Query 011854
Match_columns 476
No_of_seqs 354 out of 1684
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 05:57:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011854.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011854hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12315 DUF3633: Protein of u 100.0 1E-76 2.2E-81 555.5 15.7 208 265-472 1-212 (212)
2 KOG1703 Adaptor protein Enigma 99.9 1.1E-25 2.4E-30 241.0 5.6 334 111-475 132-479 (479)
3 KOG1701 Focal adhesion adaptor 99.8 1.8E-22 3.8E-27 205.3 -2.2 163 112-307 273-438 (468)
4 KOG2272 Focal adhesion protein 99.8 3.1E-22 6.7E-27 191.1 -2.6 166 112-314 72-252 (332)
5 KOG4577 Transcription factor L 99.8 3.1E-20 6.8E-25 180.2 -3.6 123 112-246 32-154 (383)
6 KOG1701 Focal adhesion adaptor 99.6 1.6E-17 3.6E-22 169.3 0.2 128 106-245 327-462 (468)
7 KOG2272 Focal adhesion protein 99.6 1.5E-17 3.3E-22 159.2 -0.2 125 106-245 188-312 (332)
8 KOG1044 Actin-binding LIM Zn-f 99.5 1.3E-15 2.8E-20 160.1 2.2 118 111-243 131-248 (670)
9 KOG1703 Adaptor protein Enigma 99.5 1.8E-15 3.9E-20 162.5 0.6 119 110-242 360-478 (479)
10 PF00412 LIM: LIM domain; Int 99.3 2.2E-12 4.8E-17 98.6 2.8 57 116-172 1-58 (58)
11 KOG1044 Actin-binding LIM Zn-f 99.1 1.4E-10 3.1E-15 122.6 7.4 165 113-311 16-187 (670)
12 KOG1700 Regulatory protein MLP 98.7 2.5E-09 5.4E-14 102.6 0.5 123 111-247 5-168 (200)
13 PF00412 LIM: LIM domain; Int 98.4 2.1E-07 4.6E-12 70.9 4.0 57 176-245 1-57 (58)
14 smart00132 LIM Zinc-binding do 98.3 5.6E-07 1.2E-11 62.5 2.9 37 115-151 1-38 (39)
15 KOG1700 Regulatory protein MLP 97.5 3.1E-05 6.7E-10 74.4 0.6 64 109-172 104-167 (200)
16 KOG1702 Nebulin repeat protein 97.4 1.9E-05 4.1E-10 74.8 -1.6 58 114-171 5-62 (264)
17 KOG4577 Transcription factor L 97.4 2.6E-05 5.7E-10 77.0 -1.6 70 107-176 86-158 (383)
18 KOG0490 Transcription factor, 97.1 0.0001 2.2E-09 71.3 -0.8 114 118-244 1-118 (235)
19 PF13485 Peptidase_MA_2: Pepti 96.9 0.0042 9.1E-08 53.3 7.7 107 351-470 19-127 (128)
20 smart00132 LIM Zinc-binding do 96.8 0.00096 2.1E-08 45.9 2.5 37 175-222 1-37 (39)
21 PF10026 DUF2268: Predicted Zn 84.5 1.4 3E-05 42.1 4.5 43 357-399 65-113 (195)
22 TIGR02412 pepN_strep_liv amino 75.2 8.6 0.00019 44.8 7.9 41 358-398 288-330 (831)
23 smart00726 UIM Ubiquitin-inter 73.5 2.8 6E-05 27.2 1.9 21 43-63 1-21 (26)
24 PF02809 UIM: Ubiquitin intera 71.9 2.4 5.2E-05 25.1 1.2 16 43-58 2-17 (18)
25 PF14835 zf-RING_6: zf-RING of 69.5 4.4 9.5E-05 32.1 2.6 47 141-187 8-54 (65)
26 PF01433 Peptidase_M1: Peptida 67.9 2.1 4.5E-05 44.4 0.7 44 356-399 294-339 (390)
27 KOG0320 Predicted E3 ubiquitin 67.4 2.1 4.6E-05 40.4 0.5 48 138-185 129-179 (187)
28 PF10460 Peptidase_M30: Peptid 64.5 4.7 0.0001 42.4 2.4 43 356-398 138-186 (366)
29 PRK14873 primosome assembly pr 63.7 5.1 0.00011 45.5 2.7 37 142-181 394-430 (665)
30 PF04450 BSP: Peptidase of pla 63.6 4.1 8.9E-05 39.4 1.7 92 357-467 96-192 (205)
31 KOG1280 Uncharacterized conser 62.2 4.7 0.0001 41.7 1.9 73 113-221 8-88 (381)
32 TIGR00595 priA primosomal prot 60.2 6.9 0.00015 43.0 2.9 37 142-181 224-261 (505)
33 COG4357 Zinc finger domain con 59.2 1.7 3.8E-05 36.8 -1.4 50 115-164 37-86 (105)
34 PF06114 DUF955: Domain of unk 58.4 6.1 0.00013 33.1 1.7 52 344-395 29-86 (122)
35 PF00595 PDZ: PDZ domain (Also 54.5 3.7 8.1E-05 32.8 -0.2 27 321-347 43-69 (81)
36 PF11781 RRN7: RNA polymerase 53.8 7.5 0.00016 27.1 1.2 25 141-169 9-33 (36)
37 PF14891 Peptidase_M91: Effect 51.9 6.4 0.00014 36.8 0.8 21 352-375 101-121 (174)
38 PF13699 DUF4157: Domain of un 51.5 5.6 0.00012 32.6 0.3 16 359-374 63-78 (79)
39 PHA02456 zinc metallopeptidase 49.1 5.9 0.00013 34.7 0.1 18 358-375 80-98 (141)
40 PF10367 Vps39_2: Vacuolar sor 49.0 12 0.00026 31.4 2.0 30 112-141 77-107 (109)
41 PRK14890 putative Zn-ribbon RN 48.7 15 0.00033 28.5 2.3 13 113-125 7-19 (59)
42 COG2191 Formylmethanofuran deh 48.6 8.4 0.00018 37.2 1.1 16 156-171 188-203 (206)
43 PF10263 SprT-like: SprT-like 48.5 8.4 0.00018 34.9 1.1 23 352-374 55-77 (157)
44 PF01431 Peptidase_M13: Peptid 48.2 5.7 0.00012 37.7 -0.1 15 357-371 36-50 (206)
45 COG2856 Predicted Zn peptidase 47.7 26 0.00056 34.2 4.3 55 344-398 59-120 (213)
46 PF14471 DUF4428: Domain of un 46.6 15 0.00032 27.7 1.9 30 214-245 1-30 (51)
47 smart00504 Ubox Modified RING 45.8 14 0.0003 27.9 1.7 44 141-185 2-47 (63)
48 PRK05580 primosome assembly pr 44.8 16 0.00035 41.5 2.8 11 359-369 556-566 (679)
49 PF05299 Peptidase_M61: M61 gl 43.0 15 0.00032 32.8 1.7 42 358-399 5-59 (122)
50 PF10235 Cript: Microtubule-as 42.9 15 0.00032 31.1 1.5 36 142-185 46-81 (90)
51 PF13240 zinc_ribbon_2: zinc-r 42.6 14 0.00031 23.1 1.1 8 116-123 2-9 (23)
52 PRK14559 putative protein seri 42.5 21 0.00045 40.5 3.1 11 251-261 124-134 (645)
53 PHA00527 hypothetical protein 42.1 55 0.0012 28.4 4.9 63 327-394 47-113 (129)
54 COG5504 Predicted Zn-dependent 42.1 17 0.00036 36.4 2.0 36 358-394 141-183 (280)
55 KOG2199 Signal transducing ada 41.5 16 0.00035 38.7 1.9 26 40-65 161-186 (462)
56 COG1645 Uncharacterized Zn-fin 41.1 15 0.00032 33.2 1.4 22 142-168 30-51 (131)
57 COG1198 PriA Primosomal protei 41.0 34 0.00073 39.4 4.5 49 113-182 435-484 (730)
58 PRK14015 pepN aminopeptidase N 39.9 63 0.0014 38.1 6.6 42 357-398 296-339 (875)
59 PF09943 DUF2175: Uncharacteri 39.2 8.7 0.00019 33.1 -0.4 26 116-141 5-31 (101)
60 PF13920 zf-C3HC4_3: Zinc fing 39.1 21 0.00045 26.1 1.7 42 142-184 4-48 (50)
61 PF10391 DNA_pol_lambd_f: Fing 38.1 33 0.00072 25.8 2.7 27 443-471 6-32 (52)
62 PF10083 DUF2321: Uncharacteri 37.9 17 0.00036 33.7 1.2 55 161-228 28-84 (158)
63 PF14634 zf-RING_5: zinc-RING 37.8 19 0.00042 25.6 1.4 38 143-180 2-43 (44)
64 TIGR02411 leuko_A4_hydro leuko 37.7 18 0.00039 40.6 1.7 39 359-397 281-321 (601)
65 KOG1702 Nebulin repeat protein 37.7 9.1 0.0002 37.0 -0.5 42 208-251 27-72 (264)
66 PF08394 Arc_trans_TRASH: Arch 36.9 19 0.00042 25.4 1.1 30 116-148 1-31 (37)
67 KOG1813 Predicted E3 ubiquitin 36.8 19 0.0004 36.8 1.4 45 140-185 241-287 (313)
68 PF10367 Vps39_2: Vacuolar sor 36.0 24 0.00051 29.5 1.8 13 173-185 78-90 (109)
69 PRK04023 DNA polymerase II lar 34.4 41 0.00088 39.8 3.8 37 141-185 639-675 (1121)
70 cd00162 RING RING-finger (Real 34.1 18 0.0004 24.4 0.7 39 143-181 2-43 (45)
71 KOG4739 Uncharacterized protei 33.9 24 0.00053 34.8 1.7 34 152-185 15-49 (233)
72 KOG2932 E3 ubiquitin ligase in 33.5 19 0.00042 36.9 1.0 44 142-185 92-135 (389)
73 KOG0320 Predicted E3 ubiquitin 32.3 21 0.00046 33.8 1.0 50 210-260 129-178 (187)
74 COG0308 PepN Aminopeptidase N 31.7 1.9E+02 0.004 34.1 8.8 45 355-399 305-351 (859)
75 smart00731 SprT SprT homologue 31.5 22 0.00048 32.2 1.0 20 355-374 57-76 (146)
76 PF12674 Zn_ribbon_2: Putative 31.4 24 0.00053 29.1 1.1 31 214-244 2-35 (81)
77 PF14446 Prok-RING_1: Prokaryo 31.3 25 0.00053 26.9 1.0 14 113-126 5-18 (54)
78 PF12773 DZR: Double zinc ribb 30.5 42 0.00091 24.4 2.2 11 174-184 13-23 (50)
79 PF06677 Auto_anti-p27: Sjogre 30.4 32 0.00069 24.8 1.4 22 142-167 19-40 (41)
80 TIGR02420 dksA RNA polymerase- 29.7 18 0.00039 31.3 0.1 31 111-147 78-108 (110)
81 PF09768 Peptidase_M76: Peptid 29.2 19 0.0004 34.1 0.1 16 357-372 71-86 (173)
82 cd00136 PDZ PDZ domain, also c 29.0 9.3 0.0002 29.2 -1.7 25 319-343 29-53 (70)
83 PF13834 DUF4193: Domain of un 28.0 18 0.00039 31.0 -0.2 28 213-241 71-98 (99)
84 PRK00420 hypothetical protein; 26.6 39 0.00085 29.7 1.6 22 142-167 25-46 (112)
85 PF06689 zf-C4_ClpX: ClpX C4-t 26.3 63 0.0014 23.0 2.4 32 214-245 3-34 (41)
86 KOG3552 FERM domain protein FR 26.1 23 0.00051 41.3 0.2 23 320-342 91-113 (1298)
87 KOG0978 E3 ubiquitin ligase in 26.0 18 0.00039 41.1 -0.7 29 159-187 661-692 (698)
88 PF10083 DUF2321: Uncharacteri 25.9 28 0.00061 32.3 0.6 52 113-184 28-79 (158)
89 PF01421 Reprolysin: Reprolysi 25.8 39 0.00084 31.9 1.6 25 344-368 118-142 (199)
90 COG2888 Predicted Zn-ribbon RN 25.7 25 0.00054 27.4 0.2 26 214-244 11-36 (61)
91 PF03854 zf-P11: P-11 zinc fin 24.4 37 0.00079 25.4 0.8 31 155-185 9-47 (50)
92 PF01258 zf-dskA_traR: Prokary 24.3 9.6 0.00021 26.2 -2.1 8 116-123 6-13 (36)
93 KOG3209 WW domain-containing p 24.1 9.3 0.0002 43.2 -3.3 27 316-342 937-963 (984)
94 COG2191 Formylmethanofuran deh 23.9 30 0.00065 33.5 0.4 30 213-244 173-202 (206)
95 PRK14714 DNA polymerase II lar 23.5 61 0.0013 39.4 2.8 51 112-185 666-721 (1337)
96 COG4784 Putative Zn-dependent 23.3 62 0.0013 34.0 2.5 107 346-474 108-220 (479)
97 cd04270 ZnMc_TACE_like Zinc-de 23.1 32 0.00069 34.0 0.4 22 348-369 156-179 (244)
98 PF01447 Peptidase_M4: Thermol 23.0 29 0.00063 31.9 0.1 13 358-370 136-148 (150)
99 PF06827 zf-FPG_IleRS: Zinc fi 23.0 38 0.00083 22.1 0.7 13 173-185 1-13 (30)
100 KOG3624 M13 family peptidase [ 22.9 63 0.0014 36.7 2.8 71 357-463 518-605 (687)
101 cd04267 ZnMc_ADAM_like Zinc-de 22.8 38 0.00082 31.6 0.9 25 344-369 121-145 (192)
102 COG1088 RfbB dTDP-D-glucose 4, 22.6 58 0.0013 33.7 2.1 29 421-449 184-213 (340)
103 PF13923 zf-C3HC4_2: Zinc fing 22.3 50 0.0011 22.7 1.2 28 143-170 1-28 (39)
104 PF01435 Peptidase_M48: Peptid 21.8 33 0.00072 32.4 0.3 28 345-372 73-104 (226)
105 PLN03208 E3 ubiquitin-protein 21.2 66 0.0014 31.0 2.1 29 140-169 18-46 (193)
106 PRK03564 formate dehydrogenase 20.9 1.2E+02 0.0025 31.4 4.0 28 204-233 218-245 (309)
107 cd04269 ZnMc_adamalysin_II_lik 20.6 60 0.0013 30.4 1.7 25 345-369 119-143 (194)
108 PF07607 DUF1570: Protein of u 20.2 58 0.0013 29.2 1.5 32 359-390 3-38 (128)
109 TIGR02414 pepN_proteo aminopep 20.2 55 0.0012 38.5 1.6 41 357-397 283-325 (863)
No 1
>PF12315 DUF3633: Protein of unknown function (DUF3633); InterPro: IPR022087 This domain family is found in bacteria and eukaryotes, and is approximately 210 amino acids in length. The family is found in association with PF00412 from PFAM.
Probab=100.00 E-value=1e-76 Score=555.45 Aligned_cols=208 Identities=72% Similarity=1.152 Sum_probs=199.1
Q ss_pred HhcccccccccceeeehhhhhhhhcCCCCCcccccccCCccCCcccccccccccccCCCCCccccccccccccccccceE
Q 011854 265 SIHMKLEQQIPLLLVERQALNEARDGEKNGYYHMPETRGLCLSEEQTVTTVLWRPRFGPGNQARNIITEPYKLTRRCDVT 344 (476)
Q Consensus 265 gl~~~~~~~~Pv~LV~~~aln~a~e~e~~g~~~~~e~rGlclseeq~~~s~~~~~~~~~g~ri~e~~~~p~~~~~~~ev~ 344 (476)
+|||++++++|++||+++|||+|.++|++|+++.++||||||||+|+|++++++|++++|++++++.++|+++++.|+|+
T Consensus 1 ~lnmki~q~~PllLVe~~aLN~a~~~Ek~~~~~~~~tRGLclseeq~v~sv~~~p~~~~~~~~~~~~~e~~~~~~~~eV~ 80 (212)
T PF12315_consen 1 GLNMKIEQEIPLLLVERQALNEAEEGEKIGHHHMPETRGLCLSEEQTVTSVLRRPRMGPGNQLIDMSTEPQRLTRGCEVT 80 (212)
T ss_pred CCCCcccCCCCeEEecHHHHHHHHhhccCCCCCCeeeeeeeeeeeEEEEEEEecCCcCCCCccceeeecceeeccceeEE
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEecCchhHHhhhhhhccchhhhhhhcCCCCCCcchhhhHHHHHHHHHHhhhcccCCCCCC----CCCCCcCCCCCCC
Q 011854 345 AILILYGLPRLLTGTILAHEMMHGWMRLQGFRTLSPDVEEGICQVIAHWWLISQLKSSKKVTP----TSSSSAAGTSKKG 420 (476)
Q Consensus 345 ~il~l~glp~~l~g~ilaHe~~Ha~l~~~g~~~l~~~~eEG~cq~~a~~wl~~~~~~~~~~~~----~~~~~~~~~~~~~ 420 (476)
+|+|||||||+|||||||||+||||||++|||+|+++||||||||||||||++|++++.++.. ++++|++++||||
T Consensus 81 ~Ilvl~GLPrll~gsiLAHE~mHa~Lrl~g~~~L~~~vEEGiCqvla~~wL~~~~~~~~~~~~~~s~~~s~~~~~~skkg 160 (212)
T PF12315_consen 81 AILVLYGLPRLLTGSILAHELMHAWLRLNGFPNLSPEVEEGICQVLAYLWLESELASGSGSSSSSSSSSSSSASSSSKKG 160 (212)
T ss_pred EEEEECCCCHHHHhhHHHHHHHHHHhcccCCCCCChHHHHHHHHHHHHHHHhhhhhcccCCcccccCCCCCCcccccccc
Confidence 999999999999999999999999999999999999999999999999999999998876322 2345677788999
Q ss_pred CCchhHHHHHHHHHhhhhcCCCCCChhhHHHHHHHHHHhCHHHHHHHHHhhC
Q 011854 421 TGPKFDKKLGEFFKHQIETDASPVYGDGFRAGQHAVQKYGLGRTLDHIRRTG 472 (476)
Q Consensus 421 ~~~~~~~~l~~~~~~qi~~d~s~~yG~Gfr~~~~~~~~~gl~~~l~~~~~~g 472 (476)
++|+||+||++||+||||+|+|||||||||+|++||++|||++||+|||+||
T Consensus 161 ~~s~~E~kL~~f~~~qIe~D~SpvYGdGFRaa~~av~~~GL~~tLdhir~tg 212 (212)
T PF12315_consen 161 AKSQFEKKLGEFFKHQIETDTSPVYGDGFRAANEAVEKYGLRRTLDHIRRTG 212 (212)
T ss_pred cccHHHHHHHHHHHHHhccCCCcccchHHHHHHHHHHHhCHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999999999998
No 2
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.91 E-value=1.1e-25 Score=240.95 Aligned_cols=334 Identities=44% Similarity=0.699 Sum_probs=278.6
Q ss_pred CCCcccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCcccccccccc-cccccccccCCcccCCCCc
Q 011854 111 EGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYRE-HYHPKCDVCKHFIPSNHGG 189 (476)
Q Consensus 111 ~~~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~-~f~~~C~~C~~~I~~~~~g 189 (476)
.....|.+|.-.|..+..+ ||+|..|..++.. +...||.. .-...|.+|...|..+..+
T Consensus 132 ~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~p~~~----------~~~~~~~~~~~~~~~~v~~~~~~~~~~~ 191 (479)
T KOG1703|consen 132 PLDSICGGCNSAIEHGRSV----------CFQCKRCSEPLSG----------FPKPSYHESGRSKNEDVEEASSPSSRAG 191 (479)
T ss_pred cccccccCCCcccccccch----------hhhhcccccccCC----------cccccccccccccccccccccccccccc
Confidence 3456799999988766555 8999999888822 23344444 3567899999999988878
Q ss_pred ceEEcccCccccccCCCCccCCCCccCCCCcccCCCCceEEecCCcccchhhHhhhccCCCCCCcchhhHHHHHHHhccc
Q 011854 190 LIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQPLYLDIQEFYESIHMK 269 (476)
Q Consensus 190 ~i~~~~hpfw~qkyC~~h~H~~CF~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~~~v~d~~~Cqp~~~~I~~f~~gl~~~ 269 (476)
.+.++.++||.++||+.|.++.+..|..|++....+..|+.+.+++.+|.+|....+|+.+.|++++..+..++.+..+.
T Consensus 192 ~~~~~~~~~~~~~~~~~~e~~~tp~~~~~~r~e~~~~~~~~l~~~~~~~~~~~~~~~~~~p~~~p~~~~~~~~~~~~~~~ 271 (479)
T KOG1703|consen 192 LILSRSHPFWKQKYCPSHENDGTPKCCSCERLEPLDTRYVELADGRALCLECMGSASMDSPECQPLVSAPRPASEGLHMK 271 (479)
T ss_pred ccccccchhhhhcccccccCCCCCCcccccccccccccceecccchhhhhhccCCcccCCCccCcceecccccccccccc
Confidence 89999999999999999999999999999998766888998999999999999888899999999999999999999999
Q ss_pred ccccccceeeehhhhhhhhcCCCCCcccccccCCccCCcccccccccccccCCCCCccccccccccccccccceEEEEEe
Q 011854 270 LEQQIPLLLVERQALNEARDGEKNGYYHMPETRGLCLSEEQTVTTVLWRPRFGPGNQARNIITEPYKLTRRCDVTAILIL 349 (476)
Q Consensus 270 ~~~~~Pv~LV~~~aln~a~e~e~~g~~~~~e~rGlclseeq~~~s~~~~~~~~~g~ri~e~~~~p~~~~~~~ev~~il~l 349 (476)
..+..++.+++.++++.+.++......+ ..++++|.++.++++++ ..|..++++.-+....|++.++.++
T Consensus 272 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~p~c~~c~~~i~~~---------~~i~~~~~~~h~~~~~c~~~~~~~~ 341 (479)
T KOG1703|consen 272 VEKELPLLLVESEALKKLREEEKPAEYH-NVTRPLCLSCNQKIRSV---------KVIVALGKEWHPEHFSCEVCAIVIL 341 (479)
T ss_pred cccccchhhccccccccccccccccccc-ccccccccccccCcccc---------eeEeeccccccccceeecccccccc
Confidence 9999999999999999987766544433 37889999999887553 4467888888889999999999999
Q ss_pred cCchhHHhhhhhhccchhhhhhhcCCCCCCcchhhhHHHHHHHHHHhhhcccCCC-CCCCCCC--------CcCCCCCCC
Q 011854 350 YGLPRLLTGTILAHEMMHGWMRLQGFRTLSPDVEEGICQVIAHWWLISQLKSSKK-VTPTSSS--------SAAGTSKKG 420 (476)
Q Consensus 350 ~glp~~l~g~ilaHe~~Ha~l~~~g~~~l~~~~eEG~cq~~a~~wl~~~~~~~~~-~~~~~~~--------~~~~~~~~~ 420 (476)
++.|+..+|.+++||+||+|++.++.+.+.+.++++||++ +.+|+....+-..- ..-..++ .+....+++
T Consensus 342 ~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~-~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~ 420 (479)
T KOG1703|consen 342 DGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCAL-GRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKL 420 (479)
T ss_pred CCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhc-cCeechhceeeecccCCCCCCcccccCCccchhhhHhhh
Confidence 9999999999999999999999999999999999999999 99999988765421 1111111 112233444
Q ss_pred C--CchhHHHHHHHHHhhhhcCCCCCChhhHHHHHHHHHHh--CHHHHHHHHHhhCCCC
Q 011854 421 T--GPKFDKKLGEFFKHQIETDASPVYGDGFRAGQHAVQKY--GLGRTLDHIRRTGRFP 475 (476)
Q Consensus 421 ~--~~~~~~~l~~~~~~qi~~d~s~~yG~Gfr~~~~~~~~~--gl~~~l~~~~~~g~~p 475 (476)
. +..++++.++|+.++|+.|.+++||+|||.++.+++.. ++..+++++.....|+
T Consensus 421 ~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~~ 479 (479)
T KOG1703|consen 421 FTTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHFP 479 (479)
T ss_pred ccccchhccchhHhhhhHhhccCccccccceehhhhhccccCCceeecCCccccccCCC
Confidence 3 67788999999999999999999999999999999777 7999998888776654
No 3
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.83 E-value=1.8e-22 Score=205.31 Aligned_cols=163 Identities=21% Similarity=0.482 Sum_probs=132.8
Q ss_pred CCcccccCCccccc-CceEeecCccccCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccCCCCcc
Q 011854 112 GYRICAGCNNEIGH-GRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPSNHGGL 190 (476)
Q Consensus 112 ~~~~C~~C~~~I~~-g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f~~~C~~C~~~I~~~~~g~ 190 (476)
.+.+|.+|++.|.. +..+.||++.||..||+|..|++.|.++.||..|+++||+.||... .+||.+|++.|.+ .+
T Consensus 273 ~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t-lekC~~Cg~~I~d---~i 348 (468)
T KOG1701|consen 273 YFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT-LEKCNKCGEPIMD---RI 348 (468)
T ss_pred hhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHH-HHHHhhhhhHHHH---HH
Confidence 45689999999964 3458999999999999999999999999999999999999999876 7999999999998 45
Q ss_pred eEEcccCccccccCCCCccCCCCccCCCCcccCCCCceEEecCCcccchhhHhhhccCCCCCCcchhhHHHHHHHhcccc
Q 011854 191 IEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQPLYLDIQEFYESIHMKL 270 (476)
Q Consensus 191 i~~~~hpfw~qkyC~~h~H~~CF~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~~~v~d~~~Cqp~~~~I~~f~~gl~~~~ 270 (476)
+.+.++. ||++||+|.+|.+-+ +|..|++..++++||..||++. +.++|..|..+| |+.
T Consensus 349 LrA~Gka----------yHp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~k--fAPrCs~C~~PI--------~P~ 407 (468)
T KOG1701|consen 349 LRALGKA----------YHPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHKK--FAPRCSVCGNPI--------LPR 407 (468)
T ss_pred HHhcccc----------cCCCceEEEEecccc-CCccccccCCCceeeehhhhhh--cCcchhhccCCc--------cCC
Confidence 6555544 499999999999977 8999999999999999999995 479999999998 666
Q ss_pred cccc-cceeeehhhhhhhhcCCCCC-cccccccCCccCC
Q 011854 271 EQQI-PLLLVERQALNEARDGEKNG-YYHMPETRGLCLS 307 (476)
Q Consensus 271 ~~~~-Pv~LV~~~aln~a~e~e~~g-~~~~~e~rGlcls 307 (476)
+++- -|++|.+. ..|.- --++ |-.|+-||
T Consensus 408 ~G~~etvRvvamd-------r~fHv~CY~C-EDCg~~LS 438 (468)
T KOG1701|consen 408 DGKDETVRVVAMD-------RDFHVNCYKC-EDCGLLLS 438 (468)
T ss_pred CCCcceEEEEEcc-------ccccccceeh-hhcCcccc
Confidence 5444 36666533 22311 1133 56677777
No 4
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.82 E-value=3.1e-22 Score=191.14 Aligned_cols=166 Identities=25% Similarity=0.538 Sum_probs=142.8
Q ss_pred CCcccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCccccccccccc-----ccccccccCCcccCC
Q 011854 112 GYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREH-----YHPKCDVCKHFIPSN 186 (476)
Q Consensus 112 ~~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~-----f~~~C~~C~~~I~~~ 186 (476)
..|.|++|++.| .|++|.+|+..|||.||+|..|++.|.+..|+...|+..|..|..+. -...|..|+..|..
T Consensus 72 faPcC~kC~EFi-iGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~- 149 (332)
T KOG2272|consen 72 FAPCCGKCGEFI-IGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDE- 149 (332)
T ss_pred hchhhcccccch-hhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhccc-
Confidence 468899999999 59999999999999999999999999999999999999999997652 23479999999876
Q ss_pred CCcceEEcccCccccccCCCCccCCCCccCCCCcccCCCCceEEecCCcccchhhHhhhccCCCCCCcchhhHHHHHHHh
Q 011854 187 HGGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQPLYLDIQEFYESI 266 (476)
Q Consensus 187 ~~g~i~~~~hpfw~qkyC~~h~H~~CF~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~~~v~d~~~Cqp~~~~I~~f~~gl 266 (476)
..+.|++.|| |+..|.|..|++.+..+.+-+ .|.+||+.|+++ |..++|..|.++|.
T Consensus 150 --~~l~fr~d~y----------H~yHFkCt~C~keL~sdaRev---k~eLyClrChD~--mgipiCgaC~rpIe------ 206 (332)
T KOG2272|consen 150 --QPLTFRGDPY----------HPYHFKCTTCGKELTSDAREV---KGELYCLRCHDK--MGIPICGACRRPIE------ 206 (332)
T ss_pred --ccccccCCCC----------Cccceecccccccccchhhhh---ccceeccccccc--cCCcccccccCchH------
Confidence 4689999886 777899999999887777754 789999999999 78999999997774
Q ss_pred cccccccccceeeehhhhhhhh----------cCCCCCcccccccCCccCCccccccc
Q 011854 267 HMKLEQQIPLLLVERQALNEAR----------DGEKNGYYHMPETRGLCLSEEQTVTT 314 (476)
Q Consensus 267 ~~~~~~~~Pv~LV~~~aln~a~----------e~e~~g~~~~~e~rGlclseeq~~~s 314 (476)
.++ +.|||+.| ++++.||.|+ |.+|+.++|+++.-.
T Consensus 207 -----erv------i~amgKhWHveHFvCa~CekPFlGHrHY-EkkGlaYCe~h~~qL 252 (332)
T KOG2272|consen 207 -----ERV------IFAMGKHWHVEHFVCAKCEKPFLGHRHY-EKKGLAYCETHYHQL 252 (332)
T ss_pred -----HHH------HHHhccccchhheeehhcCCcccchhhh-hhcCchhHHHHHHHH
Confidence 333 66777776 4678899998 999999999988644
No 5
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.75 E-value=3.1e-20 Score=180.22 Aligned_cols=123 Identities=29% Similarity=0.619 Sum_probs=108.6
Q ss_pred CCcccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccCCCCcce
Q 011854 112 GYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPSNHGGLI 191 (476)
Q Consensus 112 ~~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f~~~C~~C~~~I~~~~~g~i 191 (476)
..++|++|.+.|.+.-+++++++.||..|++|+.|..+|.+..|. ++|.+||+.+|.++|+.+|..|...|+... +
T Consensus 32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFs-R~~s~yCkedFfKrfGTKCsaC~~GIpPtq---V 107 (383)
T KOG4577|consen 32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFS-REGSVYCKEDFFKRFGTKCSACQEGIPPTQ---V 107 (383)
T ss_pred ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhh-cCCceeehHHHHHHhCCcchhhcCCCChHH---H
Confidence 678999999999877778999999999999999999999998776 589999999999999999999999999742 3
Q ss_pred EEcccCccccccCCCCccCCCCccCCCCcccCCCCceEEecCCcccchhhHhhhc
Q 011854 192 EYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSAI 246 (476)
Q Consensus 192 ~~~~hpfw~qkyC~~h~H~~CF~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~~~v 246 (476)
.-+...| -||..||.|..|.|.+..|+.|++++|++++|+..|+++-
T Consensus 108 VRkAqd~--------VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak 154 (383)
T KOG4577|consen 108 VRKAQDF--------VYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAK 154 (383)
T ss_pred HHHhhcc--------eeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHH
Confidence 2333322 2599999999999999999999999999999999999864
No 6
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=99.65 E-value=1.6e-17 Score=169.29 Aligned_cols=128 Identities=25% Similarity=0.533 Sum_probs=107.4
Q ss_pred ccCCCCCCcccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeec-cCCcccccccccccccccccccCCccc
Q 011854 106 VIQFPEGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFST-SENRPYHKSCYREHYHPKCDVCKHFIP 184 (476)
Q Consensus 106 ~~~~~~~~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~-~dg~~YCk~cY~~~f~~~C~~C~~~I~ 184 (476)
...+......|..|++.|. ..++.|+|+.||+.||+|..|.+.|.+..|.. .++++||-.||++.|.|+|.+|+++|.
T Consensus 327 E~cyq~tlekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~ 405 (468)
T KOG1701|consen 327 EGCYQDTLEKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPIL 405 (468)
T ss_pred hHHHHHHHHHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCcc
Confidence 3445556788999999994 78999999999999999999999999988887 688999999999999999999999999
Q ss_pred CCCCc----ceEEcccCccccccCCCCccCCCCccCCCCcccC---CCCceEEecCCcccchhhHhhh
Q 011854 185 SNHGG----LIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEP---QDTAYVALDDGRKLCLECLDSA 245 (476)
Q Consensus 185 ~~~~g----~i~~~~hpfw~qkyC~~h~H~~CF~C~~C~r~~~---~g~~y~~l~dg~~~C~~C~~~~ 245 (476)
..+.. .|...++. ||.+|++|..|+..|. .+...+.+ ||.++|+.|+-..
T Consensus 406 P~~G~~etvRvvamdr~----------fHv~CY~CEDCg~~LS~e~e~qgCyPl-d~HllCk~Ch~~R 462 (468)
T KOG1701|consen 406 PRDGKDETVRVVAMDRD----------FHVNCYKCEDCGLLLSSEEEGQGCYPL-DGHLLCKTCHLKR 462 (468)
T ss_pred CCCCCcceEEEEEcccc----------ccccceehhhcCccccccCCCCcceec-cCceeechhhhhh
Confidence 86522 24445544 4999999999998775 35677766 8999999998653
No 7
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=99.65 E-value=1.5e-17 Score=159.22 Aligned_cols=125 Identities=20% Similarity=0.518 Sum_probs=109.2
Q ss_pred ccCCCCCCcccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccC
Q 011854 106 VIQFPEGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPS 185 (476)
Q Consensus 106 ~~~~~~~~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f~~~C~~C~~~I~~ 185 (476)
+-....+.++|+.|.++| .+++|.+||+.||.+.|+|+.|.+|+-+...|++.|.+||+.||.++|+..|..|+..|.+
T Consensus 188 rChD~mgipiCgaC~rpI-eervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G 266 (332)
T KOG2272|consen 188 RCHDKMGIPICGACRRPI-EERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGG 266 (332)
T ss_pred ccccccCCcccccccCch-HHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCc
Confidence 344557899999999999 6899999999999999999999999999899999999999999999999999999999998
Q ss_pred CCCcceEEcccCccccccCCCCccCCCCccCCCCcccCCCCceEEecCCcccchhhHhhh
Q 011854 186 NHGGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSA 245 (476)
Q Consensus 186 ~~~g~i~~~~hpfw~qkyC~~h~H~~CF~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~~~ 245 (476)
. ++.+.++. | =++||.|+.|.+.+...++|+.+ |-+++|++||++.
T Consensus 267 ~---vv~al~Ka-----w-----Cv~cf~Cs~Cdkkl~~K~Kf~E~-DmkP~CKkCy~rf 312 (332)
T KOG2272|consen 267 D---VVSALNKA-----W-----CVECFSCSTCDKKLTQKNKFYEF-DMKPVCKKCYDRF 312 (332)
T ss_pred c---HHHHhhhh-----h-----ccccccccccccccccccceeee-ccchHHHHHHhhc
Confidence 4 45444433 3 45589999999999888898855 8899999999973
No 8
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.54 E-value=1.3e-15 Score=160.08 Aligned_cols=118 Identities=28% Similarity=0.662 Sum_probs=102.9
Q ss_pred CCCcccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccCCCCcc
Q 011854 111 EGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPSNHGGL 190 (476)
Q Consensus 111 ~~~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f~~~C~~C~~~I~~~~~g~ 190 (476)
.+...|++|++.|..|+.+.|+++.||..||+|..|+..|.+ +|..+||.|||++||.+.|+.+|..|.++|.+ ++
T Consensus 131 ~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fisg---kv 206 (670)
T KOG1044|consen 131 YGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFISG---KV 206 (670)
T ss_pred cCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhhh---hh
Confidence 456789999999999999999999999999999999999987 47788999999999999999999999999998 45
Q ss_pred eEEcccCccccccCCCCccCCCCccCCCCcccCCCCceEEecCCcccchhhHh
Q 011854 191 IEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLD 243 (476)
Q Consensus 191 i~~~~hpfw~qkyC~~h~H~~CF~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~ 243 (476)
+.+.+ .|||+.|-+|+.|+.++..|+.-+ +....+.-..|-.
T Consensus 207 Lqag~----------kh~HPtCARCsRCgqmF~eGEEMY-lQGs~iWHP~C~q 248 (670)
T KOG1044|consen 207 LQAGD----------KHFHPTCARCSRCGQMFGEGEEMY-LQGSEIWHPDCKQ 248 (670)
T ss_pred hhccC----------cccCcchhhhhhhccccccchhee-eccccccCCcccc
Confidence 66555 367999999999999998888766 5566666666653
No 9
>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=99.52 E-value=1.8e-15 Score=162.48 Aligned_cols=119 Identities=28% Similarity=0.616 Sum_probs=103.3
Q ss_pred CCCCcccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccCCCCc
Q 011854 110 PEGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPSNHGG 189 (476)
Q Consensus 110 ~~~~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f~~~C~~C~~~I~~~~~g 189 (476)
+...+.|.+|+.+| .++.|.+++..||+.||.|..|+++|....|+..++.+||+.||++++..+|..|..+|..-. .
T Consensus 360 ~~~~p~C~~C~~~i-~~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~-~ 437 (479)
T KOG1703|consen 360 APFRPNCKRCLLPI-LEEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGS-R 437 (479)
T ss_pred HhhCccccccCCch-HHhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhh-h
Confidence 34678999999999 599999999999999999999999999999999999999999999999999999999877322 3
Q ss_pred ceEEcccCccccccCCCCccCCCCccCCCCcccCCCCceEEecCCcccchhhH
Q 011854 190 LIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECL 242 (476)
Q Consensus 190 ~i~~~~hpfw~qkyC~~h~H~~CF~C~~C~r~~~~g~~y~~l~dg~~~C~~C~ 242 (476)
.++..+.+| |..||+|..|.+.+ .+..|+ ...++++|..|+
T Consensus 438 ~ie~~~~~~----------h~~~F~c~~c~~~l-~~~~~~-~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 438 QIEADGSPF----------HGDCFRCANCMKKL-TKKTFF-ETLDKPLCQKHF 478 (479)
T ss_pred HhhccCccc----------cccceehhhhhccc-cCCcee-ecCCccccccCC
Confidence 567777664 99999999999876 556666 668899999885
No 10
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.26 E-value=2.2e-12 Score=98.62 Aligned_cols=57 Identities=37% Similarity=1.023 Sum_probs=52.2
Q ss_pred cccCCcccccCceE-eecCccccCCCcccCCCCCCCCCceeeccCCcccccccccccc
Q 011854 116 CAGCNNEIGHGRFL-NCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHY 172 (476)
Q Consensus 116 C~~C~~~I~~g~~v-~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f 172 (476)
|.+|+++|..+..+ .++++.||+.||+|..|+.+|.+..|+..+|++||+.||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence 88999999866665 7999999999999999999999888999999999999998865
No 11
>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]
Probab=99.09 E-value=1.4e-10 Score=122.56 Aligned_cols=165 Identities=18% Similarity=0.369 Sum_probs=116.0
Q ss_pred CcccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccCCCCcceE
Q 011854 113 YRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPSNHGGLIE 192 (476)
Q Consensus 113 ~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f~~~C~~C~~~I~~~~~g~i~ 192 (476)
.-.|.+|.+.- .|+++.+.++.||..||.|..|+..|....|+.+++. .++++ ..|..+|.+. .+.
T Consensus 16 ~i~c~~c~~kc-~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~--------~~ygt--~~c~~~~~ge---vvs 81 (670)
T KOG1044|consen 16 GIKCDKCRKKC-SGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPEN--------RLYGT--DDCRAFVEGE---VVS 81 (670)
T ss_pred ceehhhhCCcc-ccceeEeeccccceeeeeccccCCCcccccceecccc--------eeecc--cchhhhccce---eEe
Confidence 34699999998 5999999999999999999999999999889887664 34444 6788888873 466
Q ss_pred EcccCccccccCCCCccCCCCccCCCCcccCCCCceEEecCCcccchhhHhhhcc------CCCCCCcchhhHHHHHHH-
Q 011854 193 YRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIM------DTNECQPLYLDIQEFYES- 265 (476)
Q Consensus 193 ~~~hpfw~qkyC~~h~H~~CF~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~~~v~------d~~~Cqp~~~~I~~f~~g- 265 (476)
..++- +|+.||.|+.|..+++.|++.. +.....+|..|-..+-. +...|..|.+.|.. |
T Consensus 82 a~gkt----------yh~~cf~cs~ck~pf~~g~~vt-~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~---gq 147 (670)
T KOG1044|consen 82 TLGKT----------YHPKCFSCSTCKSPFKSGDKVT-FSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKN---GQ 147 (670)
T ss_pred cccce----------eccccceecccCCCCCCCCeee-ecchhhhhhhhcCcccCCcccccCCccccchhhhhhc---cc
Confidence 66543 4999999999999999999865 55666899999653222 34479999888731 1
Q ss_pred hcccccccccceeeehhhhhhhhcCCCCCcccccccCCccCCcccc
Q 011854 266 IHMKLEQQIPLLLVERQALNEARDGEKNGYYHMPETRGLCLSEEQT 311 (476)
Q Consensus 266 l~~~~~~~~Pv~LV~~~aln~a~e~e~~g~~~~~e~rGlclseeq~ 311 (476)
.-.-+..+..|......+....+.+|+. ..+|..+++..+
T Consensus 148 ~llald~qwhv~cfkc~~c~~vL~gey~------skdg~pyce~dy 187 (670)
T KOG1044|consen 148 ALLALDKQWHVSCFKCKSCSAVLNGEYM------SKDGVPYCEKDY 187 (670)
T ss_pred eeeeeccceeeeeeehhhhcccccceee------ccCCCcchhhhh
Confidence 0011234444555555555555555543 335555554443
No 12
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=98.72 E-value=2.5e-09 Score=102.56 Aligned_cols=123 Identities=22% Similarity=0.436 Sum_probs=91.1
Q ss_pred CCCcccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCccccccccccccccc---------------
Q 011854 111 EGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPK--------------- 175 (476)
Q Consensus 111 ~~~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f~~~--------------- 175 (476)
.....|..|++.++..+.+...|..||+.||+|..|...|+...+..+++.+||+.||-..++++
T Consensus 5 ~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (200)
T KOG1700|consen 5 GTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLG 84 (200)
T ss_pred cccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCC
Confidence 34558999999999888888999999999999999999999989999999999999876555443
Q ss_pred --------------------------ccccCCcccCCCCcceEEcccCccccccCCCCccCCCCccCCCCcccCCCCceE
Q 011854 176 --------------------------CDVCKHFIPSNHGGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYV 229 (476)
Q Consensus 176 --------------------------C~~C~~~I~~~~~g~i~~~~hpfw~qkyC~~h~H~~CF~C~~C~r~~~~g~~y~ 229 (476)
|..|.+.+.... . +... ..-||..||+|+.|+..+ ....|.
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~E-k-~~~~----------~~~~hk~cfrc~~~~~~l-s~~~~~ 151 (200)
T KOG1700|consen 85 KDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLE-K-VTGN----------GLEFHKSCFRCTHCGKKL-SPKNYA 151 (200)
T ss_pred cccccccccccccchhHHhhhccccccccccceeeehH-H-Hhhh----------hhhhhhhheeeccccccc-CCcchh
Confidence 333333333211 0 1111 234799999999999987 445565
Q ss_pred EecCCcccchhhHhhhcc
Q 011854 230 ALDDGRKLCLECLDSAIM 247 (476)
Q Consensus 230 ~l~dg~~~C~~C~~~~v~ 247 (476)
...+.++|...+..+++
T Consensus 152 -~~~g~l~~~~~~~~~~~ 168 (200)
T KOG1700|consen 152 -ALEGVLYCKHHFAQLFK 168 (200)
T ss_pred -hcCCccccchhhheeec
Confidence 55788888887766544
No 13
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=98.43 E-value=2.1e-07 Score=70.90 Aligned_cols=57 Identities=19% Similarity=0.445 Sum_probs=43.9
Q ss_pred ccccCCcccCCCCcceEEcccCccccccCCCCccCCCCccCCCCcccCCCCceEEecCCcccchhhHhhh
Q 011854 176 CDVCKHFIPSNHGGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSA 245 (476)
Q Consensus 176 C~~C~~~I~~~~~g~i~~~~hpfw~qkyC~~h~H~~CF~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~~~ 245 (476)
|..|+++|.+.. ..+.+.++ .||+.||+|..|++.+..+. |+ ..++++||..||.+.
T Consensus 1 C~~C~~~I~~~~-~~~~~~~~----------~~H~~Cf~C~~C~~~l~~~~-~~-~~~~~~~C~~c~~~~ 57 (58)
T PF00412_consen 1 CARCGKPIYGTE-IVIKAMGK----------FWHPECFKCSKCGKPLNDGD-FY-EKDGKPYCKDCYQKR 57 (58)
T ss_dssp BTTTSSBESSSS-EEEEETTE----------EEETTTSBETTTTCBTTTSS-EE-EETTEEEEHHHHHHH
T ss_pred CCCCCCCccCcE-EEEEeCCc----------EEEccccccCCCCCccCCCe-eE-eECCEEECHHHHhhh
Confidence 889999999754 22235543 36999999999999886555 65 568899999999864
No 14
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.28 E-value=5.6e-07 Score=62.51 Aligned_cols=37 Identities=46% Similarity=1.106 Sum_probs=33.5
Q ss_pred ccccCCcccccC-ceEeecCccccCCCcccCCCCCCCC
Q 011854 115 ICAGCNNEIGHG-RFLNCLDVFWHPECFCCHACHQPIT 151 (476)
Q Consensus 115 ~C~~C~~~I~~g-~~v~algk~wH~~CF~C~~C~~~L~ 151 (476)
.|.+|+++|..+ ..+.++++.||+.||+|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 489999999766 7788999999999999999999885
No 15
>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]
Probab=97.48 E-value=3.1e-05 Score=74.43 Aligned_cols=64 Identities=19% Similarity=0.444 Sum_probs=57.0
Q ss_pred CCCCCcccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCcccccccccccc
Q 011854 109 FPEGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHY 172 (476)
Q Consensus 109 ~~~~~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f 172 (476)
+......|.+|.+.+++.+.+...+..||..||+|..|+..|+...|...++.+||+.++.+++
T Consensus 104 ~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 104 FAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF 167 (200)
T ss_pred hhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence 3445678999999999889999999999999999999999999999999999999998876653
No 16
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=97.42 E-value=1.9e-05 Score=74.75 Aligned_cols=58 Identities=22% Similarity=0.615 Sum_probs=53.2
Q ss_pred cccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCccccccccccc
Q 011854 114 RICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREH 171 (476)
Q Consensus 114 ~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~ 171 (476)
..|..|++.+++-+.|+++++.||..||+|..|+.+|....|--.+.++||..+|.+.
T Consensus 5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq 62 (264)
T KOG1702|consen 5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQ 62 (264)
T ss_pred chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccc
Confidence 4688999999988999999999999999999999999988887679999999999875
No 17
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=97.35 E-value=2.6e-05 Score=77.05 Aligned_cols=70 Identities=23% Similarity=0.486 Sum_probs=57.0
Q ss_pred cCCCCCCcccccCCcccccCceE-eecCccccCCCcccCCCCCCCC-Cceeec-cCCcccccccccccccccc
Q 011854 107 IQFPEGYRICAGCNNEIGHGRFL-NCLDVFWHPECFCCHACHQPIT-DIEFST-SENRPYHKSCYREHYHPKC 176 (476)
Q Consensus 107 ~~~~~~~~~C~~C~~~I~~g~~v-~algk~wH~~CF~C~~C~~~L~-~~~f~~-~dg~~YCk~cY~~~f~~~C 176 (476)
-+|....-.|..|...|.+.++| +|.+.+||..||.|..|+..|. +.+||. .|+++.|+.+|..-...-|
T Consensus 86 dFfKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~ 158 (383)
T KOG4577|consen 86 DFFKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC 158 (383)
T ss_pred HHHHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence 34566677899999999888776 6889999999999999999995 556664 7899999999987543444
No 18
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.07 E-value=0.0001 Score=71.30 Aligned_cols=114 Identities=23% Similarity=0.442 Sum_probs=88.0
Q ss_pred cCCcccccCceEeecCccccCCCcccCCCCCCCC--CceeeccCCcccccccccc--cccccccccCCcccCCCCcceEE
Q 011854 118 GCNNEIGHGRFLNCLDVFWHPECFCCHACHQPIT--DIEFSTSENRPYHKSCYRE--HYHPKCDVCKHFIPSNHGGLIEY 193 (476)
Q Consensus 118 ~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~--~~~f~~~dg~~YCk~cY~~--~f~~~C~~C~~~I~~~~~g~i~~ 193 (476)
+|+..|.+...+.+.+..||..|..|..|...+. ...|.. +|..||+.+|.. .+..+|..|...|...+ .
T Consensus 1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~-----~ 74 (235)
T KOG0490|consen 1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLD-----E 74 (235)
T ss_pred CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHH-----H
Confidence 4777786555677779999999999999999998 677777 999999999998 78899999999885432 1
Q ss_pred cccCccccccCCCCccCCCCccCCCCcccCCCCceEEecCCcccchhhHhh
Q 011854 194 RAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDS 244 (476)
Q Consensus 194 ~~hpfw~qkyC~~h~H~~CF~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~~ 244 (476)
....| ... |--||.|..|.+....++.+.+.......|...+.+
T Consensus 75 ler~f------~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~ 118 (235)
T KOG0490|consen 75 LERAF------EKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE 118 (235)
T ss_pred HHHhh------cCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence 11122 112 667999999999877777777555557888888765
No 19
>PF13485 Peptidase_MA_2: Peptidase MA superfamily
Probab=96.87 E-value=0.0042 Score=53.33 Aligned_cols=107 Identities=21% Similarity=0.252 Sum_probs=65.0
Q ss_pred CchhHHhhhhhhccchhhhhhhcC--CCCCCcchhhhHHHHHHHHHHhhhcccCCCCCCCCCCCcCCCCCCCCCchhHHH
Q 011854 351 GLPRLLTGTILAHEMMHGWMRLQG--FRTLSPDVEEGICQVIAHWWLISQLKSSKKVTPTSSSSAAGTSKKGTGPKFDKK 428 (476)
Q Consensus 351 glp~~l~g~ilaHe~~Ha~l~~~g--~~~l~~~~eEG~cq~~a~~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 428 (476)
+.+..-...+|+||+.|+|+.... ...++..+.||+++.++..|-. ........ . -..+....++ .
T Consensus 19 ~~~~~~~~~~l~HE~~H~~~~~~~~~~~~~~~W~~EG~A~y~~~~~~~-~~~~~~~~-~---------~~~~~~~~~~-~ 86 (128)
T PF13485_consen 19 GSDEDWLDRVLAHELAHQWFGNYFGGDDNAPRWFNEGLAEYVEGRIED-EFDEDLKQ-A---------IESGSLPPLE-P 86 (128)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHcCCCccCchHHHHHHHHHHhcCccc-hhHHHHHH-H---------HHcCCCCChH-H
Confidence 344443447999999999987652 2478899999999999954311 00000000 0 0000111111 2
Q ss_pred HHHHHHhhhhcCCCCCChhhHHHHHHHHHHhCHHHHHHHHHh
Q 011854 429 LGEFFKHQIETDASPVYGDGFRAGQHAVQKYGLGRTLDHIRR 470 (476)
Q Consensus 429 l~~~~~~qi~~d~s~~yG~Gfr~~~~~~~~~gl~~~l~~~~~ 470 (476)
|...+.. ...+.+..|.-|+-.+....+++|...+.+-|+.
T Consensus 87 l~~~~~~-~~~~~~~~Y~~~~~~~~~L~~~~G~~~~~~~l~~ 127 (128)
T PF13485_consen 87 LNSSFDF-SWEDDSLAYYQGYLFVRFLEEKYGREKFKAFLRE 127 (128)
T ss_pred Hhccccc-cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 2222211 5667777999999999999999997777766653
No 20
>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=96.80 E-value=0.00096 Score=45.95 Aligned_cols=37 Identities=19% Similarity=0.325 Sum_probs=27.5
Q ss_pred cccccCCcccCCCCcceEEcccCccccccCCCCccCCCCccCCCCccc
Q 011854 175 KCDVCKHFIPSNHGGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERME 222 (476)
Q Consensus 175 ~C~~C~~~I~~~~~g~i~~~~hpfw~qkyC~~h~H~~CF~C~~C~r~~ 222 (476)
+|..|+++|.+.. ..+.+.+ ..||+.||+|..|++.|
T Consensus 1 ~C~~C~~~i~~~~-~~~~~~~----------~~~H~~Cf~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGGE-LVLRALG----------KVWHPECFKCSKCGKPL 37 (39)
T ss_pred CccccCCcccCCc-EEEEeCC----------ccccccCCCCcccCCcC
Confidence 5899999998752 2344443 34699999999999866
No 21
>PF10026 DUF2268: Predicted Zn-dependent protease (DUF2268); InterPro: IPR018728 This domain, found in various hypothetical bacterial proteins, as well as predicted zinc dependent proteases, has no known function.
Probab=84.48 E-value=1.4 Score=42.14 Aligned_cols=43 Identities=19% Similarity=0.183 Sum_probs=31.7
Q ss_pred hhhhhhccchhhhhhh------cCCCCCCcchhhhHHHHHHHHHHhhhc
Q 011854 357 TGTILAHEMMHGWMRL------QGFRTLSPDVEEGICQVIAHWWLISQL 399 (476)
Q Consensus 357 ~g~ilaHe~~Ha~l~~------~g~~~l~~~~eEG~cq~~a~~wl~~~~ 399 (476)
.-++||||+-|++-.- .+...|+..|-||+.+.++..-.....
T Consensus 65 l~~~iaHE~hH~~r~~~~~~~~~~~TLld~~I~EGlAe~f~~~~~g~~~ 113 (195)
T PF10026_consen 65 LPALIAHEYHHNCRYEQIGWDPEDTTLLDSLIMEGLAEYFAEELYGEEY 113 (195)
T ss_pred HHHHHHHHHHHHHHHhccCCCCCCCCHHHHHHHhhHHHHHHHHHcCCCC
Confidence 3579999998886422 234567899999999988887755544
No 22
>TIGR02412 pepN_strep_liv aminopeptidase N, Streptomyces lividans type. This family is a subset of the members of the zinc metallopeptidase family M1 (pfam01433), with a single member characterized in Streptomyces lividans 66 and designated aminopeptidase N. The spectrum of activity may differ somewhat from the aminopeptidase N clade of E. coli and most other Proteobacteria, well separated phylogenetically within the M1 family. The M1 family also includes leukotriene A-4 hydrolase/aminopeptidase (with a bifunctional active site).
Probab=75.21 E-value=8.6 Score=44.81 Aligned_cols=41 Identities=20% Similarity=0.271 Sum_probs=31.0
Q ss_pred hhhhhccchhhhhh-hcCCCC-CCcchhhhHHHHHHHHHHhhh
Q 011854 358 GTILAHEMMHGWMR-LQGFRT-LSPDVEEGICQVIAHWWLISQ 398 (476)
Q Consensus 358 g~ilaHe~~Ha~l~-~~g~~~-l~~~~eEG~cq~~a~~wl~~~ 398 (476)
..+||||+.|-|.. +-...- -+..+-|||..+|+++|++..
T Consensus 288 ~~viaHElAHqWFGnlVT~~wW~dlWLnEGFAty~e~~~~~~~ 330 (831)
T TIGR02412 288 AGVILHEMAHMWFGDLVTMRWWNDLWLNESFAEYMGTLASAEA 330 (831)
T ss_pred HHHHHHHHHHHHhCCEeccccccchhHHHHHHHHHHHHHHHhc
Confidence 46999999999975 212221 236899999999999999753
No 23
>smart00726 UIM Ubiquitin-interacting motif. Present in proteasome subunit S5a and other ubiquitin-associated proteins.
Probab=73.49 E-value=2.8 Score=27.17 Aligned_cols=21 Identities=38% Similarity=0.569 Sum_probs=15.7
Q ss_pred ccchHHHHHHHhhhhhhhhcC
Q 011854 43 QENEDIDRAIALSLLEENQKG 63 (476)
Q Consensus 43 ~~~e~~~~a~~~sl~e~~~~~ 63 (476)
.|+|+|..||++|+.|.+...
T Consensus 1 ~EDe~Lq~Ai~lSl~e~e~~~ 21 (26)
T smart00726 1 DEDEDLQLALELSLQEAEESX 21 (26)
T ss_pred ChHHHHHHHHHHhHHHhhhcc
Confidence 367888888888887766543
No 24
>PF02809 UIM: Ubiquitin interaction motif; InterPro: IPR003903 The Ubiquitin Interacting Motif (UIM), or 'LALAL-motif', is a stretch of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin [,]. In addition, the UIM is found, often in tandem or triplet arrays, in a variety of proteins either involved in ubiquitination and ubiquitin metabolism, or known to interact with ubiquitin-like modifiers. Among the UIM proteins are two different subgroups of the UBP (ubiquitin carboxy-terminal hydrolase) family of deubiquitinating enzymes, one F-box protein, one family of HECT-containing ubiquitin-ligases (E3s) from plants, and several proteins containing ubiquitin-associated UBA and/or UBX domains []. In most of these proteins, the UIM occurs in multiple copies and in association with other domains such as UBA (IPR015940 from INTERPRO), UBX (IPR001012 from INTERPRO), ENTH, EH (IPR000261 from INTERPRO), VHS (IPR002014 from INTERPRO), SH3 (IPR001452 from INTERPRO), HECT (IPR000569 from INTERPRO), VWFA (IPR002035 from INTERPRO), EF-hand calcium-binding, WD-40 (IPR001680 from INTERPRO), F-box (IPR001810 from INTERPRO), LIM (IPR001781 from INTERPRO), protein kinase (IPR000719 from INTERPRO), ankyrin (IPR002110 from INTERPRO), PX (IPR001683 from INTERPRO), phosphatidylinositol 3- and 4-kinase (IPR000403 from INTERPRO), C2 (IPR000008 from INTERPRO), OTU (IPR003323 from INTERPRO), dnaJ (IPR001623 from INTERPRO), RING-finger (IPR001841 from INTERPRO) or FYVE-finger (IPR017455 from INTERPRO). UIMs have been shown to bind ubiquitin and to serve as a specific targeting signal important for monoubiquitination. Thus, UIMs may have several functions in ubiquitin metabolism each of which may require different numbers of UIMs [, , ]. The UIM is unlikely to form an independent folding domain. Instead, based on the spacing of the conserved residues, the motif probably forms a short alpha-helix that can be embedded into different protein folds []. Some proteins known to contain an UIM are listed below: Eukaryotic PSD4/RPN-10/S5, a multi-ubiquitin binding subunit of the 26S proteasome. Vertebrate Machado-Joseph disease protein 1 (Ataxin-3), which acts as a histone-binding protein that regulates transcription; defects in Ataxin-3 cause the neurodegenerative disorder Machado-Joseph disease (MJD). Vertebrate epsin and epsin2. Vertebrate hepatocyte growth factor-regulated tyrosine kinase substrate (HRS). Mammalian epidermal growth factor receptor substrate 15 (EPS15), which is involved in cell growth regulation. Mammalian epidermal growth factor receptor substrate EPS15R. Drosophila melanogaster (Fruit fly) liquid facets (lqf), an epsin. Yeast VPS27 vacuolar sorting protein, which is required for membrane traffic to the vacuole. ; PDB: 2KDE_A 2KDF_A 1YX6_A 1YX5_A 1YX4_A 1P9C_A 1UEL_B 1P9D_S 2KLZ_A.
Probab=71.86 E-value=2.4 Score=25.08 Aligned_cols=16 Identities=50% Similarity=0.800 Sum_probs=12.3
Q ss_pred ccchHHHHHHHhhhhh
Q 011854 43 QENEDIDRAIALSLLE 58 (476)
Q Consensus 43 ~~~e~~~~a~~~sl~e 58 (476)
.|+++|.+||++|+.|
T Consensus 2 ~Ed~~L~~Al~~S~~e 17 (18)
T PF02809_consen 2 DEDEDLQRALEMSLEE 17 (18)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHhhhcc
Confidence 4677888888888764
No 25
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=69.45 E-value=4.4 Score=32.07 Aligned_cols=47 Identities=17% Similarity=0.367 Sum_probs=23.5
Q ss_pred cccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccCCC
Q 011854 141 FCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPSNH 187 (476)
Q Consensus 141 F~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f~~~C~~C~~~I~~~~ 187 (476)
.+|+.|...|...---..=...||..|-...++..|.+|+.+-...+
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD 54 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQD 54 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHH
Confidence 57888877776542223456789999999888999999998765433
No 26
>PF01433 Peptidase_M1: Peptidase family M1 This is family M1 in the peptidase classification.; InterPro: IPR014782 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M1 (clan MA(E)), the type example being aminopeptidase N from Homo sapiens (Human). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Membrane alanine aminopeptidase (3.4.11.2 from EC) is part of the HEXXH+E group; it consists entirely of aminopeptidases, spread across a wide variety of species []. Functional studies show that CD13/APN catalyzes the removal of single amino acids from the amino terminus of small peptides and probably plays a role in their final digestion; one family member (leukotriene-A4 hydrolase) is known to hydrolyse the epoxide leukotriene-A4 to form an inflammatory mediator []. This hydrolase has been shown to have aminopeptidase activity [], and the zinc ligands of the M1 family were identified by site-directed mutagenesis on this enzyme [] CD13 participates in trimming peptides bound to MHC class II molecules [] and cleaves MIP-1 chemokine, which alters target cell specificity from basophils to eosinophils []. CD13 acts as a receptor for specific strains of RNA viruses (coronaviruses) which cause a relatively large percentage of upper respiratory trace infections. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 2XQ0_A 2XPY_A 2XPZ_A 3SE6_B 3EBH_A 3EBG_A 3T8V_A 3Q44_A 3Q43_A 3EBI_A ....
Probab=67.88 E-value=2.1 Score=44.41 Aligned_cols=44 Identities=18% Similarity=0.255 Sum_probs=32.9
Q ss_pred Hhhhhhhccchhhhhhh-cCCCCC-CcchhhhHHHHHHHHHHhhhc
Q 011854 356 LTGTILAHEMMHGWMRL-QGFRTL-SPDVEEGICQVIAHWWLISQL 399 (476)
Q Consensus 356 l~g~ilaHe~~Ha~l~~-~g~~~l-~~~~eEG~cq~~a~~wl~~~~ 399 (476)
....+||||++|-|..- -....= ...+-|||+..++++|++...
T Consensus 294 ~~~~~iahElahqWfGn~vt~~~w~d~WL~Eg~a~y~~~~~~~~~~ 339 (390)
T PF01433_consen 294 EIASLIAHELAHQWFGNLVTPKWWSDLWLNEGFATYLEYLILEKLF 339 (390)
T ss_dssp HHHHHHHHHHHTTTBTTTEEESSGGGHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHhccCCccccchhhhHHHHHHHHHHHHhHhhcc
Confidence 33568999999999752 122222 367999999999999999866
No 27
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.37 E-value=2.1 Score=40.35 Aligned_cols=48 Identities=19% Similarity=0.499 Sum_probs=37.9
Q ss_pred CCCcccCCCCCCCCCce-eeccCCccccccccccc--ccccccccCCcccC
Q 011854 138 PECFCCHACHQPITDIE-FSTSENRPYHKSCYREH--YHPKCDVCKHFIPS 185 (476)
Q Consensus 138 ~~CF~C~~C~~~L~~~~-f~~~dg~~YCk~cY~~~--f~~~C~~C~~~I~~ 185 (476)
..||.|..|-....... +.-+-|.+||+.|-+.. ...+|..|++.|+.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 45788998877776654 55688999999998764 45699999998875
No 28
>PF10460 Peptidase_M30: Peptidase M30; InterPro: IPR019501 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This family contains metallopeptidases belonging to MEROPS peptidase family M30 (hyicolysin family, clan MA). Hyicolysin has a zinc ion which is liganded by two histidine and one glutamate residue.
Probab=64.51 E-value=4.7 Score=42.43 Aligned_cols=43 Identities=21% Similarity=0.181 Sum_probs=31.5
Q ss_pred Hhhhhhhccchhhh---hh--hcCC-CCCCcchhhhHHHHHHHHHHhhh
Q 011854 356 LTGTILAHEMMHGW---MR--LQGF-RTLSPDVEEGICQVIAHWWLISQ 398 (476)
Q Consensus 356 l~g~ilaHe~~Ha~---l~--~~g~-~~l~~~~eEG~cq~~a~~wl~~~ 398 (476)
.+-+|||||++|.- .+ +.|- ...+..++||+-+++.++.-...
T Consensus 138 ~~~sTlAHEfQHmInfy~~~v~~g~~~~~dtWLnE~lS~~aEdl~s~~~ 186 (366)
T PF10460_consen 138 TVYSTLAHEFQHMINFYQRGVLHGKQYAMDTWLNEMLSMSAEDLYSSKI 186 (366)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHHhcCC
Confidence 34689999999875 22 2232 35789999999999999764443
No 29
>PRK14873 primosome assembly protein PriA; Provisional
Probab=63.74 E-value=5.1 Score=45.51 Aligned_cols=37 Identities=22% Similarity=0.562 Sum_probs=20.6
Q ss_pred ccCCCCCCCCCceeeccCCcccccccccccccccccccCC
Q 011854 142 CCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKH 181 (476)
Q Consensus 142 ~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f~~~C~~C~~ 181 (476)
+|..|+.+|+ |...++.+.|+-|-.......|..|+.
T Consensus 394 ~C~~C~~~L~---~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs 430 (665)
T PRK14873 394 RCRHCTGPLG---LPSAGGTPRCRWCGRAAPDWRCPRCGS 430 (665)
T ss_pred ECCCCCCcee---EecCCCeeECCCCcCCCcCccCCCCcC
Confidence 6788877775 223345565666644333445555554
No 30
>PF04450 BSP: Peptidase of plants and bacteria; InterPro: IPR007541 These basic secretory proteins (BSPs) are believed to be part of the plants defence mechanism against pathogens [].
Probab=63.56 E-value=4.1 Score=39.44 Aligned_cols=92 Identities=24% Similarity=0.341 Sum_probs=56.5
Q ss_pred hhhhhhccchhhhhhhcCCCCCCcchhhhHHHHHHHHHHhhhcccCCCCCCCCCCCcCCCCCCCCCchhHH--HHHHHHH
Q 011854 357 TGTILAHEMMHGWMRLQGFRTLSPDVEEGICQVIAHWWLISQLKSSKKVTPTSSSSAAGTSKKGTGPKFDK--KLGEFFK 434 (476)
Q Consensus 357 ~g~ilaHe~~Ha~l~~~g~~~l~~~~eEG~cq~~a~~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~l~~~~~ 434 (476)
.-.+|-||+||+|+.- |...-|..+-|||...+-+.= ...+.. ..+.+....|+. ...+||+
T Consensus 96 i~Gvl~HE~~H~~Q~~-~~~~~P~~liEGIADyVRl~a---G~~~~~------------w~~p~~~~~wd~gY~~TA~FL 159 (205)
T PF04450_consen 96 IIGVLYHEMVHCWQWD-GRGTAPGGLIEGIADYVRLKA---GYAPPH------------WKRPGGGDSWDDGYRTTARFL 159 (205)
T ss_pred HHHHHHHHHHHHhhcC-CCCCCChhheecHHHHHHHHc---CCCCcc------------ccCCCCCCCcccccHHHHHHH
Confidence 3458999999999987 556788999999999886651 111100 001010012332 5567777
Q ss_pred hhhhcCCCCCChhhH-HHHHHHHHHhCH--HHHHHH
Q 011854 435 HQIETDASPVYGDGF-RAGQHAVQKYGL--GRTLDH 467 (476)
Q Consensus 435 ~qi~~d~s~~yG~Gf-r~~~~~~~~~gl--~~~l~~ 467 (476)
.=+|... ||.|| |..++++.+.+. ..+++.
T Consensus 160 ~wle~~~---~~~gfV~~LN~~m~~~~y~~~~~~~~ 192 (205)
T PF04450_consen 160 DWLEDNR---YGKGFVRRLNEAMRRDKYSSDDFWKE 192 (205)
T ss_pred HHHHhcc---cCccHHHHHHHHHhhCCCCcHhHHHH
Confidence 7777632 66676 888888866554 444443
No 31
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=62.21 E-value=4.7 Score=41.71 Aligned_cols=73 Identities=22% Similarity=0.375 Sum_probs=42.7
Q ss_pred CcccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCccccccccccc--------ccccccccCCccc
Q 011854 113 YRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREH--------YHPKCDVCKHFIP 184 (476)
Q Consensus 113 ~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~--------f~~~C~~C~~~I~ 184 (476)
...|.+|++.-. -..|++|-.|.. .-.|..||... -+|.|..|...-.
T Consensus 8 ~v~CdgC~k~~~------------t~rrYkCL~C~D------------yDlC~sCyen~~tt~~H~~dHPmqcil~~~df 63 (381)
T KOG1280|consen 8 GVSCDGCGKTAF------------TFRRYKCLRCSD------------YDLCFSCYENGATTPIHDEDHPMQCILSRVDF 63 (381)
T ss_pred Cceeccccccce------------eeeeeEeeeecc------------hhHHHHHhhcCCCCcccCCCCceeEEeeccce
Confidence 346888987542 233556666621 23577777543 2456666654332
Q ss_pred CCCCcceEEcccCccccccCCCCccCCCCccCCCCcc
Q 011854 185 SNHGGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERM 221 (476)
Q Consensus 185 ~~~~g~i~~~~hpfw~qkyC~~h~H~~CF~C~~C~r~ 221 (476)
. +-|.+.|+ +|+-+.||+|-.|++.
T Consensus 64 e-----L~f~Ge~i-------~~y~~qSftCPyC~~~ 88 (381)
T KOG1280|consen 64 E-----LYFGGEPI-------SHYDPQSFTCPYCGIM 88 (381)
T ss_pred e-----eEecCccc-------cccccccccCCccccc
Confidence 2 33444443 5667779999999974
No 32
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=60.22 E-value=6.9 Score=42.95 Aligned_cols=37 Identities=22% Similarity=0.598 Sum_probs=19.1
Q ss_pred ccCCCCCCCCCceeeccCCcccccccccc-cccccccccCC
Q 011854 142 CCHACHQPITDIEFSTSENRPYHKSCYRE-HYHPKCDVCKH 181 (476)
Q Consensus 142 ~C~~C~~~L~~~~f~~~dg~~YCk~cY~~-~f~~~C~~C~~ 181 (476)
+|..|+.+|+ |...++.+.|+.|-.. .+...|..|+.
T Consensus 224 ~C~~C~~~l~---~h~~~~~l~Ch~Cg~~~~~~~~Cp~C~s 261 (505)
T TIGR00595 224 CCPNCDVSLT---YHKKEGKLRCHYCGYQEPIPKTCPQCGS 261 (505)
T ss_pred CCCCCCCceE---EecCCCeEEcCCCcCcCCCCCCCCCCCC
Confidence 5677766664 3334556666655332 22335555543
No 33
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=59.23 E-value=1.7 Score=36.82 Aligned_cols=50 Identities=22% Similarity=0.497 Sum_probs=34.5
Q ss_pred ccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCcccc
Q 011854 115 ICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYH 164 (476)
Q Consensus 115 ~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YC 164 (476)
.|..|+..+..-.+....-..+++.+..|.+|...|+-.+|.....-|||
T Consensus 37 aCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~EY~~~~~Cp~C 86 (105)
T COG4357 37 ACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAEYGMCGSCPYC 86 (105)
T ss_pred hHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHHHhhcCCCCCc
Confidence 36677777755455665567788888888888888877666654544444
No 34
>PF06114 DUF955: Domain of unknown function (DUF955); InterPro: IPR010359 This is a family of bacterial and viral proteins with undetermined function. A conserved H-E-X-X-H motif is suggestive of a catalytic active site and shows similarity to IPR001915 from INTERPRO.; PDB: 3DTE_A 3DTK_A 3DTI_A.
Probab=58.44 E-value=6.1 Score=33.10 Aligned_cols=52 Identities=21% Similarity=0.098 Sum_probs=32.6
Q ss_pred EEEEEecCchhHHhhhhhhccchhhhhhhcCC------CCCCcchhhhHHHHHHHHHH
Q 011854 344 TAILILYGLPRLLTGTILAHEMMHGWMRLQGF------RTLSPDVEEGICQVIAHWWL 395 (476)
Q Consensus 344 ~~il~l~glp~~l~g~ilaHe~~Ha~l~~~g~------~~l~~~~eEG~cq~~a~~wl 395 (476)
..|++-..++..-.-.+||||++|.++...+. ........|--++.+|...|
T Consensus 29 ~~I~in~~~~~~~~~f~laHELgH~~~~~~~~~~~~~~~~~~~~~~E~~An~fA~~lL 86 (122)
T PF06114_consen 29 PIIFINSNLSPERQRFTLAHELGHILLHHGDETFNYYLNYFFNERQEREANAFAAALL 86 (122)
T ss_dssp TEEEEESSS-HHHHHHHHHHHHHHHHHHH-HHHHHHHHHH--THHHHHHHHHHHHHHH
T ss_pred CEEEECCCCCHHHHHHHHHHHHHHHHhhhccccchhhccccchhhHHHHHHHHHHHHh
Confidence 45667777888777889999999999987541 23344444555555554443
No 35
>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=54.53 E-value=3.7 Score=32.77 Aligned_cols=27 Identities=15% Similarity=0.199 Sum_probs=22.1
Q ss_pred CCCCCccccccccccccccccceEEEE
Q 011854 321 FGPGNQARNIITEPYKLTRRCDVTAIL 347 (476)
Q Consensus 321 ~~~g~ri~e~~~~p~~~~~~~ev~~il 347 (476)
+++||+|++||+.+++.....++..+|
T Consensus 43 l~~GD~Il~INg~~v~~~~~~~~~~~l 69 (81)
T PF00595_consen 43 LKVGDRILEINGQSVRGMSHDEVVQLL 69 (81)
T ss_dssp SSTTEEEEEETTEESTTSBHHHHHHHH
T ss_pred cchhhhhheeCCEeCCCCCHHHHHHHH
Confidence 889999999999999988776654433
No 36
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=53.83 E-value=7.5 Score=27.09 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=18.2
Q ss_pred cccCCCCCCCCCceeeccCCccccccccc
Q 011854 141 FCCHACHQPITDIEFSTSENRPYHKSCYR 169 (476)
Q Consensus 141 F~C~~C~~~L~~~~f~~~dg~~YCk~cY~ 169 (476)
+.|..|+.. .|...||..||..|-.
T Consensus 9 ~~C~~C~~~----~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 9 EPCPVCGSR----WFYSDDGFYYCDRCGH 33 (36)
T ss_pred CcCCCCCCe----EeEccCCEEEhhhCce
Confidence 347788765 4667899999987743
No 37
>PF14891 Peptidase_M91: Effector protein
Probab=51.88 E-value=6.4 Score=36.84 Aligned_cols=21 Identities=29% Similarity=0.664 Sum_probs=17.3
Q ss_pred chhHHhhhhhhccchhhhhhhcCC
Q 011854 352 LPRLLTGTILAHEMMHGWMRLQGF 375 (476)
Q Consensus 352 lp~~l~g~ilaHe~~Ha~l~~~g~ 375 (476)
.|-.+ +|+|||.|||=.++|-
T Consensus 101 ~~p~v---~L~HEL~HA~~~~~Gt 121 (174)
T PF14891_consen 101 RPPFV---VLYHELIHAYDYMNGT 121 (174)
T ss_pred HHHHH---HHHHHHHHHHHHHCCC
Confidence 34455 9999999999999985
No 38
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=51.49 E-value=5.6 Score=32.56 Aligned_cols=16 Identities=38% Similarity=0.584 Sum_probs=12.9
Q ss_pred hhhhccchhhhhhhcC
Q 011854 359 TILAHEMMHGWMRLQG 374 (476)
Q Consensus 359 ~ilaHe~~Ha~l~~~g 374 (476)
++||||++|++....|
T Consensus 63 ~llaHEl~Hv~Qq~~g 78 (79)
T PF13699_consen 63 ALLAHELAHVVQQRRG 78 (79)
T ss_pred hhHhHHHHHHHhhccC
Confidence 4899999999976543
No 39
>PHA02456 zinc metallopeptidase motif-containing protein
Probab=49.09 E-value=5.9 Score=34.66 Aligned_cols=18 Identities=39% Similarity=0.702 Sum_probs=14.1
Q ss_pred hhhhhccchhhhhhhc-CC
Q 011854 358 GTILAHEMMHGWMRLQ-GF 375 (476)
Q Consensus 358 g~ilaHe~~Ha~l~~~-g~ 375 (476)
.-|||||+.|+|+.-. |+
T Consensus 80 ~~TL~HEL~H~WQ~RsYG~ 98 (141)
T PHA02456 80 RDTLAHELNHAWQFRTYGL 98 (141)
T ss_pred HHHHHHHHHHHHhhhccce
Confidence 4599999999998654 53
No 40
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=48.96 E-value=12 Score=31.37 Aligned_cols=30 Identities=20% Similarity=0.431 Sum_probs=20.9
Q ss_pred CCcccccCCcccccCceEe-ecCccccCCCc
Q 011854 112 GYRICAGCNNEIGHGRFLN-CLDVFWHPECF 141 (476)
Q Consensus 112 ~~~~C~~C~~~I~~g~~v~-algk~wH~~CF 141 (476)
....|..|+++|..+.++. -.|..+|..|+
T Consensus 77 ~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 77 ESTKCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCCccCcCCcCCCceEEEeCCCeEEecccc
Confidence 3567999999997655543 34567887775
No 41
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=48.72 E-value=15 Score=28.54 Aligned_cols=13 Identities=31% Similarity=0.577 Sum_probs=7.7
Q ss_pred CcccccCCccccc
Q 011854 113 YRICAGCNNEIGH 125 (476)
Q Consensus 113 ~~~C~~C~~~I~~ 125 (476)
.+.|..|+..|..
T Consensus 7 ~~~CtSCg~~i~~ 19 (59)
T PRK14890 7 PPKCTSCGIEIAP 19 (59)
T ss_pred CccccCCCCcccC
Confidence 3456666666643
No 42
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=48.55 E-value=8.4 Score=37.18 Aligned_cols=16 Identities=19% Similarity=0.443 Sum_probs=12.2
Q ss_pred eccCCccccccccccc
Q 011854 156 STSENRPYHKSCYREH 171 (476)
Q Consensus 156 ~~~dg~~YCk~cY~~~ 171 (476)
...+|++.|+.||...
T Consensus 188 ~~~ng~~vC~~C~~~~ 203 (206)
T COG2191 188 VVLNGKPVCKPCAEKK 203 (206)
T ss_pred hhcCCceecccccccc
Confidence 3468899999998754
No 43
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=48.50 E-value=8.4 Score=34.85 Aligned_cols=23 Identities=30% Similarity=0.222 Sum_probs=18.9
Q ss_pred chhHHhhhhhhccchhhhhhhcC
Q 011854 352 LPRLLTGTILAHEMMHGWMRLQG 374 (476)
Q Consensus 352 lp~~l~g~ilaHe~~Ha~l~~~g 374 (476)
.|...+-.||.|||.|+|+.+.+
T Consensus 55 ~~~~~~~~tL~HEm~H~~~~~~~ 77 (157)
T PF10263_consen 55 NPEEELIDTLLHEMAHAAAYVFG 77 (157)
T ss_pred hHHHHHHHHHHHHHHHHHhhhcc
Confidence 45566678999999999998873
No 44
>PF01431 Peptidase_M13: Peptidase family M13 This is family M13 in the peptidase classification. ; InterPro: IPR018497 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M13 (neprilysin family, clan MA(E)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk [, ]. The family includes eukaryotic and prokaryotic oligopeptidases, as well as some of the proteins responsible for the molecular basis of the blood group antigens e.g. Kell []. Neprilysin (3.4.24.11 from EC), is another member of this group, it is variously known as common acute lymphoblastic leukemia antigen (CALLA), enkephalinase (gp100) and neutral endopeptidase metalloendopeptidase (NEP). It is a plasma membrane-bound mammalian enzyme that is able to digest biologically-active peptides, including enkephalins []. The zinc ligands of neprilysin are known and are analogous to those in thermolysin, a related peptidase [, ]. Neprilysins, like thermolysin, are inhibited by phosphoramidon, which appears to selectively inhibit this family in mammals. The enzymes are all oligopeptidases, digesting oligo- and polypeptides, but not proteins []. Neprilysin consists of a short cytoplasmic domain, a membrane-spanning region and a large extracellular domain. The cytoplasmic domain contains a conformationally-restrained octapeptide, which is thought to act as a stop transfer sequence that prevents proteolysis and secretion [, ].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QPJ_A 1R1I_A 1R1J_A 1Y8J_A 1R1H_A 1DMT_A 2YB9_A 3DWB_A 3ZUK_A.
Probab=48.15 E-value=5.7 Score=37.69 Aligned_cols=15 Identities=53% Similarity=0.809 Sum_probs=13.2
Q ss_pred hhhhhhccchhhhhh
Q 011854 357 TGTILAHEMMHGWMR 371 (476)
Q Consensus 357 ~g~ilaHe~~Ha~l~ 371 (476)
.|+|||||++|+.-.
T Consensus 36 lG~ilahel~hafd~ 50 (206)
T PF01431_consen 36 LGFILAHELMHAFDP 50 (206)
T ss_dssp HHHHHHHHHHHCTST
T ss_pred HHHHHHHHHHHHHHH
Confidence 499999999999865
No 45
>COG2856 Predicted Zn peptidase [Amino acid transport and metabolism]
Probab=47.70 E-value=26 Score=34.19 Aligned_cols=55 Identities=20% Similarity=0.059 Sum_probs=36.9
Q ss_pred EEEEEecCchhHHhhhhhhccchhhhhhhcC------CCC-CCcchhhhHHHHHHHHHHhhh
Q 011854 344 TAILILYGLPRLLTGTILAHEMMHGWMRLQG------FRT-LSPDVEEGICQVIAHWWLISQ 398 (476)
Q Consensus 344 ~~il~l~glp~~l~g~ilaHe~~Ha~l~~~g------~~~-l~~~~eEG~cq~~a~~wl~~~ 398 (476)
..|++-...+...--=|||||+.|++|.-.+ .++ -....-|--|+.+|---|-..
T Consensus 59 ~~I~iN~n~~~~r~rFtlAHELGH~llH~~~~~~~~~~~~~~~~~~~E~~AN~FAa~lLmP~ 120 (213)
T COG2856 59 PVIYINANNSLERKRFTLAHELGHALLHTDLNTRFDAEPTLQQDRKIEAEANAFAAELLMPE 120 (213)
T ss_pred ceEEEeCCCCHHHHHHHHHHHHhHHHhccccchhhhcccccchhHHHHHHHHHHHHHHhCCh
Confidence 4455555555544446999999999997643 123 234556788999998887644
No 46
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=46.62 E-value=15 Score=27.66 Aligned_cols=30 Identities=23% Similarity=0.664 Sum_probs=21.7
Q ss_pred ccCCCCcccCCCCceEEecCCcccchhhHhhh
Q 011854 214 RCCSCERMEPQDTAYVALDDGRKLCLECLDSA 245 (476)
Q Consensus 214 ~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~~~ 245 (476)
.|..|+.-++.-.++- +.|| .+|..|+.++
T Consensus 1 ~C~iCg~kigl~~~~k-~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFK-IKDG-YICKDCLKKL 30 (51)
T ss_pred CCCcccccccccccee-ccCc-cchHHHHHHh
Confidence 4788887665444443 6788 6999999886
No 47
>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=45.81 E-value=14 Score=27.93 Aligned_cols=44 Identities=14% Similarity=0.239 Sum_probs=32.3
Q ss_pred cccCCCCCCCCCceeeccCCcccccccccccc--cccccccCCcccC
Q 011854 141 FCCHACHQPITDIEFSTSENRPYHKSCYREHY--HPKCDVCKHFIPS 185 (476)
Q Consensus 141 F~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f--~~~C~~C~~~I~~ 185 (476)
|.|..|+..+.+. .....|..||+.|..+.+ ...|..|++.+..
T Consensus 2 ~~Cpi~~~~~~~P-v~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMKDP-VILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCCCC-EECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence 5788898888774 444678999999876432 4578888887754
No 48
>PRK05580 primosome assembly protein PriA; Validated
Probab=44.75 E-value=16 Score=41.55 Aligned_cols=11 Identities=18% Similarity=0.030 Sum_probs=8.0
Q ss_pred hhhhccchhhh
Q 011854 359 TILAHEMMHGW 369 (476)
Q Consensus 359 ~ilaHe~~Ha~ 369 (476)
+.+.||+.-.|
T Consensus 556 ~~~~~d~~~f~ 566 (679)
T PRK05580 556 ALLAQDYDAFA 566 (679)
T ss_pred HHHhCCHHHHH
Confidence 57789886655
No 49
>PF05299 Peptidase_M61: M61 glycyl aminopeptidase; InterPro: IPR007963 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M61 (glycyl aminopeptidase family, clan MA(E)).The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example is glycyl aminopeptidase from Sphingomonas capsulata.
Probab=42.98 E-value=15 Score=32.76 Aligned_cols=42 Identities=24% Similarity=0.342 Sum_probs=30.1
Q ss_pred hhhhhccchhhhh--hhcC---------CCCCC--cchhhhHHHHHHHHHHhhhc
Q 011854 358 GTILAHEMMHGWM--RLQG---------FRTLS--PDVEEGICQVIAHWWLISQL 399 (476)
Q Consensus 358 g~ilaHe~~Ha~l--~~~g---------~~~l~--~~~eEG~cq~~a~~wl~~~~ 399 (476)
-.++|||+-|+|- |+.. -|+.+ ..+-||+-+.++.+-|-+..
T Consensus 5 l~l~sHEffH~WnvkrirP~~l~p~dy~~~~~t~~LWv~EG~T~Y~~~l~l~RaG 59 (122)
T PF05299_consen 5 LGLLSHEFFHSWNVKRIRPAELGPFDYEKPNYTELLWVYEGFTSYYGDLLLVRAG 59 (122)
T ss_pred hhhhhhhccccccceEeccccccCCCCCCCCCCCCEeeeeCcHHHHHHHHHHHcC
Confidence 4689999999995 3322 12222 57899999999998876543
No 50
>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=42.88 E-value=15 Score=31.09 Aligned_cols=36 Identities=19% Similarity=0.558 Sum_probs=23.9
Q ss_pred ccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccC
Q 011854 142 CCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPS 185 (476)
Q Consensus 142 ~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f~~~C~~C~~~I~~ 185 (476)
.|..|...+.. .|.-||..|..+ .-.|+-|++.|.+
T Consensus 46 ~C~~CK~~v~q------~g~~YCq~CAYk--kGiCamCGKki~d 81 (90)
T PF10235_consen 46 KCKICKTKVHQ------PGAKYCQTCAYK--KGICAMCGKKILD 81 (90)
T ss_pred ccccccccccc------CCCccChhhhcc--cCcccccCCeecc
Confidence 45555544422 366789999655 3589999998865
No 51
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=42.65 E-value=14 Score=23.06 Aligned_cols=8 Identities=50% Similarity=1.306 Sum_probs=4.0
Q ss_pred cccCCccc
Q 011854 116 CAGCNNEI 123 (476)
Q Consensus 116 C~~C~~~I 123 (476)
|..|+..|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 44455554
No 52
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=42.48 E-value=21 Score=40.55 Aligned_cols=11 Identities=45% Similarity=0.739 Sum_probs=7.0
Q ss_pred CCCcchhhHHH
Q 011854 251 ECQPLYLDIQE 261 (476)
Q Consensus 251 ~Cqp~~~~I~~ 261 (476)
+|||+...+++
T Consensus 124 d~~p~~~s~~~ 134 (645)
T PRK14559 124 DCQPLQPSPLE 134 (645)
T ss_pred ecCCCccCHHH
Confidence 57877665543
No 53
>PHA00527 hypothetical protein
Probab=42.11 E-value=55 Score=28.41 Aligned_cols=63 Identities=22% Similarity=0.277 Sum_probs=40.4
Q ss_pred cccccccccccccccceEEEE-EecCchhHHhhhhhhccchhhhhhh---cCCCCCCcchhhhHHHHHHHHH
Q 011854 327 ARNIITEPYKLTRRCDVTAIL-ILYGLPRLLTGTILAHEMMHGWMRL---QGFRTLSPDVEEGICQVIAHWW 394 (476)
Q Consensus 327 i~e~~~~p~~~~~~~ev~~il-~l~glp~~l~g~ilaHe~~Ha~l~~---~g~~~l~~~~eEG~cq~~a~~w 394 (476)
.+--+|.+.-.+...++--+| |..|.. |||+||.+|+-.-+ -|...-|-+.-|-.|-+|+-|.
T Consensus 47 mla~~~~S~~~s~~~~~L~~~GVFNGK~-----~T~~HECAH~AF~vC~~VGV~~E~G~ANETYCY~~~R~~ 113 (129)
T PHA00527 47 MLAGATQSYCNTETGENLYLLGVFNGKA-----ATLVHECAHVAFYVCRDVGVTTEPGDANETYCYMLDRMF 113 (129)
T ss_pred hhhccccccccccCCCeEEEEEEeccHH-----HHHHHHHHHHHHHHHHhcCcccCCCccchhHHHHHHHHH
Confidence 344455555555554443333 666654 59999999987532 2555556677788998887765
No 54
>COG5504 Predicted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=42.06 E-value=17 Score=36.39 Aligned_cols=36 Identities=28% Similarity=0.285 Sum_probs=24.2
Q ss_pred hhhhhccchhhhhhhcC-------CCCCCcchhhhHHHHHHHHH
Q 011854 358 GTILAHEMMHGWMRLQG-------FRTLSPDVEEGICQVIAHWW 394 (476)
Q Consensus 358 g~ilaHe~~Ha~l~~~g-------~~~l~~~~eEG~cq~~a~~w 394 (476)
-|+||||+ |--.|+.. ...|+.-|-||+.|-.++-=
T Consensus 141 ~aliaHE~-HH~~R~~~i~~~eg~vtLle~lV~EGLAE~av~E~ 183 (280)
T COG5504 141 PALIAHEY-HHNCRLRYIDYGEGSVTLLEALVMEGLAEHAVFEL 183 (280)
T ss_pred HHHHHHHH-HhhheecccccCCCceeHHHHHHHHHHHHHHHHHH
Confidence 46999999 54555532 13557889999998655443
No 55
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=41.52 E-value=16 Score=38.71 Aligned_cols=26 Identities=42% Similarity=0.542 Sum_probs=22.4
Q ss_pred CccccchHHHHHHHhhhhhhhhcCCC
Q 011854 40 PLEQENEDIDRAIALSLLEENQKGEN 65 (476)
Q Consensus 40 ~~~~~~e~~~~a~~~sl~e~~~~~~~ 65 (476)
...+|+|||..||++||.|.++.+|.
T Consensus 161 ~~k~EeEdiaKAi~lSL~E~~~Q~k~ 186 (462)
T KOG2199|consen 161 SSKQEEEDIAKAIELSLKEQEKQKKL 186 (462)
T ss_pred cccccHHHHHHHHHhhHHHHhhchhh
Confidence 44789999999999999998887664
No 56
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=41.08 E-value=15 Score=33.17 Aligned_cols=22 Identities=23% Similarity=0.720 Sum_probs=15.3
Q ss_pred ccCCCCCCCCCceeeccCCcccccccc
Q 011854 142 CCHACHQPITDIEFSTSENRPYHKSCY 168 (476)
Q Consensus 142 ~C~~C~~~L~~~~f~~~dg~~YCk~cY 168 (476)
.|..|+.|| |- ++|.+||.-|-
T Consensus 30 hCp~Cg~PL----F~-KdG~v~CPvC~ 51 (131)
T COG1645 30 HCPKCGTPL----FR-KDGEVFCPVCG 51 (131)
T ss_pred hCcccCCcc----ee-eCCeEECCCCC
Confidence 366777776 33 79999887763
No 57
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=40.99 E-value=34 Score=39.39 Aligned_cols=49 Identities=18% Similarity=0.415 Sum_probs=31.3
Q ss_pred CcccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCcccccccccc-cccccccccCCc
Q 011854 113 YRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYRE-HYHPKCDVCKHF 182 (476)
Q Consensus 113 ~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~-~f~~~C~~C~~~ 182 (476)
.-.|..|+.. ++|..|+.+|+- ....+.+.|+-|-.+ ..-..|..|+..
T Consensus 435 ~l~C~~Cg~v------------------~~Cp~Cd~~lt~---H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 435 LLLCRDCGYI------------------AECPNCDSPLTL---HKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred eeecccCCCc------------------ccCCCCCcceEE---ecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 4679999965 478999888753 333466767666544 233356666544
No 58
>PRK14015 pepN aminopeptidase N; Provisional
Probab=39.92 E-value=63 Score=38.07 Aligned_cols=42 Identities=19% Similarity=0.361 Sum_probs=29.2
Q ss_pred hhhhhhccchhhhhhhc-CCCCC-CcchhhhHHHHHHHHHHhhh
Q 011854 357 TGTILAHEMMHGWMRLQ-GFRTL-SPDVEEGICQVIAHWWLISQ 398 (476)
Q Consensus 357 ~g~ilaHe~~Ha~l~~~-g~~~l-~~~~eEG~cq~~a~~wl~~~ 398 (476)
..++||||+.|-|..=. -+..- ...+-|||.-++.+.|.+..
T Consensus 296 i~~vIaHElaHqWFGNlVT~~~W~dLWLnEGFAty~e~~~~~~~ 339 (875)
T PRK14015 296 IESVIAHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSADL 339 (875)
T ss_pred HHHHHHHHHHHHHHhCcceecchhhhhhhhHHHHHHHHHHHHHh
Confidence 45799999999996310 11222 25679999999988886643
No 59
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=39.16 E-value=8.7 Score=33.06 Aligned_cols=26 Identities=31% Similarity=0.561 Sum_probs=12.6
Q ss_pred cccCCcccccCceEeec-CccccCCCc
Q 011854 116 CAGCNNEIGHGRFLNCL-DVFWHPECF 141 (476)
Q Consensus 116 C~~C~~~I~~g~~v~al-gk~wH~~CF 141 (476)
|.-|+++|+.|+..++. +..-|-.||
T Consensus 5 C~iCg~~I~~gqlFTF~~kG~VH~~C~ 31 (101)
T PF09943_consen 5 CYICGKPIYEGQLFTFTKKGPVHYECF 31 (101)
T ss_pred EEecCCeeeecceEEEecCCcEeHHHH
Confidence 55566655555544332 234444444
No 60
>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=39.07 E-value=21 Score=26.05 Aligned_cols=42 Identities=19% Similarity=0.497 Sum_probs=28.9
Q ss_pred ccCCCCCCCCCceeeccCCcc-ccccccccc--ccccccccCCccc
Q 011854 142 CCHACHQPITDIEFSTSENRP-YHKSCYREH--YHPKCDVCKHFIP 184 (476)
Q Consensus 142 ~C~~C~~~L~~~~f~~~dg~~-YCk~cY~~~--f~~~C~~C~~~I~ 184 (476)
.|..|........+ ..=|.. +|..|+.+. ...+|..|.++|.
T Consensus 4 ~C~iC~~~~~~~~~-~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENPRDVVL-LPCGHLCFCEECAERLLKRKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSBSSEEE-ETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred CCccCCccCCceEE-eCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence 56677766555433 356777 999998775 4679999999886
No 61
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=38.08 E-value=33 Score=25.84 Aligned_cols=27 Identities=22% Similarity=0.503 Sum_probs=18.5
Q ss_pred CCChhhHHHHHHHHHHhCHHHHHHHHHhh
Q 011854 443 PVYGDGFRAGQHAVQKYGLGRTLDHIRRT 471 (476)
Q Consensus 443 ~~yG~Gfr~~~~~~~~~gl~~~l~~~~~~ 471 (476)
-|||-|-..|.+-++ .|++ +|+.|+..
T Consensus 6 ~I~GVG~~tA~~w~~-~G~r-tl~Dl~~~ 32 (52)
T PF10391_consen 6 GIWGVGPKTARKWYA-KGIR-TLEDLRKS 32 (52)
T ss_dssp TSTT--HHHHHHHHH-TT---SHHHHHHG
T ss_pred hcccccHHHHHHHHH-hCCC-CHHHHhhh
Confidence 499999999999998 8875 56666653
No 62
>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=37.94 E-value=17 Score=33.73 Aligned_cols=55 Identities=16% Similarity=0.356 Sum_probs=36.2
Q ss_pred cccccccccccccccccccCCcccCCC--CcceEEcccCccccccCCCCccCCCCccCCCCcccCCCCce
Q 011854 161 RPYHKSCYREHYHPKCDVCKHFIPSNH--GGLIEYRAHPFWVQKYCPSHEHDGTPRCCSCERMEPQDTAY 228 (476)
Q Consensus 161 ~~YCk~cY~~~f~~~C~~C~~~I~~~~--~g~i~~~~hpfw~qkyC~~h~H~~CF~C~~C~r~~~~g~~y 228 (476)
.-||.+|-.+. -..|..|+.+|.+.. .|.+.+.. ||+.- --|..|+++.|+....
T Consensus 28 ~~fC~kCG~~t-I~~Cp~C~~~IrG~y~v~gv~~~g~-----------~~~~P-sYC~~CGkpyPWt~~~ 84 (158)
T PF10083_consen 28 EKFCSKCGAKT-ITSCPNCSTPIRGDYHVEGVFGLGG-----------HYEAP-SYCHNCGKPYPWTENA 84 (158)
T ss_pred HHHHHHhhHHH-HHHCcCCCCCCCCceecCCeeeeCC-----------CCCCC-hhHHhCCCCCchHHHH
Confidence 45899997665 578999999999853 23343322 22211 1388999988876543
No 63
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=37.81 E-value=19 Score=25.62 Aligned_cols=38 Identities=21% Similarity=0.550 Sum_probs=23.5
Q ss_pred cCCCCCCCC--CceeeccCCcccccccccccc--cccccccC
Q 011854 143 CHACHQPIT--DIEFSTSENRPYHKSCYREHY--HPKCDVCK 180 (476)
Q Consensus 143 C~~C~~~L~--~~~f~~~dg~~YCk~cY~~~f--~~~C~~C~ 180 (476)
|..|...+. ...+...=|..+|..|..... ...|..|+
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~~~~~~CP~C~ 43 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLKGKSVKCPICR 43 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhcCCCCCCcCCC
Confidence 566666662 233444567888888877665 44666665
No 64
>TIGR02411 leuko_A4_hydro leukotriene A-4 hydrolase/aminopeptidase. Members of this family represent a distinctive subset within the zinc metallopeptidase family M1 (pfam01433). The majority of the members of pfam01433 are aminopeptidases, but the sequences in this family for which the function is known are leukotriene A-4 hydrolase. A dual epoxide hydrolase and aminopeptidase activity at the same active site is indicated. The physiological substrate for aminopeptidase activity is not known.
Probab=37.70 E-value=18 Score=40.65 Aligned_cols=39 Identities=18% Similarity=0.207 Sum_probs=29.2
Q ss_pred hhhhccchhhhhhh-cCCCCC-CcchhhhHHHHHHHHHHhh
Q 011854 359 TILAHEMMHGWMRL-QGFRTL-SPDVEEGICQVIAHWWLIS 397 (476)
Q Consensus 359 ~ilaHe~~Ha~l~~-~g~~~l-~~~~eEG~cq~~a~~wl~~ 397 (476)
.+||||++|-|..- -....= ...+-|||+-.+.+.+++.
T Consensus 281 ~viaHElAHqWfGNlVT~~~W~d~WLnEGfaty~e~~~~~~ 321 (601)
T TIGR02411 281 DVIAHELAHSWSGNLVTNCSWEHFWLNEGWTVYLERRIVGR 321 (601)
T ss_pred hhHHHHHHhhccCceeecCCchHHHHHhhHHHHHHHHHHHH
Confidence 59999999999851 122222 3689999999999987663
No 65
>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]
Probab=37.66 E-value=9.1 Score=37.01 Aligned_cols=42 Identities=21% Similarity=0.246 Sum_probs=29.3
Q ss_pred ccCCCCccCCCCcccCCCCceEEecCCcccchhhHhhh----ccCCCC
Q 011854 208 EHDGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSA----IMDTNE 251 (476)
Q Consensus 208 ~H~~CF~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~~~----v~d~~~ 251 (476)
||..||.|..|+..+. =..|- -.+.++||-.+|... +.|+|+
T Consensus 27 whk~cfkce~c~mtln-mKnyK-gy~kkpycn~hYpkq~at~~adTPE 72 (264)
T KOG1702|consen 27 WHKQCFKCEVCGMTLN-MKNYK-GYDKKPYCNPHYPKQVATVMADTPE 72 (264)
T ss_pred HHHHhheeeeccCChh-hhhcc-ccccCCCcCcccccceeeeecCCHH
Confidence 7999999999996542 22332 247899999999743 445543
No 66
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=36.86 E-value=19 Score=25.37 Aligned_cols=30 Identities=27% Similarity=0.671 Sum_probs=20.3
Q ss_pred cccCCcccccC-ceEeecCccccCCCcccCCCCC
Q 011854 116 CAGCNNEIGHG-RFLNCLDVFWHPECFCCHACHQ 148 (476)
Q Consensus 116 C~~C~~~I~~g-~~v~algk~wH~~CF~C~~C~~ 148 (476)
|.-|+++|... ..++..++.|| |.|..|..
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~ 31 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLS 31 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE---EECHHHHH
Confidence 77899998533 34677888888 55555543
No 67
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.79 E-value=19 Score=36.78 Aligned_cols=45 Identities=22% Similarity=0.418 Sum_probs=32.8
Q ss_pred CcccCCCCCCCCCceeeccCCcccccccccccc--cccccccCCcccC
Q 011854 140 CFCCHACHQPITDIEFSTSENRPYHKSCYREHY--HPKCDVCKHFIPS 185 (476)
Q Consensus 140 CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f--~~~C~~C~~~I~~ 185 (476)
=|.|..|.+.+... ....-+..+|+.|....| +++|.+|++.+.+
T Consensus 241 Pf~c~icr~~f~~p-Vvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 241 PFKCFICRKYFYRP-VVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred Cccccccccccccc-hhhcCCceeehhhhccccccCCcceeccccccc
Confidence 37788888776543 223467788999987654 4799999998876
No 68
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=36.01 E-value=24 Score=29.50 Aligned_cols=13 Identities=31% Similarity=0.713 Sum_probs=9.4
Q ss_pred cccccccCCcccC
Q 011854 173 HPKCDVCKHFIPS 185 (476)
Q Consensus 173 ~~~C~~C~~~I~~ 185 (476)
...|.+|++.|..
T Consensus 78 ~~~C~vC~k~l~~ 90 (109)
T PF10367_consen 78 STKCSVCGKPLGN 90 (109)
T ss_pred CCCccCcCCcCCC
Confidence 3578888887765
No 69
>PRK04023 DNA polymerase II large subunit; Validated
Probab=34.38 E-value=41 Score=39.84 Aligned_cols=37 Identities=19% Similarity=0.266 Sum_probs=20.1
Q ss_pred cccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccC
Q 011854 141 FCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPS 185 (476)
Q Consensus 141 F~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f~~~C~~C~~~I~~ 185 (476)
|+|..|+.. .....+|..|-.......|..|+..+..
T Consensus 639 frCP~CG~~--------Te~i~fCP~CG~~~~~y~CPKCG~El~~ 675 (1121)
T PRK04023 639 RRCPFCGTH--------TEPVYRCPRCGIEVEEDECEKCGREPTP 675 (1121)
T ss_pred ccCCCCCCC--------CCcceeCccccCcCCCCcCCCCCCCCCc
Confidence 566666654 1222356666554444556666665554
No 70
>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=34.10 E-value=18 Score=24.44 Aligned_cols=39 Identities=15% Similarity=0.502 Sum_probs=18.3
Q ss_pred cCCCCCCCCCceeeccCCcccccccccccc---cccccccCC
Q 011854 143 CHACHQPITDIEFSTSENRPYHKSCYREHY---HPKCDVCKH 181 (476)
Q Consensus 143 C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f---~~~C~~C~~ 181 (476)
|..|...+........=|..||..|....+ ..+|..|+.
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRT 43 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHHHHhCcCCCCCCCC
Confidence 455555542222222245566666654332 235666654
No 71
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=33.88 E-value=24 Score=34.83 Aligned_cols=34 Identities=21% Similarity=0.402 Sum_probs=27.1
Q ss_pred Cceee-ccCCcccccccccccccccccccCCcccC
Q 011854 152 DIEFS-TSENRPYHKSCYREHYHPKCDVCKHFIPS 185 (476)
Q Consensus 152 ~~~f~-~~dg~~YCk~cY~~~f~~~C~~C~~~I~~ 185 (476)
...|+ ..-..++|..|......+.|..|++.|..
T Consensus 15 ~~~f~LTaC~HvfC~~C~k~~~~~~C~lCkk~ir~ 49 (233)
T KOG4739|consen 15 QDPFFLTACRHVFCEPCLKASSPDVCPLCKKSIRI 49 (233)
T ss_pred CCceeeeechhhhhhhhcccCCccccccccceeee
Confidence 33444 46778999999998888899999999765
No 72
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=33.49 E-value=19 Score=36.91 Aligned_cols=44 Identities=18% Similarity=0.420 Sum_probs=26.9
Q ss_pred ccCCCCCCCCCceeeccCCcccccccccccccccccccCCcccC
Q 011854 142 CCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIPS 185 (476)
Q Consensus 142 ~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f~~~C~~C~~~I~~ 185 (476)
.|..|+.+|.-.+--.--...||.+|....--..|..|...|.-
T Consensus 92 fCd~Cd~PI~IYGRmIPCkHvFCl~CAr~~~dK~Cp~C~d~Vqr 135 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKHVFCLECARSDSDKICPLCDDRVQR 135 (389)
T ss_pred eecccCCcceeeecccccchhhhhhhhhcCccccCcCcccHHHH
Confidence 35566666654333333456677777665545588999887653
No 73
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.28 E-value=21 Score=33.85 Aligned_cols=50 Identities=26% Similarity=0.563 Sum_probs=35.4
Q ss_pred CCCCccCCCCcccCCCCceEEecCCcccchhhHhhhccCCCCCCcchhhHH
Q 011854 210 DGTPRCCSCERMEPQDTAYVALDDGRKLCLECLDSAIMDTNECQPLYLDIQ 260 (476)
Q Consensus 210 ~~CF~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~~~v~d~~~Cqp~~~~I~ 260 (476)
..||.|-.|-........ +.-+=|.++|.+|.+.++..+..|--|...|.
T Consensus 129 ~~~~~CPiCl~~~sek~~-vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVP-VSTKCGHVFCSQCIKDALKNTNKCPTCRKKIT 178 (187)
T ss_pred ccccCCCceecchhhccc-cccccchhHHHHHHHHHHHhCCCCCCcccccc
Confidence 457888888643222222 23467899999999999988899988886663
No 74
>COG0308 PepN Aminopeptidase N [Amino acid transport and metabolism]
Probab=31.66 E-value=1.9e+02 Score=34.14 Aligned_cols=45 Identities=20% Similarity=0.280 Sum_probs=32.7
Q ss_pred HHhhhhhhccchhhhhh-hcCCC-CCCcchhhhHHHHHHHHHHhhhc
Q 011854 355 LLTGTILAHEMMHGWMR-LQGFR-TLSPDVEEGICQVIAHWWLISQL 399 (476)
Q Consensus 355 ~l~g~ilaHe~~Ha~l~-~~g~~-~l~~~~eEG~cq~~a~~wl~~~~ 399 (476)
+-+.+++|||+.|.|-. +--+. --...+-|||--++.+.|.++..
T Consensus 305 ~~~~~viaHElaHqWfGnlVT~~~W~~lWLnEgfat~~e~~~~~~~~ 351 (859)
T COG0308 305 ENVEEVIAHELAHQWFGNLVTMKWWDDLWLNEGFATFREVLWSEDLG 351 (859)
T ss_pred HHHHHHHHHHHhhhcccceeeccCHHHHHHhhhhHHHHHHHHHHHhc
Confidence 44456999999999963 10111 12378999999999999998765
No 75
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=31.54 E-value=22 Score=32.17 Aligned_cols=20 Identities=30% Similarity=0.285 Sum_probs=16.0
Q ss_pred HHhhhhhhccchhhhhhhcC
Q 011854 355 LLTGTILAHEMMHGWMRLQG 374 (476)
Q Consensus 355 ~l~g~ilaHe~~Ha~l~~~g 374 (476)
..+-.||.|||.|+++.+.|
T Consensus 57 ~~l~~~l~HEm~H~~~~~~g 76 (146)
T smart00731 57 DRLRETLLHELCHAALYLFG 76 (146)
T ss_pred HHHHhhHHHHHHHHHHHHhC
Confidence 34456999999999998754
No 76
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=31.43 E-value=24 Score=29.06 Aligned_cols=31 Identities=26% Similarity=0.534 Sum_probs=20.8
Q ss_pred ccCCCCcccCCCCceEEecCC---cccchhhHhh
Q 011854 214 RCCSCERMEPQDTAYVALDDG---RKLCLECLDS 244 (476)
Q Consensus 214 ~C~~C~r~~~~g~~y~~l~dg---~~~C~~C~~~ 244 (476)
.|-+|+.++.....|....|| .-||.-||..
T Consensus 2 ~CQSCGMPl~~~~~~Gte~dGs~s~~YC~yCy~~ 35 (81)
T PF12674_consen 2 FCQSCGMPLSKDEDFGTEADGSKSEDYCSYCYQN 35 (81)
T ss_pred cCCcCcCccCCccccccccCCCCchhHHHHHhcC
Confidence 378888877555434444454 3699999975
No 77
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=31.27 E-value=25 Score=26.94 Aligned_cols=14 Identities=21% Similarity=0.501 Sum_probs=9.9
Q ss_pred CcccccCCcccccC
Q 011854 113 YRICAGCNNEIGHG 126 (476)
Q Consensus 113 ~~~C~~C~~~I~~g 126 (476)
..+|..|++.|.++
T Consensus 5 ~~~C~~Cg~~~~~~ 18 (54)
T PF14446_consen 5 GCKCPVCGKKFKDG 18 (54)
T ss_pred CccChhhCCcccCC
Confidence 45788888888543
No 78
>PF12773 DZR: Double zinc ribbon
Probab=30.47 E-value=42 Score=24.37 Aligned_cols=11 Identities=27% Similarity=0.655 Sum_probs=5.1
Q ss_pred ccccccCCccc
Q 011854 174 PKCDVCKHFIP 184 (476)
Q Consensus 174 ~~C~~C~~~I~ 184 (476)
..|..|+..+.
T Consensus 13 ~fC~~CG~~l~ 23 (50)
T PF12773_consen 13 KFCPHCGTPLP 23 (50)
T ss_pred cCChhhcCChh
Confidence 44455544443
No 79
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=30.40 E-value=32 Score=24.76 Aligned_cols=22 Identities=27% Similarity=0.761 Sum_probs=13.6
Q ss_pred ccCCCCCCCCCceeeccCCccccccc
Q 011854 142 CCHACHQPITDIEFSTSENRPYHKSC 167 (476)
Q Consensus 142 ~C~~C~~~L~~~~f~~~dg~~YCk~c 167 (476)
.|..|+.||-. .++|+.||-.|
T Consensus 19 ~Cp~C~~PL~~----~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPLMR----DKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCeeEE----ecCCCEECCCC
Confidence 45667766633 35777777655
No 80
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=29.68 E-value=18 Score=31.29 Aligned_cols=31 Identities=35% Similarity=0.760 Sum_probs=19.0
Q ss_pred CCCcccccCCcccccCceEeecCccccCCCcccCCCC
Q 011854 111 EGYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACH 147 (476)
Q Consensus 111 ~~~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~ 147 (476)
...+.|..|+++|. -..+.+ -|++..|..|.
T Consensus 78 g~yG~C~~Cge~I~-~~RL~a-----~P~a~~Cv~Cq 108 (110)
T TIGR02420 78 GEYGYCEECGEEIG-LRRLEA-----RPTATLCIDCK 108 (110)
T ss_pred CCCCchhccCCccc-HHHHhh-----CCCccccHHhH
Confidence 45679999999994 333433 24444555553
No 81
>PF09768 Peptidase_M76: Peptidase M76 family; InterPro: IPR019165 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. Mitochondrial inner membrane protease ATP23 has two roles in the assembly of mitochondrial ATPase. Firstly, it acts as a protease that removes the N-terminal 10 residues of mitochondrial ATPase CF(0) subunit 6 (ATP6) at the intermembrane space side. Secondly, it is involved in the correct assembly of the membrane-embedded ATPase CF(0) particle, probably mediating association of ATP6 with the subunit 9 ring [, ].; GO: 0004222 metalloendopeptidase activity
Probab=29.20 E-value=19 Score=34.08 Aligned_cols=16 Identities=25% Similarity=0.490 Sum_probs=12.8
Q ss_pred hhhhhhccchhhhhhh
Q 011854 357 TGTILAHEMMHGWMRL 372 (476)
Q Consensus 357 ~g~ilaHe~~Ha~l~~ 372 (476)
...||+|||.|||=.+
T Consensus 71 l~~~l~HELIHayD~c 86 (173)
T PF09768_consen 71 LEDTLTHELIHAYDHC 86 (173)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3569999999999544
No 82
>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=28.99 E-value=9.3 Score=29.23 Aligned_cols=25 Identities=16% Similarity=0.049 Sum_probs=19.1
Q ss_pred ccCCCCCccccccccccccccccce
Q 011854 319 PRFGPGNQARNIITEPYKLTRRCDV 343 (476)
Q Consensus 319 ~~~~~g~ri~e~~~~p~~~~~~~ev 343 (476)
..+.+||+|++||++++......++
T Consensus 29 ~gl~~GD~I~~Ing~~v~~~~~~~~ 53 (70)
T cd00136 29 AGLQAGDVILAVNGTDVKNLTLEDV 53 (70)
T ss_pred cCCCCCCEEEEECCEECCCCCHHHH
Confidence 3578999999999999876644333
No 83
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=28.00 E-value=18 Score=31.04 Aligned_cols=28 Identities=25% Similarity=0.656 Sum_probs=19.3
Q ss_pred CccCCCCcccCCCCceEEecCCcccchhh
Q 011854 213 PRCCSCERMEPQDTAYVALDDGRKLCLEC 241 (476)
Q Consensus 213 F~C~~C~r~~~~g~~y~~l~dg~~~C~~C 241 (476)
|+|++|--+- ...+-....+|.++|..|
T Consensus 71 FTCssCFLV~-HRSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 71 FTCSSCFLVH-HRSQLAREKDGQPICRDC 98 (99)
T ss_pred eeeeeeeeEe-chhhhccccCCCEecccc
Confidence 8999998432 223334355789999988
No 84
>PRK00420 hypothetical protein; Validated
Probab=26.60 E-value=39 Score=29.68 Aligned_cols=22 Identities=14% Similarity=0.324 Sum_probs=11.8
Q ss_pred ccCCCCCCCCCceeeccCCccccccc
Q 011854 142 CCHACHQPITDIEFSTSENRPYHKSC 167 (476)
Q Consensus 142 ~C~~C~~~L~~~~f~~~dg~~YCk~c 167 (476)
.|..|+.+|. -.++|+.||..|
T Consensus 25 ~CP~Cg~pLf----~lk~g~~~Cp~C 46 (112)
T PRK00420 25 HCPVCGLPLF----ELKDGEVVCPVH 46 (112)
T ss_pred CCCCCCCcce----ecCCCceECCCC
Confidence 4555665552 225676665554
No 85
>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=26.27 E-value=63 Score=22.99 Aligned_cols=32 Identities=31% Similarity=0.680 Sum_probs=20.8
Q ss_pred ccCCCCcccCCCCceEEecCCcccchhhHhhh
Q 011854 214 RCCSCERMEPQDTAYVALDDGRKLCLECLDSA 245 (476)
Q Consensus 214 ~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~~~ 245 (476)
+|+-|++......+.+.-.++-..|..|-..+
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~~ 34 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQA 34 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHHH
Confidence 58999998766666665555788999997653
No 86
>KOG3552 consensus FERM domain protein FRM-8 [General function prediction only]
Probab=26.06 E-value=23 Score=41.27 Aligned_cols=23 Identities=30% Similarity=0.423 Sum_probs=19.4
Q ss_pred cCCCCCccccccccccccccccc
Q 011854 320 RFGPGNQARNIITEPYKLTRRCD 342 (476)
Q Consensus 320 ~~~~g~ri~e~~~~p~~~~~~~e 342 (476)
.+.+||.|+.||++||+..+++.
T Consensus 91 KL~PGDQIl~vN~Epv~daprer 113 (1298)
T KOG3552|consen 91 KLQPGDQILAVNGEPVKDAPRER 113 (1298)
T ss_pred cccCCCeEEEecCcccccccHHH
Confidence 46799999999999999776654
No 87
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=26.03 E-value=18 Score=41.12 Aligned_cols=29 Identities=21% Similarity=0.544 Sum_probs=19.3
Q ss_pred CCccccccccccccc---ccccccCCcccCCC
Q 011854 159 ENRPYHKSCYREHYH---PKCDVCKHFIPSNH 187 (476)
Q Consensus 159 dg~~YCk~cY~~~f~---~~C~~C~~~I~~~~ 187 (476)
-++.||..|-..++. -+|..|+.....++
T Consensus 661 C~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 661 CGHVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred cchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 445667777655443 47999988777655
No 88
>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=25.89 E-value=28 Score=32.27 Aligned_cols=52 Identities=21% Similarity=0.390 Sum_probs=35.3
Q ss_pred CcccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCcccccccccccccccccccCCccc
Q 011854 113 YRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHPKCDVCKHFIP 184 (476)
Q Consensus 113 ~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f~~~C~~C~~~I~ 184 (476)
...|.+||.... -.|..|+.+|.+..| .+|.++=..+|. --..|+.|+++.+
T Consensus 28 ~~fC~kCG~~tI----------------~~Cp~C~~~IrG~y~--v~gv~~~g~~~~--~PsYC~~CGkpyP 79 (158)
T PF10083_consen 28 EKFCSKCGAKTI----------------TSCPNCSTPIRGDYH--VEGVFGLGGHYE--APSYCHNCGKPYP 79 (158)
T ss_pred HHHHHHhhHHHH----------------HHCcCCCCCCCCcee--cCCeeeeCCCCC--CChhHHhCCCCCc
Confidence 345889988653 378899999987533 255555455554 2347999998765
No 89
>PF01421 Reprolysin: Reprolysin (M12B) family zinc metalloprotease This Prosite motif covers only the active site.; InterPro: IPR001590 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M12, subfamily M12B (adamalysin family, clan (MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. The adamalysins are zinc dependent endopeptidases found in snake venom. There are some mammalian proteins such as P78325 from SWISSPROT, and fertilin Q28472 from SWISSPROT. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes. CD156 (also called ADAM8 (3.4.24 from EC) or MS2 human) has been implicated in extravasation of leukocytes. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2E3X_A 2W15_A 2W14_A 2W13_A 2W12_A 1ND1_A 3K7L_A 2DW2_A 2DW0_B 2DW1_A ....
Probab=25.84 E-value=39 Score=31.87 Aligned_cols=25 Identities=28% Similarity=0.258 Sum_probs=18.2
Q ss_pred EEEEEecCchhHHhhhhhhccchhh
Q 011854 344 TAILILYGLPRLLTGTILAHEMMHG 368 (476)
Q Consensus 344 ~~il~l~glp~~l~g~ilaHe~~Ha 368 (476)
-+|....+.....++.++|||++|.
T Consensus 118 ~~i~~~~~~~~~~~a~~~AHelGH~ 142 (199)
T PF01421_consen 118 CGIVEDHSRSGLSFAVIIAHELGHN 142 (199)
T ss_dssp EEEEE-SSSSHHHHHHHHHHHHHHH
T ss_pred CcEeeeccchhHHHHHHHHHHHHHh
Confidence 3455555567778899999999984
No 90
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=25.70 E-value=25 Score=27.42 Aligned_cols=26 Identities=27% Similarity=0.511 Sum_probs=13.0
Q ss_pred ccCCCCcccCCCCceEEecCCcccchhhHhh
Q 011854 214 RCCSCERMEPQDTAYVALDDGRKLCLECLDS 244 (476)
Q Consensus 214 ~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~~ 244 (476)
.|.+|+..|..++.|+ ...|.+|-+.
T Consensus 11 ~CtSCg~~i~p~e~~v-----~F~CPnCGe~ 36 (61)
T COG2888 11 VCTSCGREIAPGETAV-----KFPCPNCGEV 36 (61)
T ss_pred eeccCCCEeccCCcee-----EeeCCCCCce
Confidence 4555555554444444 3445555443
No 91
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=24.37 E-value=37 Score=25.38 Aligned_cols=31 Identities=13% Similarity=0.328 Sum_probs=13.6
Q ss_pred eeccCCcccccccccc--------cccccccccCCcccC
Q 011854 155 FSTSENRPYHKSCYRE--------HYHPKCDVCKHFIPS 185 (476)
Q Consensus 155 f~~~dg~~YCk~cY~~--------~f~~~C~~C~~~I~~ 185 (476)
++...|-+-|.+||.= .....|..|+++++.
T Consensus 9 Wf~~k~Li~C~dHYLCl~CLt~ml~~s~~C~iC~~~LPt 47 (50)
T PF03854_consen 9 WFANKGLIKCSDHYLCLNCLTLMLSRSDRCPICGKPLPT 47 (50)
T ss_dssp -S--SSEEE-SS-EEEHHHHHHT-SSSSEETTTTEE---
T ss_pred hhcCCCeeeecchhHHHHHHHHHhccccCCCcccCcCcc
Confidence 4455666667666632 234567777776664
No 92
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=24.28 E-value=9.6 Score=26.20 Aligned_cols=8 Identities=38% Similarity=1.161 Sum_probs=3.9
Q ss_pred cccCCccc
Q 011854 116 CAGCNNEI 123 (476)
Q Consensus 116 C~~C~~~I 123 (476)
|..|+++|
T Consensus 6 C~~CGe~I 13 (36)
T PF01258_consen 6 CEDCGEPI 13 (36)
T ss_dssp -TTTSSBE
T ss_pred ccccCChH
Confidence 55555555
No 93
>KOG3209 consensus WW domain-containing protein [General function prediction only]
Probab=24.13 E-value=9.3 Score=43.16 Aligned_cols=27 Identities=22% Similarity=0.144 Sum_probs=23.3
Q ss_pred cccccCCCCCccccccccccccccccc
Q 011854 316 LWRPRFGPGNQARNIITEPYKLTRRCD 342 (476)
Q Consensus 316 ~~~~~~~~g~ri~e~~~~p~~~~~~~e 342 (476)
.+..||++||.|+||||++-+...+..
T Consensus 937 ~rdGrm~VGDqi~eINGesTkgmtH~r 963 (984)
T KOG3209|consen 937 IRDGRMRVGDQITEINGESTKGMTHDR 963 (984)
T ss_pred cccCceeecceEEEecCcccCCCcHHH
Confidence 467899999999999999998887754
No 94
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=23.91 E-value=30 Score=33.49 Aligned_cols=30 Identities=20% Similarity=0.593 Sum_probs=22.5
Q ss_pred CccCCCCcccCCCCceEEecCCcccchhhHhh
Q 011854 213 PRCCSCERMEPQDTAYVALDDGRKLCLECLDS 244 (476)
Q Consensus 213 F~C~~C~r~~~~g~~y~~l~dg~~~C~~C~~~ 244 (476)
-+|..|+.++. .....+.+|+++|..|+..
T Consensus 173 v~C~kCGE~~~--e~~~~~~ng~~vC~~C~~~ 202 (206)
T COG2191 173 VRCSKCGELFM--EPRAVVLNGKPVCKPCAEK 202 (206)
T ss_pred eeccccCcccc--cchhhhcCCceeccccccc
Confidence 48999997653 2334466999999999875
No 95
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.49 E-value=61 Score=39.36 Aligned_cols=51 Identities=24% Similarity=0.387 Sum_probs=0.0
Q ss_pred CCcccccCCcccccCceEeecCccccCCCcccCCCCCCCCCceeeccCCcccccccccccccc-----cccccCCcccC
Q 011854 112 GYRICAGCNNEIGHGRFLNCLDVFWHPECFCCHACHQPITDIEFSTSENRPYHKSCYREHYHP-----KCDVCKHFIPS 185 (476)
Q Consensus 112 ~~~~C~~C~~~I~~g~~v~algk~wH~~CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~~~f~~-----~C~~C~~~I~~ 185 (476)
+...|..|+..+. =+.|..|+.++ .-...|..|-.+.-.. .|..|+.+...
T Consensus 666 ~~rkCPkCG~~t~---------------~~fCP~CGs~t--------e~vy~CPsCGaev~~des~a~~CP~CGtplv~ 721 (1337)
T PRK14714 666 GRRRCPSCGTETY---------------ENRCPDCGTHT--------EPVYVCPDCGAEVPPDESGRVECPRCDVELTP 721 (1337)
T ss_pred EEEECCCCCCccc---------------cccCcccCCcC--------CCceeCccCCCccCCCccccccCCCCCCcccc
No 96
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=23.28 E-value=62 Score=33.98 Aligned_cols=107 Identities=24% Similarity=0.294 Sum_probs=60.8
Q ss_pred EEEecCchhHHh-----hhhhhccchhhhhhhcCCCCCCcchhhhHHHHHHHHHHhhhcccCCCCCCCCCCCcCCCCCCC
Q 011854 346 ILILYGLPRLLT-----GTILAHEMMHGWMRLQGFRTLSPDVEEGICQVIAHWWLISQLKSSKKVTPTSSSSAAGTSKKG 420 (476)
Q Consensus 346 il~l~glp~~l~-----g~ilaHe~~Ha~l~~~g~~~l~~~~eEG~cq~~a~~wl~~~~~~~~~~~~~~~~~~~~~~~~~ 420 (476)
|++-.||-.++- .++|+|||.|+--+. |..+-+.+-+|+|.--+.-..|.+...... ..-.|
T Consensus 108 lYitRGLlAland~sEvAAVl~HEmgHVtAnH-gi~rQ~~e~a~~ia~rvva~vl~~~~agk~------------A~~rG 174 (479)
T COG4784 108 LYITRGLLALANDSSEVAAVLAHEMGHVTANH-GIQRQQREAAEVIASRVVAEVLGSDAAGKQ------------ALIRG 174 (479)
T ss_pred EEEehhHHHHcCCHHHHHHHHHhhhhheecch-hHHHHHHHHHHHHHHHHHHHHhCCcchhhH------------HHhhh
Confidence 466677766553 679999999987655 566666777887765444444333221000 01112
Q ss_pred CCchhHHHHHHHHHhhhhcCCCCCChhhHHHHHH-HHHHhCHHHHHHHHHhhCCC
Q 011854 421 TGPKFDKKLGEFFKHQIETDASPVYGDGFRAGQH-AVQKYGLGRTLDHIRRTGRF 474 (476)
Q Consensus 421 ~~~~~~~~l~~~~~~qi~~d~s~~yG~Gfr~~~~-~~~~~gl~~~l~~~~~~g~~ 474 (476)
+ -+|+.|=++| |--.+ +-|-|..-+ -|+-|-..++|+.+..+-+|
T Consensus 175 k-----lrla~fsRnq-ELqAD---~iG~~~lgeAGYDP~A~~rfl~sm~ay~~F 220 (479)
T COG4784 175 K-----LRLAQFSRNQ-ELQAD---AIGIKMLGEAGYDPYAAARFLQSMAAYTDF 220 (479)
T ss_pred h-----HHHhhhccch-hhhhh---hhhHHHHHhcCCChHHHHHHHHHHHhhhhh
Confidence 1 3555554443 43333 446665433 35666677888887777665
No 97
>cd04270 ZnMc_TACE_like Zinc-dependent metalloprotease; TACE_like subfamily. TACE, the tumor-necrosis factor-alpha converting enzyme, releases soluble TNF-alpha from transmembrane pro-TNF-alpha.
Probab=23.12 E-value=32 Score=34.01 Aligned_cols=22 Identities=32% Similarity=0.581 Sum_probs=15.3
Q ss_pred EecCc--hhHHhhhhhhccchhhh
Q 011854 348 ILYGL--PRLLTGTILAHEMMHGW 369 (476)
Q Consensus 348 ~l~gl--p~~l~g~ilaHe~~Ha~ 369 (476)
+.+|. |...+..|+|||++|.+
T Consensus 156 ~~~~~~~~~~~~a~t~AHElGHnl 179 (244)
T cd04270 156 VNYGKRVPTKESDLVTAHELGHNF 179 (244)
T ss_pred eccCCccchhHHHHHHHHHHHHhc
Confidence 34554 44446679999999975
No 98
>PF01447 Peptidase_M4: Thermolysin metallopeptidase, catalytic domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification. ; InterPro: IPR013856 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases that belong to the MEROPS peptidase family M4 (thermolysin family, clan MA(E)). The protein fold of the peptidase domain of thermolysin, is the type example for members of the clan MA. The thermolysin family is composed only of secreted eubacterial endopeptidases. The zinc-binding residues are H-142, H-146 and E-166, with E-143 acting as the catalytic residue. Thermolysin also contains 4 calcium-binding sites, which contribute to its unusual thermostability. The family also includes enzymes from a number of pathogens, including Legionella and Listeria, and the protein pseudolysin, all with a substrate specificity for an aromatic residue in the P1' position. Three-dimensional structure analysis has shown that the enzymes undergo a hinge-bend motion during catalysis. Pseudolysin has a broader specificity, acting on large molecules such as elastin and collagen, possibly due to its wider active site cleft []. This entry represents a domain found in peptidase M4 family members.; GO: 0004222 metalloendopeptidase activity; PDB: 3NQX_A 3NQZ_B 3NQY_B 1BQB_A 1U4G_A 1EZM_A 3DBK_A 1ESP_A 1NPC_A 1LND_E ....
Probab=23.02 E-value=29 Score=31.91 Aligned_cols=13 Identities=38% Similarity=0.618 Sum_probs=10.6
Q ss_pred hhhhhccchhhhh
Q 011854 358 GTILAHEMMHGWM 370 (476)
Q Consensus 358 g~ilaHe~~Ha~l 370 (476)
--|+|||++|+..
T Consensus 136 lDVvaHEltHGVt 148 (150)
T PF01447_consen 136 LDVVAHELTHGVT 148 (150)
T ss_dssp HHHHHHHHHHHHH
T ss_pred cceeeeccccccc
Confidence 3599999999864
No 99
>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=22.96 E-value=38 Score=22.12 Aligned_cols=13 Identities=31% Similarity=0.728 Sum_probs=7.6
Q ss_pred cccccccCCcccC
Q 011854 173 HPKCDVCKHFIPS 185 (476)
Q Consensus 173 ~~~C~~C~~~I~~ 185 (476)
+.+|..|...|..
T Consensus 1 G~~C~rC~~~~~~ 13 (30)
T PF06827_consen 1 GEKCPRCWNYIED 13 (30)
T ss_dssp TSB-TTT--BBEE
T ss_pred CCcCccCCCcceE
Confidence 4679999988875
No 100
>KOG3624 consensus M13 family peptidase [Amino acid transport and metabolism]
Probab=22.88 E-value=63 Score=36.72 Aligned_cols=71 Identities=20% Similarity=0.362 Sum_probs=0.0
Q ss_pred hhhhhhccchhhh----hhhcCCCCCCcchhhhHHHHHHHHHHhhhcccCCCCCCCCCCCcCCCCCCCCCchhHHHHHHH
Q 011854 357 TGTILAHEMMHGW----MRLQGFRTLSPDVEEGICQVIAHWWLISQLKSSKKVTPTSSSSAAGTSKKGTGPKFDKKLGEF 432 (476)
Q Consensus 357 ~g~ilaHe~~Ha~----l~~~g~~~l~~~~eEG~cq~~a~~wl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~ 432 (476)
.|.+|+||++|++ +.-....++.+ |.+.+..... .+..+=
T Consensus 518 iG~vigHEl~H~FD~~G~~~D~~Gn~~~-------------ww~~~s~~~f-----------------------~~~~qC 561 (687)
T KOG3624|consen 518 IGFVIGHELTHGFDDQGRQYDESGNLRD-------------WWDTESESEF-----------------------QERAQC 561 (687)
T ss_pred HHHHHHHHHhhcccccccccCCCccccc-------------CCCHhHHHHH-----------------------HHHHHH
Q ss_pred HHhhhhcCCCC-------------CChhhHHHHHHHHHHhCHHH
Q 011854 433 FKHQIETDASP-------------VYGDGFRAGQHAVQKYGLGR 463 (476)
Q Consensus 433 ~~~qi~~d~s~-------------~yG~Gfr~~~~~~~~~gl~~ 463 (476)
+.+|-.+=..| +=..|+|.|..|+.+..+..
T Consensus 562 ~~~qy~~y~~~~~~ng~~t~~EnIAD~~Gl~~A~~AY~~~~~~~ 605 (687)
T KOG3624|consen 562 LVKQYSNYLDPRRLNGSKTLGENIADNGGLKLAYRAYKKWKLDL 605 (687)
T ss_pred HHHHHhccCCCcccCCccccchhhcchhhHHHHHHHHHHHHHhc
No 101
>cd04267 ZnMc_ADAM_like Zinc-dependent metalloprotease, ADAM_like or reprolysin_like subgroup. The adamalysin_like or ADAM family of metalloproteases contains proteolytic domains from snake venoms, proteases from the mammalian reproductive tract, and the tumor necrosis factor alpha convertase, TACE. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
Probab=22.79 E-value=38 Score=31.65 Aligned_cols=25 Identities=32% Similarity=0.456 Sum_probs=16.9
Q ss_pred EEEEEecCchhHHhhhhhhccchhhh
Q 011854 344 TAILILYGLPRLLTGTILAHEMMHGW 369 (476)
Q Consensus 344 ~~il~l~glp~~l~g~ilaHe~~Ha~ 369 (476)
.+|....+. ....+.|+|||++|..
T Consensus 121 ~~v~~~~~~-~~~~~~~~aHElGH~l 145 (192)
T cd04267 121 VGVVEDTGF-TLLTALTMAHELGHNL 145 (192)
T ss_pred eEEEecCCc-ceeehhhhhhhHHhhc
Confidence 345545543 4566889999999954
No 102
>COG1088 RfbB dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]
Probab=22.58 E-value=58 Score=33.69 Aligned_cols=29 Identities=28% Similarity=0.492 Sum_probs=22.0
Q ss_pred CCchh-HHHHHHHHHhhhhcCCCCCChhhH
Q 011854 421 TGPKF-DKKLGEFFKHQIETDASPVYGDGF 449 (476)
Q Consensus 421 ~~~~~-~~~l~~~~~~qi~~d~s~~yG~Gf 449 (476)
.+-|| ||-+=-...+-|+..+=||||||-
T Consensus 184 GPyqfpEKlIP~~I~nal~g~~lpvYGdG~ 213 (340)
T COG1088 184 GPYQFPEKLIPLMIINALLGKPLPVYGDGL 213 (340)
T ss_pred CCCcCchhhhHHHHHHHHcCCCCceecCCc
Confidence 34477 455556778888999999999994
No 103
>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=22.30 E-value=50 Score=22.73 Aligned_cols=28 Identities=21% Similarity=0.506 Sum_probs=17.9
Q ss_pred cCCCCCCCCCceeeccCCcccccccccc
Q 011854 143 CHACHQPITDIEFSTSENRPYHKSCYRE 170 (476)
Q Consensus 143 C~~C~~~L~~~~f~~~dg~~YCk~cY~~ 170 (476)
|..|...+.+.-....=|..||+.|..+
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~ 28 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEK 28 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHH
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHH
Confidence 4566666666434556788888888654
No 104
>PF01435 Peptidase_M48: Peptidase family M48 This is family M48 in the peptidase classification. ; InterPro: IPR001915 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M48 (Ste24 endopeptidase family, clan M-); members of both subfamily are represented. The members of this set of proteins are mostly described as probable protease htpX homologue (3.4.24 from EC) or CAAX prenyl protease 1, which proteolytically removes the C-terminal three residues of farnesylated proteins. They are integral membrane proteins associated with the endoplasmic reticulum and Golgi, binding one zinc ion per subunit. In Saccharomyces cerevisiae (Baker's yeast) Ste24p is required for the first NH2-terminal proteolytic processing event within the a-factor precursor, which takes place after COOH-terminal CAAX modification is complete. The Ste24p contains multiple predicted membrane spans, a zinc metalloprotease motif (HEXXH), and a COOH-terminal ER retrieval signal (KKXX). The HEXXH protease motif is critical for Ste24p activity, since Ste24p fails to function when conserved residues within this motif are mutated. The Ste24p homologues occur in a diverse group of organisms, including Escherichia coli, Schizosaccharomyces pombe (Fission yeast), Haemophilus influenzae, and Homo sapiens (Human), which indicates that the gene is highly conserved throughout evolution. Ste24p and the proteins related to it define a subfamily of proteins that are likely to function as intracellular, membrane-associated zinc metalloproteases []. HtpX is a zinc-dependent endoprotease member of the membrane-localized proteolytic system in E. coli, which participates in the proteolytic quality control of membrane proteins in conjunction with FtsH, a membrane-bound and ATP-dependent protease. Biochemical characterisation revealed that HtpX undergoes self-degradation upon cell disruption or membrane solubilization. It can also degraded casein and cleaves solubilized membrane proteins, for example, SecY []. Expression of HtpX in the plasma membrane is under the control of CpxR, with the metalloproteinase active site of HtpX located on the cytosolic side of the membrane. This suggests a potential role for HtpX in the response to mis-folded proteins [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis, 0016020 membrane; PDB: 3CQB_A 3C37_B.
Probab=21.83 E-value=33 Score=32.40 Aligned_cols=28 Identities=36% Similarity=0.432 Sum_probs=18.8
Q ss_pred EEEEecCchhHHh----hhhhhccchhhhhhh
Q 011854 345 AILILYGLPRLLT----GTILAHEMMHGWMRL 372 (476)
Q Consensus 345 ~il~l~glp~~l~----g~ilaHe~~Ha~l~~ 372 (476)
.|++-.||-..++ .++||||+.|...+-
T Consensus 73 ~I~v~~~ll~~~~~~el~aVlaHElgH~~~~h 104 (226)
T PF01435_consen 73 RIVVTSGLLESLSEDELAAVLAHELGHIKHRH 104 (226)
T ss_dssp EEEEEHHHHHHSSHHHHHHHHHHHHHHHHTTH
T ss_pred EEEEeChhhhcccHHHHHHHHHHHHHHHHcCC
Confidence 3455555543333 579999999987765
No 105
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=21.24 E-value=66 Score=30.97 Aligned_cols=29 Identities=21% Similarity=0.405 Sum_probs=15.8
Q ss_pred CcccCCCCCCCCCceeeccCCccccccccc
Q 011854 140 CFCCHACHQPITDIEFSTSENRPYHKSCYR 169 (476)
Q Consensus 140 CF~C~~C~~~L~~~~f~~~dg~~YCk~cY~ 169 (476)
.|.|..|...+.+. ....-|..||..|-.
T Consensus 18 ~~~CpICld~~~dP-VvT~CGH~FC~~CI~ 46 (193)
T PLN03208 18 DFDCNICLDQVRDP-VVTLCGHLFCWPCIH 46 (193)
T ss_pred ccCCccCCCcCCCc-EEcCCCchhHHHHHH
Confidence 35666665555443 223456667777753
No 106
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=20.93 E-value=1.2e+02 Score=31.42 Aligned_cols=28 Identities=32% Similarity=0.622 Sum_probs=19.9
Q ss_pred CCCCccCCCCccCCCCcccCCCCceEEecC
Q 011854 204 CPSHEHDGTPRCCSCERMEPQDTAYVALDD 233 (476)
Q Consensus 204 C~~h~H~~CF~C~~C~r~~~~g~~y~~l~d 233 (476)
|...||-.=-.|..|+. ..+-.|+.+++
T Consensus 218 C~teW~~~R~~C~~Cg~--~~~l~y~~~~~ 245 (309)
T PRK03564 218 CESEWHVVRVKCSNCEQ--SGKLHYWSLDS 245 (309)
T ss_pred CCCcccccCccCCCCCC--CCceeeeeecC
Confidence 67778877778999985 35566765544
No 107
>cd04269 ZnMc_adamalysin_II_like Zinc-dependent metalloprotease; adamalysin_II_like subfamily. Adamalysin II is a snake venom zinc endopeptidase. This subfamily contains other snake venom metalloproteinases, as well as membrane-anchored metalloproteases belonging to the ADAM family. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions.
Probab=20.61 E-value=60 Score=30.40 Aligned_cols=25 Identities=24% Similarity=0.240 Sum_probs=16.5
Q ss_pred EEEEecCchhHHhhhhhhccchhhh
Q 011854 345 AILILYGLPRLLTGTILAHEMMHGW 369 (476)
Q Consensus 345 ~il~l~glp~~l~g~ilaHe~~Ha~ 369 (476)
+|....+-....+..|+|||++|..
T Consensus 119 ~v~~~~~~~~~~~a~~~AHElGH~l 143 (194)
T cd04269 119 GVVQDHSRNLLLFAVTMAHELGHNL 143 (194)
T ss_pred EEEEeCCcchHHHHHHHHHHHHhhc
Confidence 3444444334566789999999864
No 108
>PF07607 DUF1570: Protein of unknown function (DUF1570); InterPro: IPR011464 This entry represents hypothetical proteins confined to bacteria.
Probab=20.22 E-value=58 Score=29.20 Aligned_cols=32 Identities=28% Similarity=0.352 Sum_probs=22.9
Q ss_pred hhhhccchhhhhhhcCC-CCC---CcchhhhHHHHH
Q 011854 359 TILAHEMMHGWMRLQGF-RTL---SPDVEEGICQVI 390 (476)
Q Consensus 359 ~ilaHe~~Ha~l~~~g~-~~l---~~~~eEG~cq~~ 390 (476)
+||+||..|--+.--|. +++ |..+-|||...+
T Consensus 3 ~T~~HEa~HQl~~N~Gl~~r~~~~P~Wv~EGlA~yF 38 (128)
T PF07607_consen 3 ATIAHEATHQLAFNTGLHPRLADWPRWVSEGLATYF 38 (128)
T ss_pred hHHHHHHHHHHHHHccccccCCCCchHHHHhHHHHc
Confidence 69999999976654462 344 577888887743
No 109
>TIGR02414 pepN_proteo aminopeptidase N, Escherichia coli type. The M1 family of zinc metallopeptidases contains a number of distinct, well-separated clades of proteins with aminopeptidase activity. Several are designated aminopeptidase N, EC 3.4.11.2, after the Escherichia coli enzyme, suggesting a similar activity profile. This family consists of all aminopeptidases closely related to E. coli PepN and presumed to have similar (not identical) function. Nearly all are found in Proteobacteria, but members are found also in Cyanobacteria, plants, and apicomplexan parasites. This family differs greatly in sequence from the family of aminopeptidases typified by Streptomyces lividans PepN (TIGR02412), from the membrane bound aminopeptidase N family in animals, etc.
Probab=20.16 E-value=55 Score=38.51 Aligned_cols=41 Identities=20% Similarity=0.358 Sum_probs=27.8
Q ss_pred hhhhhhccchhhhhhh-cCCCCC-CcchhhhHHHHHHHHHHhh
Q 011854 357 TGTILAHEMMHGWMRL-QGFRTL-SPDVEEGICQVIAHWWLIS 397 (476)
Q Consensus 357 ~g~ilaHe~~Ha~l~~-~g~~~l-~~~~eEG~cq~~a~~wl~~ 397 (476)
..++||||+.|-|..= --+..- ...+-|||.-++..+|.+.
T Consensus 283 i~~VIaHElaHqWfGNlVT~~~W~~LWLnEGfAty~e~~~~~~ 325 (863)
T TIGR02414 283 IESVIAHEYFHNWTGNRVTCRDWFQLSLKEGLTVFRDQEFSAD 325 (863)
T ss_pred HHHHHHHHHHHHHhcceeeecchhhhhhhhhHHHHHHHHHHHH
Confidence 3479999999999521 011111 2568999999888877553
Done!