADRCGKLKVGDRILAVNGQSILNLSHADIVSLIKDAG 827 (984)
T ss_pred ChhHhhccccccceEEEecCeeeeccCchhHHHHHHhcC
Confidence 8999999999999999863 5666777788888877653
No 58
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=36.36 E-value=21 Score=30.42 Aligned_cols=15 Identities=7% Similarity=-0.086 Sum_probs=11.5
Q ss_pred ccCCcccCCCCCCCC
Q psy11904 132 KKGEHLVLVTADPEK 146 (199)
Q Consensus 132 kKGiCAMCGk~~~~~ 146 (199)
+.|.|++||.++...
T Consensus 19 Q~G~CaiC~~~l~~~ 33 (157)
T PHA02565 19 QNGICPLCKRELDGD 33 (157)
T ss_pred hCCcCCCCCCccCCC
Confidence 457999999887643
No 59
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=36.03 E-value=13 Score=28.03 Aligned_cols=22 Identities=9% Similarity=0.131 Sum_probs=12.2
Q ss_pred cccCCcccCCCCCCCCCCcceee
Q psy11904 131 YKKGEHLVLVTADPEKGDKFALI 153 (199)
Q Consensus 131 YkKGiCAMCGk~~~~~~~~~~~i 153 (199)
.+.|.|++||++.+.. ...+++
T Consensus 20 ~q~~~C~iC~~~~~~~-~~~~~v 41 (81)
T PF02945_consen 20 EQGGRCAICGKPLPGE-SRKLVV 41 (81)
T ss_dssp HTTTE-TTT-SEEETT-CGGCEE
T ss_pred HhCCcCcCCCCCcccC-CCccee
Confidence 4557999999865555 333433
No 60
>TIGR01713 typeII_sec_gspC general secretion pathway protein C. This model represents GspC, protein C of the main terminal branch of the general secretion pathway, also called type II secretion. This system transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=35.89 E-value=56 Score=28.82 Aligned_cols=45 Identities=16% Similarity=0.182 Sum_probs=33.4
Q ss_pred cccccccCCCCeeeEEEEeecccch-hhHHhhhhcccc-ceEEEEEeee
Q psy11904 4 CAETWALNNGDRITSVRISFRHMVY-EDALTILSYASP-YEVQIETEKE 50 (199)
Q Consensus 4 a~~~~~l~~GD~i~s~ti~F~n~~y-EDAl~iL~~a~P-Ykv~~~l~re 50 (199)
.++..-|++||.|.+ |....+.. +|++.+++...| =.+.++++|.
T Consensus 203 ~a~~aGLr~GDvIv~--ING~~i~~~~~~~~~l~~~~~~~~v~l~V~R~ 249 (259)
T TIGR01713 203 LFYKSGLQDGDIAVA--LNGLDLRDPEQAFQALQMLREETNLTLTVERD 249 (259)
T ss_pred HHHHcCCCCCCEEEE--ECCEEcCCHHHHHHHHHhcCCCCeEEEEEEEC
Confidence 345566999999999 77776654 566888887666 4788888874
No 61
>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=35.51 E-value=17 Score=21.34 Aligned_cols=21 Identities=24% Similarity=0.499 Sum_probs=15.1
Q ss_pred CCcCCccccc-----ccCCcccCCCC
Q psy11904 122 GSHYCQACAY-----KKGEHLVLVTA 142 (199)
Q Consensus 122 G~kYCQ~CAY-----kKGiCAMCGk~ 142 (199)
||.||..|.. ....|.+|...
T Consensus 19 ~H~~c~~C~~~~~~~~~~~Cp~C~~~ 44 (45)
T cd00162 19 GHVFCRSCIDKWLKSGKNTCPLCRTP 44 (45)
T ss_pred CChhcHHHHHHHHHhCcCCCCCCCCc
Confidence 6788888864 25678888764
No 62
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=35.32 E-value=42 Score=26.17 Aligned_cols=41 Identities=12% Similarity=0.176 Sum_probs=26.9
Q ss_pred cccchhhcccccCCCcCCcccccccCCcccCCCCCCCCCCcceeeecceEEEEec
Q psy11904 109 ESCKICRQKVHQVGSHYCQACAYKKGEHLVLVTADPEKGDKFALISGEHLVLVTA 163 (199)
Q Consensus 109 skCkiCK~kVhQ~G~kYCQ~CAYkKGiCAMCGk~~~~~~~~~~~i~g~~~~~~~~ 163 (199)
..|+.|.+...-....+ -.|+-||.. ..-+++|+-|.|...
T Consensus 71 ~~C~~Cg~~~~~~~~~~--------~~CP~Cgs~------~~~i~~G~El~i~~i 111 (114)
T PRK03681 71 CWCETCQQYVTLLTQRV--------RRCPQCHGD------MLRIVADDGLQIRRI 111 (114)
T ss_pred EEcccCCCeeecCCccC--------CcCcCcCCC------CcEEccCCeEEEEEE
Confidence 47888887654422221 358999943 356899999988643
No 63
>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=35.19 E-value=10 Score=30.55 Aligned_cols=25 Identities=24% Similarity=0.505 Sum_probs=14.6
Q ss_pred cccCcccchhhcccccCCCcCCccc
Q psy11904 105 TQKFESCKICRQKVHQVGSHYCQAC 129 (199)
Q Consensus 105 ~~~~skCkiCK~kVhQ~G~kYCQ~C 129 (199)
+.+..+|.+|....-...+.||..|
T Consensus 52 G~~~~rCIiCg~~~g~sdAYYC~eC 76 (106)
T PF03660_consen 52 GSLQGRCIICGSGPGVSDAYYCWEC 76 (106)
T ss_dssp SSTTSB-TTTSSSB--EE-EE-HHH
T ss_pred CCcCceEEEecCCCCcccceehhhh
Confidence 3445799999955544568999988
No 64
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=35.16 E-value=19 Score=30.74 Aligned_cols=37 Identities=14% Similarity=0.076 Sum_probs=26.0
Q ss_pred cccchhhcccccCCCcCCcccccc------cCCcccCCCCCCCCC
Q psy11904 109 ESCKICRQKVHQVGSHYCQACAYK------KGEHLVLVTADPEKG 147 (199)
Q Consensus 109 skCkiCK~kVhQ~G~kYCQ~CAYk------KGiCAMCGk~~~~~~ 147 (199)
.+|..|.+.+. |..|...-.+- -.-|+-||++.|-..
T Consensus 40 ~~Cp~C~~~Ir--G~y~v~gv~~~g~~~~~PsYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 40 TSCPNCSTPIR--GDYHVEGVFGLGGHYEAPSYCHNCGKPYPWTE 82 (158)
T ss_pred HHCcCCCCCCC--CceecCCeeeeCCCCCCChhHHhCCCCCchHH
Confidence 47888888876 55666554443 346999999999743
No 65
>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=33.84 E-value=21 Score=21.81 Aligned_cols=21 Identities=29% Similarity=0.994 Sum_probs=14.0
Q ss_pred ccchhhcccccCCCcCCccccc
Q psy11904 110 SCKICRQKVHQVGSHYCQACAY 131 (199)
Q Consensus 110 kCkiCK~kVhQ~G~kYCQ~CAY 131 (199)
.|..|.+.|.. .++.|..|-|
T Consensus 2 ~CP~C~~~V~~-~~~~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEVPE-SAKFCPHCGY 22 (26)
T ss_pred cCCCCcCCchh-hcCcCCCCCC
Confidence 68888888876 4565555443
No 66
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.53 E-value=54 Score=25.70 Aligned_cols=41 Identities=15% Similarity=0.229 Sum_probs=26.8
Q ss_pred cccchhhcccccCCCcCCcccccccCCcccCCCCCCCCCCcceeeecceEEEEec
Q psy11904 109 ESCKICRQKVHQVGSHYCQACAYKKGEHLVLVTADPEKGDKFALISGEHLVLVTA 163 (199)
Q Consensus 109 skCkiCK~kVhQ~G~kYCQ~CAYkKGiCAMCGk~~~~~~~~~~~i~g~~~~~~~~ 163 (199)
-.|+.|.+...-... ....|+.||.. ..-|++|+-|.|...
T Consensus 72 ~~C~~Cg~~~~~~~~--------~~~~CP~Cgs~------~~~i~~G~El~I~~i 112 (117)
T PRK00564 72 LECKDCSHVFKPNAL--------DYGVCEKCHSK------NVIITQGNEMRLLSL 112 (117)
T ss_pred EEhhhCCCccccCCc--------cCCcCcCCCCC------ceEEecCCEEEEEEE
Confidence 478888765544221 22359999944 356899999988643
No 67
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=33.15 E-value=39 Score=26.31 Aligned_cols=40 Identities=15% Similarity=0.126 Sum_probs=27.5
Q ss_pred cccchhhcccccCCCcCCcccccccCCcccCCCCCCCCCCcceeeecceEEEEec
Q psy11904 109 ESCKICRQKVHQVGSHYCQACAYKKGEHLVLVTADPEKGDKFALISGEHLVLVTA 163 (199)
Q Consensus 109 skCkiCK~kVhQ~G~kYCQ~CAYkKGiCAMCGk~~~~~~~~~~~i~g~~~~~~~~ 163 (199)
..|..|.....-... ...|+-||.. ..-|++|+-|.|...
T Consensus 71 ~~C~~Cg~~~~~~~~---------~~~CP~Cgs~------~~~i~~G~El~I~~i 110 (115)
T TIGR00100 71 CECEDCSEEVSPEID---------LYRCPKCHGI------MLQVRAGKELNLKSI 110 (115)
T ss_pred EEcccCCCEEecCCc---------CccCcCCcCC------CcEEecCCeEEEEEE
Confidence 478888876654321 2469999943 356899999988754
No 68
>PF07660 STN: Secretin and TonB N terminus short domain; InterPro: IPR011662 This is a conserved region found at the N-terminal region of bacterial proteins involved in either protein secretion or the uptake of selective substrates, including: Bundle-forming pilus protein B, an outer-membrane protein absolutely required for pilus biogenesis, and for enteropathogenic Escherichia coli localized adherence and autoaggregation []. PilQ, which is required for type IV pilus biogenesis and competence and is thought to function both as a pore for exit of the pilus and as a channel for entry of haem and antimicrobial agents and uptake of transforming DNA []. PupB, a specific receptor for the siderophores ferric pseudobactin BN8 and ferric pseudobactin BN7, iron chelating molecules that allow the organism to extract iron from the environment, especially under iron-restricted conditions []. TonB, which couples the electrochemical potential of the cytoplasmic membrane to the active transport of iron-siderophores and vitamin B12 across the outer membrane []. ; GO: 0019867 outer membrane; PDB: 2D1U_A 1ZZV_A 2W75_B 2O5P_A 2W77_A 2W16_A 2W6U_B 2W6T_A 2W76_B 2W78_B ....
Probab=32.69 E-value=58 Score=20.98 Aligned_cols=29 Identities=24% Similarity=0.338 Sum_probs=20.1
Q ss_pred eEEEEeecccchhhHHhhhhccccceEEE
Q psy11904 17 TSVRISFRHMVYEDALTILSYASPYEVQI 45 (199)
Q Consensus 17 ~s~ti~F~n~~yEDAl~iL~~a~PYkv~~ 45 (199)
..+++.+.|+.-|+||..|-.-.++..++
T Consensus 14 ~~vsl~~~~~~~~~~L~~ll~~t~l~y~~ 42 (52)
T PF07660_consen 14 KKVSLDVKNMSLEEALDQLLKGTGLTYKI 42 (52)
T ss_dssp BE--EE-EEE-HHHHHHHHTTTSTEEEEE
T ss_pred cceeEEcCCcCHHHHHHHHHccCCcEEEE
Confidence 35568999999999999988777766655
No 69
>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=32.41 E-value=7.8 Score=24.23 Aligned_cols=10 Identities=30% Similarity=1.075 Sum_probs=7.4
Q ss_pred CCcCCccccc
Q psy11904 122 GSHYCQACAY 131 (199)
Q Consensus 122 G~kYCQ~CAY 131 (199)
||.||..|+.
T Consensus 18 GH~fC~~C~~ 27 (39)
T PF13923_consen 18 GHSFCKECIE 27 (39)
T ss_dssp SEEEEHHHHH
T ss_pred CCchhHHHHH
Confidence 7778887764
No 70
>KOG2272|consensus
Probab=31.68 E-value=26 Score=32.68 Aligned_cols=52 Identities=25% Similarity=0.429 Sum_probs=37.5
Q ss_pred cccchhhhhhccCCCcccCcccchhhccccc-----CCCcCCcccccccC--CcccCCCCCC
Q psy11904 90 ENKALTASKARFNPYTQKFESCKICRQKVHQ-----VGSHYCQACAYKKG--EHLVLVTADP 144 (199)
Q Consensus 90 eNKLLSs~K~R~nPY~~~~skCkiCK~kVhQ-----~G~kYCQ~CAYkKG--iCAMCGk~~~ 144 (199)
.|-+|.- |-|||-.|.-+|..|+.-+.. .|..||..|--+-| ||.-|-++.-
T Consensus 148 D~~~l~f---r~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe 206 (332)
T KOG2272|consen 148 DEQPLTF---RGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE 206 (332)
T ss_pred ccccccc---cCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchH
Confidence 3467743 668888888899999987753 46789999976554 4666655554
No 71
>COG3814 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.48 E-value=32 Score=29.40 Aligned_cols=39 Identities=36% Similarity=0.413 Sum_probs=27.3
Q ss_pred ccccCCCCeeeEEEEeecccc-----hhhHHhhhhccccceEEEEEe
Q psy11904 7 TWALNNGDRITSVRISFRHMV-----YEDALTILSYASPYEVQIETE 48 (199)
Q Consensus 7 ~~~l~~GD~i~s~ti~F~n~~-----yEDAl~iL~~a~PYkv~~~l~ 48 (199)
-|.|.++|.-.|+|++|++.. -=|||+. .+.| .|.|+|+
T Consensus 71 fwdl~v~dtgFsv~lsF~~vpe~l~iPf~Al~~--FyDp-svnf~Le 114 (157)
T COG3814 71 FWDLKVTDTGFSVTLSFSGVPEKLYIPFDALRG--FYDP-SVNFELE 114 (157)
T ss_pred eecceecccceEEEEEeCCcceEEEeehHHhhh--hcCC-CccEEEE
Confidence 489999999999999999753 2356553 3333 4555555
No 72
>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=31.44 E-value=19 Score=26.58 Aligned_cols=12 Identities=8% Similarity=-0.277 Sum_probs=8.4
Q ss_pred ccCCcccCCCCC
Q psy11904 132 KKGEHLVLVTAD 143 (199)
Q Consensus 132 kKGiCAMCGk~~ 143 (199)
+.-+|.+||-+-
T Consensus 29 k~~VCnlCGFNP 40 (61)
T PF05715_consen 29 KSQVCNLCGFNP 40 (61)
T ss_pred hhhhhcccCCCC
Confidence 344799999654
No 73
>KOG3580|consensus
Probab=29.98 E-value=45 Score=34.70 Aligned_cols=45 Identities=20% Similarity=0.228 Sum_probs=35.2
Q ss_pred ccccccccCCCCeeeEEE-EeecccchhhHHhhhhccccceEEEEEe
Q psy11904 3 HCAETWALNNGDRITSVR-ISFRHMVYEDALTILSYASPYEVQIETE 48 (199)
Q Consensus 3 ~a~~~~~l~~GD~i~s~t-i~F~n~~yEDAl~iL~~a~PYkv~~~l~ 48 (199)
-|++.++|+|||.|+-+. +.-+||..-||-+++..+.- |+++.+-
T Consensus 231 LAardgnlqEGDiiLkINGtvteNmSLtDar~LIEkS~G-KL~lvVl 276 (1027)
T KOG3580|consen 231 LAARDGNLQEGDIILKINGTVTENMSLTDARKLIEKSRG-KLQLVVL 276 (1027)
T ss_pred hhhccCCcccccEEEEECcEeeccccchhHHHHHHhccC-ceEEEEE
Confidence 488999999999999853 34589999999999988764 5555443
No 74
>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=27.62 E-value=19 Score=24.65 Aligned_cols=22 Identities=41% Similarity=0.699 Sum_probs=17.9
Q ss_pred hhhhhhhhhhhcccCcccccCC
Q psy11904 51 IYFIMVCSKCEKKLGKVITPDN 72 (199)
Q Consensus 51 Iyf~MVC~KCEKKL~KLaTPD~ 72 (199)
|+....|..||++|-.+-+-|+
T Consensus 15 I~~~fIC~~CE~~iv~~~~~d~ 36 (46)
T PF10764_consen 15 IYGKFICSDCEKEIVNTETDDP 36 (46)
T ss_pred EECeEehHHHHHHhccCCCCCC
Confidence 4466789999999998877775
No 75
>KOG1892|consensus
Probab=26.47 E-value=63 Score=35.38 Aligned_cols=51 Identities=25% Similarity=0.306 Sum_probs=40.3
Q ss_pred ccccccccCCCCeeeEEE-EeecccchhhHHhhhhccccceEEEEEee--ehhhh
Q psy11904 3 HCAETWALNNGDRITSVR-ISFRHMVYEDALTILSYASPYEVQIETEK--EIYFI 54 (199)
Q Consensus 3 ~a~~~~~l~~GD~i~s~t-i~F~n~~yEDAl~iL~~a~PYkv~~~l~r--eIyf~ 54 (199)
||+--++|..||||+||. =+.=.|..|+|-.++-+..| .|.|++.| .||.+
T Consensus 972 aAd~DGRL~aGDQLLsVdG~SLiGisQErAA~lmtrtg~-vV~leVaKqgAiyhG 1025 (1629)
T KOG1892|consen 972 AADHDGRLEAGDQLLSVDGHSLIGISQERAARLMTRTGN-VVHLEVAKQGAIYHG 1025 (1629)
T ss_pred ccccccccccCceeeeecCcccccccHHHHHHHHhccCC-eEEEehhhhhhHHHH
Confidence 677889999999999943 13446889999999999887 58888865 46654
No 76
>PF07943 PBP5_C: Penicillin-binding protein 5, C-terminal domain; InterPro: IPR012907 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry contains proteins that are annotated as penicillin-binding protein 5 and 6. These belong to MEROPS peptidase family S11 (D-Ala-D-Ala carboxypeptidase A family, clan SE). Penicillin-binding protein 5 expressed by Escherichia coli functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain (IPR001967 from INTERPRO) is the catalytic domain. The C-terminal domain, this entry, is organised into a sandwich of two anti-parallel beta-sheets, and has a relatively hydrophobic surface as compared to the N-terminal domain. Its precise function is unknown; it may mediate interactions with other cell wall-synthesising enzymes, thus allowing the protein to be recruited to areas of active cell wall synthesis. It may also function as a linker domain that positions the active site in the catalytic domain closer to the peptidoglycan layer, to allow it to interact with cell wall peptides []. ; GO: 0009002 serine-type D-Ala-D-Ala carboxypeptidase activity, 0006508 proteolysis; PDB: 3A3J_A 3MFD_B 1XP4_D 3MZD_A 1NZU_A 1NJ4_A 1Z6F_A 3MZF_A 1NZO_A 3MZE_A ....
Probab=26.15 E-value=69 Score=22.50 Aligned_cols=20 Identities=5% Similarity=0.228 Sum_probs=17.2
Q ss_pred cccCCCCeeeEEEEeecccc
Q psy11904 8 WALNNGDRITSVRISFRHMV 27 (199)
Q Consensus 8 ~~l~~GD~i~s~ti~F~n~~ 27 (199)
..+..||+|+.++|+.++..
T Consensus 58 aPi~kG~~vG~~~v~~~~~~ 77 (91)
T PF07943_consen 58 APIKKGQVVGTLTVYLDGKL 77 (91)
T ss_dssp SGBGTTSEEEEEEEEETTEE
T ss_pred CcccCCCEEEEEEEEECCEE
Confidence 57899999999999887654
No 77
>PF13806 Rieske_2: Rieske-like [2Fe-2S] domain; PDB: 2JO6_A 3C0D_A 3D89_A 2JZA_A.
Probab=26.15 E-value=69 Score=24.36 Aligned_cols=54 Identities=22% Similarity=0.394 Sum_probs=36.9
Q ss_pred CCCCCCcceeeecceEEEEecCCCCCCcccccccccc-cCCceeeeeccC---ceeeccC
Q psy11904 143 DPEKGDKFALISGEHLVLVTADPEKGDKFAFDNHAFK-EGTPIIRTLEDD---KLKVSVP 198 (199)
Q Consensus 143 ~~~~~~~~~~i~g~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~---~~~~~~~ 198 (199)
+++.+.....+.|+.+.|.-. ..|..||.||.--- .+-|+.+-+-.| ...|.-|
T Consensus 11 L~~~~~~~~~v~g~~Ialf~~--~~~~vyAi~n~Cph~~~~~Ls~G~i~~~~g~~~V~CP 68 (104)
T PF13806_consen 11 LPPGEGRAVEVDGRQIALFRV--RDGEVYAIDNRCPHSQAGPLSDGLIGDGNGEPCVACP 68 (104)
T ss_dssp SCTTSEEEEEETTEEEEEEEE--STTEEEEEESBETTTTSSCGCGSEEEECTTEEEEEET
T ss_pred CCCCCcEEEEECCeEEEEEEe--CCCCEEEEeccCCccCCcccceeEEccCCCCEEEECC
Confidence 566677788888888888877 66899999997665 466655544333 3455444
No 78
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=25.78 E-value=33 Score=24.98 Aligned_cols=44 Identities=25% Similarity=0.160 Sum_probs=27.7
Q ss_pred cccchhhcccccCCCcCCcccccccCCcccCCCCCCCCCCcceeeecceE
Q psy11904 109 ESCKICRQKVHQVGSHYCQACAYKKGEHLVLVTADPEKGDKFALISGEHL 158 (199)
Q Consensus 109 skCkiCK~kVhQ~G~kYCQ~CAYkKGiCAMCGk~~~~~~~~~~~i~g~~~ 158 (199)
-+|..|..-.--- +-|-..-.|..||+.+.+.++--+.|.||-+
T Consensus 12 VkCp~C~n~q~vF------sha~t~V~C~~Cg~~L~~PtGGKa~i~~~i~ 55 (59)
T PRK00415 12 VKCPDCGNEQVVF------SHASTVVRCLVCGKTLAEPTGGKAKIKGEIL 55 (59)
T ss_pred EECCCCCCeEEEE------ecCCcEEECcccCCCcccCCCcceeeehhhh
Confidence 4788887633110 1133455899999999996655566666644
No 79
>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=25.08 E-value=13 Score=24.20 Aligned_cols=23 Identities=17% Similarity=0.388 Sum_probs=17.3
Q ss_pred CCc-CCccccccc----CCcccCCCCCC
Q psy11904 122 GSH-YCQACAYKK----GEHLVLVTADP 144 (199)
Q Consensus 122 G~k-YCQ~CAYkK----GiCAMCGk~~~ 144 (199)
||. +|..|+.+- ..|.+|-++..
T Consensus 21 gH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 21 GHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp CEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 566 888888776 89999987654
No 80
>PRK00420 hypothetical protein; Validated
Probab=24.98 E-value=34 Score=27.40 Aligned_cols=21 Identities=19% Similarity=0.574 Sum_probs=13.1
Q ss_pred Ccccchhhccccc--CCCcCCcc
Q psy11904 108 FESCKICRQKVHQ--VGSHYCQA 128 (199)
Q Consensus 108 ~skCkiCK~kVhQ--~G~kYCQ~ 128 (199)
...|..|...+-. .|..||+.
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~ 45 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPV 45 (112)
T ss_pred cCCCCCCCCcceecCCCceECCC
Confidence 3578888886653 45555544
No 81
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=24.69 E-value=89 Score=20.91 Aligned_cols=38 Identities=18% Similarity=0.384 Sum_probs=23.7
Q ss_pred ceee-ecceEEEEecC--CCCCCcccccccccccCCceeeeecc
Q psy11904 150 FALI-SGEHLVLVTAD--PEKGDKFAFDNHAFKEGTPIIRTLED 190 (199)
Q Consensus 150 ~~~i-~g~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~ 190 (199)
.|.| +|+-+.+.+.+ +..||.+++.... +.++++.|..
T Consensus 11 ~P~i~~gd~v~i~~~~~~~~~G~iv~~~~~~---~~~~ikrl~~ 51 (84)
T cd06462 11 EPTIPDGDLVLVDKSSYEPKRGDIVVFRLPG---GELTVKRVIG 51 (84)
T ss_pred cCcccCCCEEEEEecCCCCcCCEEEEEEcCC---CcEEEEEEEE
Confidence 3544 45544444444 5889999987654 5788877643
No 82
>KOG2836|consensus
Probab=24.32 E-value=30 Score=29.78 Aligned_cols=30 Identities=27% Similarity=0.234 Sum_probs=23.3
Q ss_pred ccchhhHHh-------------hhhccccceEEEEEeeehhhh
Q psy11904 25 HMVYEDALT-------------ILSYASPYEVQIETEKEIYFI 54 (199)
Q Consensus 25 n~~yEDAl~-------------iL~~a~PYkv~~~l~reIyf~ 54 (199)
.|+||||++ -|.|-+-|+-+-+|+..-.+.
T Consensus 123 gmkyedave~ir~krrga~n~kql~~lekyrpk~rlr~k~~~g 165 (173)
T KOG2836|consen 123 GMKYEDAVEMIRQKRRGAINSKQLLYLEKYRPKMRLRFKDPNG 165 (173)
T ss_pred cccHHHHHHHHHHHhhccccHHHHHHHHHhCccceeeccCCCC
Confidence 599999975 477889999888888665443
No 83
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=24.01 E-value=38 Score=30.88 Aligned_cols=32 Identities=22% Similarity=0.617 Sum_probs=24.1
Q ss_pred hccCCCcccCcccchhhcc-----cccCCCcCCcccc
Q psy11904 99 ARFNPYTQKFESCKICRQK-----VHQVGSHYCQACA 130 (199)
Q Consensus 99 ~R~nPY~~~~skCkiCK~k-----VhQ~G~kYCQ~CA 130 (199)
.++.-|+.....|+.|.+. +.+-+.+||..|-
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 4556677677899999764 4667889999993
No 84
>PRK10139 serine endoprotease; Provisional
Probab=23.53 E-value=1.1e+02 Score=28.88 Aligned_cols=45 Identities=18% Similarity=0.214 Sum_probs=25.6
Q ss_pred CccccccccCCCCeeeEEEEeecccch-hhHHhhhhccc-cceEEEEEee
Q psy11904 2 SHCAETWALNNGDRITSVRISFRHMVY-EDALTILSYAS-PYEVQIETEK 49 (199)
Q Consensus 2 s~a~~~~~l~~GD~i~s~ti~F~n~~y-EDAl~iL~~a~-PYkv~~~l~r 49 (199)
|||++. -|++||+|++ |....+.. +|....|.... --.|.+++.|
T Consensus 301 SpA~~A-GL~~GDvIl~--InG~~V~s~~dl~~~l~~~~~g~~v~l~V~R 347 (455)
T PRK10139 301 SGSAKA-GVKAGDIITS--LNGKPLNSFAELRSRIATTEPGTKVKLGLLR 347 (455)
T ss_pred ChHHHC-CCCCCCEEEE--ECCEECCCHHHHHHHHHhcCCCCEEEEEEEE
Confidence 566654 4899999998 54444332 33333443322 2357777765
No 85
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=23.06 E-value=1.4e+02 Score=24.28 Aligned_cols=51 Identities=24% Similarity=0.266 Sum_probs=33.5
Q ss_pred CcccCCCCCCCCCC-------------cceeeecceEEEEecCCCCCCcccccccccccCCce--eeeecc
Q psy11904 135 EHLVLVTADPEKGD-------------KFALISGEHLVLVTADPEKGDKFAFDNHAFKEGTPI--IRTLED 190 (199)
Q Consensus 135 iCAMCGk~~~~~~~-------------~~~~i~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~ 190 (199)
+|++||-.-+.... -.+|-.|...+|+-.=+-||--| ..|.||.+ ||-.++
T Consensus 21 iCpeC~~EW~~~~~~~~~~~~~~kDsnG~~L~dGDsV~liKDLkVKGss~-----~~K~GTkVknIrL~d~ 86 (109)
T TIGR00686 21 ICPSCLYEWNENEVNDDDDELIVKDCNGNLLANGDSVILIKDLKVKGSSL-----VLKKGTKIKNIRLVNG 86 (109)
T ss_pred ECccccccccccccccccCCceEEcCCCCCccCCCEEEEEeeccccCccc-----ceeCccEEEEEEecCC
Confidence 78888876654321 23455688888888777788654 46889976 554433
No 86
>KOG4458|consensus
Probab=23.02 E-value=35 Score=26.00 Aligned_cols=33 Identities=24% Similarity=0.481 Sum_probs=22.4
Q ss_pred hhccCCCcccCcccchhhcccccCCCcCCcccccccCCcc
Q psy11904 98 KARFNPYTQKFESCKICRQKVHQVGSHYCQACAYKKGEHL 137 (199)
Q Consensus 98 K~R~nPY~~~~skCkiCK~kVhQ~G~kYCQ~CAYkKGiCA 137 (199)
|.+++||.--.--=-.|+-.+|... ||+.|||-
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 4678898743233345666888754 99999995
No 87
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=22.85 E-value=48 Score=23.74 Aligned_cols=10 Identities=30% Similarity=0.879 Sum_probs=4.8
Q ss_pred cccchhhccc
Q psy11904 109 ESCKICRQKV 118 (199)
Q Consensus 109 skCkiCK~kV 118 (199)
.+|..|..++
T Consensus 6 ~~C~~Cg~~~ 15 (54)
T PF14446_consen 6 CKCPVCGKKF 15 (54)
T ss_pred ccChhhCCcc
Confidence 3445554444
No 88
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=22.65 E-value=29 Score=26.84 Aligned_cols=40 Identities=15% Similarity=0.206 Sum_probs=24.2
Q ss_pred cccchhhcccccCCCcCCcccccccCCcccCCCCCCCCCCcceeeecceEEEEec
Q psy11904 109 ESCKICRQKVHQVGSHYCQACAYKKGEHLVLVTADPEKGDKFALISGEHLVLVTA 163 (199)
Q Consensus 109 skCkiCK~kVhQ~G~kYCQ~CAYkKGiCAMCGk~~~~~~~~~~~i~g~~~~~~~~ 163 (199)
..|..|.....-.... -.|+.||.. ..-|++|+-|.|...
T Consensus 71 ~~C~~Cg~~~~~~~~~---------~~CP~Cgs~------~~~i~~G~el~i~~i 110 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFD---------FSCPRCGSP------DVEIISGRELRIKSI 110 (113)
T ss_dssp EEETTTS-EEECHHCC---------HH-SSSSSS-------EEEEESS-EEEEEE
T ss_pred EECCCCCCEEecCCCC---------CCCcCCcCC------CcEEccCCeEEEEEE
Confidence 4888888865442211 249999944 456999999988653
No 89
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=22.63 E-value=79 Score=21.87 Aligned_cols=19 Identities=37% Similarity=0.621 Sum_probs=13.1
Q ss_pred ecCCCCCCcccccccccccCCce
Q psy11904 162 TADPEKGDKFAFDNHAFKEGTPI 184 (199)
Q Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~ 184 (199)
.-||++||.. +....|||.
T Consensus 10 iYd~~~Gd~~----~~i~pGt~f 28 (50)
T cd00730 10 IYDPAEGDPD----EGIPPGTPF 28 (50)
T ss_pred EECCCCCCcc----cCcCCCCCH
Confidence 4588888853 566777774
No 90
>PHA02929 N1R/p28-like protein; Provisional
Probab=22.55 E-value=39 Score=30.08 Aligned_cols=37 Identities=27% Similarity=0.423 Sum_probs=27.7
Q ss_pred Ccccchhhcccc-------------cCCCcCCcccc----cccCCcccCCCCCC
Q psy11904 108 FESCKICRQKVH-------------QVGSHYCQACA----YKKGEHLVLVTADP 144 (199)
Q Consensus 108 ~skCkiCK~kVh-------------Q~G~kYCQ~CA----YkKGiCAMCGk~~~ 144 (199)
...|.||-..+. .=||.||..|- -.+..|+||-.++.
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~~~tCPlCR~~~~ 227 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhcCCCCCCCCCEee
Confidence 358999987643 23788999996 35779999987654
No 91
>COG3684 LacD Tagatose-1,6-bisphosphate aldolase [Carbohydrate transport and metabolism]
Probab=22.50 E-value=29 Score=32.39 Aligned_cols=60 Identities=27% Similarity=0.234 Sum_probs=43.0
Q ss_pred ccccCCcccCCCCCCCCCCcceeeecceEEEEecCCCCCCc---ccccccccccCCceeeeeccCceeeccCC
Q psy11904 130 AYKKGEHLVLVTADPEKGDKFALISGEHLVLVTADPEKGDK---FAFDNHAFKEGTPIIRTLEDDKLKVSVPG 199 (199)
Q Consensus 130 AYkKGiCAMCGk~~~~~~~~~~~i~g~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 199 (199)
||-+-+=+-|+-. ..|.+ +-.+|-||.-||+ |.-..|...|++-+.-.---|-|||.||+
T Consensus 147 a~ierigsec~ae------di~f~----lE~ltyd~~~~d~~eyak~kp~kV~~a~k~fsd~GadvlKvevPv 209 (306)
T COG3684 147 AYIERIGSECHAE------DLPFF----LEPLTYDPRIGDKEEYAKRKPQKVIEAMKEFSDSGADVLKVEVPV 209 (306)
T ss_pred HHHHHHHHHhhhc------CCcee----EeeeecCCCCCChHHHHhhchHHHHHHHHHhccCCCceEEeecce
Confidence 5555555666622 23333 5678999999999 66666888888877766677899999995
No 92
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.97 E-value=55 Score=32.44 Aligned_cols=21 Identities=14% Similarity=0.314 Sum_probs=16.3
Q ss_pred CCcCCcccccccC---CcccCCCC
Q psy11904 122 GSHYCQACAYKKG---EHLVLVTA 142 (199)
Q Consensus 122 G~kYCQ~CAYkKG---iCAMCGk~ 142 (199)
+.-.|+.|-|... .|.-||..
T Consensus 407 ~~l~Ch~Cg~~~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 407 RRLRCHHCGYQEPIPKACPECGST 430 (679)
T ss_pred CeEECCCCcCCCCCCCCCCCCcCC
Confidence 3346999999865 79999875
No 93
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=21.94 E-value=38 Score=29.65 Aligned_cols=29 Identities=21% Similarity=0.669 Sum_probs=19.3
Q ss_pred CCCcccCcccchhhcccc-----cCCCcCCcccc
Q psy11904 102 NPYTQKFESCKICRQKVH-----QVGSHYCQACA 130 (199)
Q Consensus 102 nPY~~~~skCkiCK~kVh-----Q~G~kYCQ~CA 130 (199)
.-|+.....|..|.+.+. .-+..||..|-
T Consensus 239 ~Vy~R~g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 239 QVYGREGEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred EEcCCCCCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 345544568999987664 23568888883
No 94
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.52 E-value=42 Score=29.56 Aligned_cols=29 Identities=31% Similarity=0.757 Sum_probs=19.5
Q ss_pred cCCCcccCcccchhhcccc-----cCCCcCCccc
Q psy11904 101 FNPYTQKFESCKICRQKVH-----QVGSHYCQAC 129 (199)
Q Consensus 101 ~nPY~~~~skCkiCK~kVh-----Q~G~kYCQ~C 129 (199)
+.-|+.....|..|.+.|. +-+..||..|
T Consensus 237 ~~Vy~R~g~pCprCG~~I~~~~~~gR~t~~CP~C 270 (272)
T PRK14810 237 HRVYQRTGEPCLNCKTPIRRVVVAGRSSHYCPHC 270 (272)
T ss_pred EeecCCCCCcCCCCCCeeEEEEECCCccEECcCC
Confidence 3455555678999987664 3456788877
No 95
>PHA02054 hypothetical protein
Probab=21.13 E-value=51 Score=26.02 Aligned_cols=14 Identities=43% Similarity=0.555 Sum_probs=11.0
Q ss_pred EEEEecCCCCCCcc
Q psy11904 158 LVLVTADPEKGDKF 171 (199)
Q Consensus 158 ~~~~~~~~~~~~~~ 171 (199)
.-||.||||.||--
T Consensus 15 ~h~v~a~pe~Gsyd 28 (94)
T PHA02054 15 VHLVSANPEVGSYD 28 (94)
T ss_pred hheeecCCCCCCHH
Confidence 34789999999843
No 96
>cd03539 Rieske_RO_Alpha_S5H This alignment model represents the N-terminal rieske iron-sulfur domain of the oxygenase alpha subunit (NagG) of salicylate 5-hydroxylase (S5H). S5H converts salicylate (2-hydroxybenzoate), a metabolic intermediate of phenanthrene, to gentisate (2,5-dihydroxybenzoate) as part of an alternate pathway for naphthalene catabolism. S5H is a multicomponent enzyme made up of NagGH (the oxygenase components), NagAa (the ferredoxin reductase component), and NagAb (the ferredoxin component). The oxygenase component is made up of alpha (NagG) and beta (NagH) subunits.
Probab=21.04 E-value=2.4e+02 Score=22.07 Aligned_cols=45 Identities=27% Similarity=0.326 Sum_probs=31.2
Q ss_pred CCCCCCcceeeecceEEEEecCCCCCCcccccccccccCCceeeee
Q psy11904 143 DPEKGDKFALISGEHLVLVTADPEKGDKFAFDNHAFKEGTPIIRTL 188 (199)
Q Consensus 143 ~~~~~~~~~~i~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 188 (199)
+++.++-..+.-|+..+||+.+ +.|..+||+|----.|.|+.+..
T Consensus 10 l~~~g~~~~~~~~~~~v~v~r~-~dg~v~A~~n~C~Hrg~~L~~g~ 54 (129)
T cd03539 10 IPNPGDFKRTLIGERSVIMTRD-PDGGINVVENVCAHRGMRFCRER 54 (129)
T ss_pred CCCCCCEEEEEECCcEEEEEEC-CCCCEEEEeccCcCCCCEeeeec
Confidence 4444555555456666666655 46899999998888899988643
No 97
>PLN00209 ribosomal protein S27; Provisional
Probab=20.89 E-value=62 Score=25.25 Aligned_cols=45 Identities=16% Similarity=0.026 Sum_probs=31.7
Q ss_pred cccchhhcccccCCCcCCcccccccCCcccCCCCCCC-CCCcceeeecceEE
Q psy11904 109 ESCKICRQKVHQVGSHYCQACAYKKGEHLVLVTADPE-KGDKFALISGEHLV 159 (199)
Q Consensus 109 skCkiCK~kVhQ~G~kYCQ~CAYkKGiCAMCGk~~~~-~~~~~~~i~g~~~~ 159 (199)
-+|..|..---- =+.|--.-.|..||+.+.+ +++|+-|..|=.|.
T Consensus 37 VkCp~C~n~q~V------FShA~t~V~C~~Cg~~L~~PTGGKa~l~~gc~fr 82 (86)
T PLN00209 37 VKCQGCFNITTV------FSHSQTVVVCGSCQTVLCQPTGGKARLTEGCSFR 82 (86)
T ss_pred EECCCCCCeeEE------EecCceEEEccccCCEeeccCCCCeEecCCceEE
Confidence 589888762211 0124556689999999998 78888888886654
No 98
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=20.65 E-value=53 Score=25.25 Aligned_cols=28 Identities=25% Similarity=0.342 Sum_probs=20.6
Q ss_pred ecccchhhHHhhhhccccceEEEEEeeeh
Q psy11904 23 FRHMVYEDALTILSYASPYEVQIETEKEI 51 (199)
Q Consensus 23 F~n~~yEDAl~iL~~a~PYkv~~~l~reI 51 (199)
.++|.++||+.+|++ +|++..-.+.+-|
T Consensus 20 IrG~~v~~A~~~L~f-~pkk~a~~i~klL 47 (103)
T TIGR01044 20 IRGKSVSQALDILRF-TPKKAAPLIKKVL 47 (103)
T ss_pred HcCCcHHHHHHHHhh-CCHhHHHHHHHHH
Confidence 367999999999997 5777655555433
No 99
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=20.49 E-value=57 Score=25.42 Aligned_cols=46 Identities=17% Similarity=0.015 Sum_probs=31.7
Q ss_pred CcccchhhcccccCCCcCCcccccccCCcccCCCCCCC-CCCcceeeecceEE
Q psy11904 108 FESCKICRQKVHQVGSHYCQACAYKKGEHLVLVTADPE-KGDKFALISGEHLV 159 (199)
Q Consensus 108 ~skCkiCK~kVhQ~G~kYCQ~CAYkKGiCAMCGk~~~~-~~~~~~~i~g~~~~ 159 (199)
.-+|..|..-.--- +-|--.-.|..||+.+.+ .++++-|..|=.|.
T Consensus 35 ~VkCp~C~n~q~VF------ShA~t~V~C~~Cg~~L~~PTGGKa~l~~gc~fr 81 (85)
T PTZ00083 35 DVKCPGCSQITTVF------SHAQTVVLCGGCSSQLCQPTGGKAKLTEGCSFR 81 (85)
T ss_pred EEECCCCCCeeEEE------ecCceEEEccccCCEeeccCCCCeEecCCceEE
Confidence 35898887622110 114455689999999988 78888888886653
No 100
>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=20.17 E-value=27 Score=20.95 Aligned_cols=21 Identities=19% Similarity=0.654 Sum_probs=9.4
Q ss_pred ccchhhccccc-----CCCcCCcccc
Q psy11904 110 SCKICRQKVHQ-----VGSHYCQACA 130 (199)
Q Consensus 110 kCkiCK~kVhQ-----~G~kYCQ~CA 130 (199)
+|..|...+.. ....||..|.
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 67777765432 2346777664
Done!