Query psy16524
Match_columns 453
No_of_seqs 223 out of 377
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 23:28:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16524.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16524hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3865|consensus 100.0 1E-143 2E-148 1061.1 34.2 377 2-451 11-390 (402)
2 KOG3780|consensus 99.9 9.6E-20 2.1E-24 187.0 31.8 284 7-401 6-318 (427)
3 PF02752 Arrestin_C: Arrestin 99.7 3.1E-16 6.6E-21 134.6 15.0 129 246-403 2-136 (136)
4 PF00339 Arrestin_N: Arrestin 99.2 3.9E-10 8.4E-15 98.7 14.2 123 9-149 2-135 (149)
5 PF03643 Vps26: Vacuolar prote 97.8 0.011 2.5E-07 59.6 25.1 206 18-327 34-244 (275)
6 PF13002 LDB19: Arrestin_N ter 96.6 0.048 1E-06 52.5 13.5 40 97-141 49-88 (191)
7 PF08737 Rgp1: Rgp1; InterPro 96.2 1.1 2.4E-05 47.7 22.0 54 239-292 293-347 (415)
8 PF00339 Arrestin_N: Arrestin 95.5 0.031 6.7E-07 48.8 5.9 42 252-293 2-45 (149)
9 PF00927 Transglut_C: Transglu 94.0 0.64 1.4E-05 39.6 10.1 75 250-329 2-76 (107)
10 PF07070 Spo0M: SpoOM protein; 93.0 5.5 0.00012 39.3 15.8 125 245-404 9-136 (218)
11 PF07070 Spo0M: SpoOM protein; 88.6 3.6 7.7E-05 40.6 9.8 95 16-139 16-115 (218)
12 KOG3780|consensus 87.5 20 0.00043 37.3 15.3 45 251-295 7-53 (427)
13 smart00809 Alpha_adaptinC2 Ada 81.2 31 0.00066 28.8 12.2 71 244-328 2-72 (104)
14 PF01835 A2M_N: MG2 domain; I 81.1 3.3 7.2E-05 34.4 5.1 26 251-276 2-27 (99)
15 PF03643 Vps26: Vacuolar prote 80.8 27 0.00058 35.6 12.3 103 259-400 34-145 (275)
16 PF04744 Monooxygenase_B: Mono 77.5 6.3 0.00014 41.8 6.7 74 251-327 249-333 (381)
17 PF01345 DUF11: Domain of unkn 76.6 8.3 0.00018 30.7 5.9 41 246-286 23-63 (76)
18 PF00207 A2M: Alpha-2-macroglo 76.2 8.1 0.00017 32.2 5.9 40 245-286 52-91 (92)
19 PF10633 NPCBM_assoc: NPCBM-as 71.4 13 0.00028 29.9 5.9 59 261-329 2-60 (78)
20 TIGR01451 B_ant_repeat conserv 70.5 8.7 0.00019 29.4 4.4 32 255-286 3-34 (53)
21 PF07705 CARDB: CARDB; InterP 70.3 55 0.0012 26.3 9.7 68 249-329 4-71 (101)
22 PF07919 Gryzun: Gryzun, putat 65.9 29 0.00063 37.4 8.8 77 244-332 466-542 (554)
23 TIGR03079 CH4_NH3mon_ox_B meth 61.6 37 0.0008 36.3 8.3 72 250-324 267-349 (399)
24 PF07919 Gryzun: Gryzun, putat 59.1 1.5E+02 0.0034 31.9 12.9 39 244-282 168-208 (554)
25 PF06159 DUF974: Protein of un 58.1 24 0.00053 35.1 6.1 31 260-290 10-40 (249)
26 KOG0452|consensus 57.6 10 0.00022 42.6 3.5 151 57-299 708-882 (892)
27 PF13199 Glyco_hydro_66: Glyco 57.2 24 0.00052 39.4 6.4 28 254-281 1-28 (559)
28 PF11355 DUF3157: Protein of u 47.1 54 0.0012 32.2 6.3 42 251-299 100-143 (199)
29 PF09478 CBM49: Carbohydrate b 47.0 50 0.0011 27.0 5.3 39 250-288 2-41 (80)
30 PF06030 DUF916: Bacterial pro 47.0 42 0.00092 29.9 5.2 29 261-290 24-52 (121)
31 COG2373 Large extracellular al 45.9 77 0.0017 39.9 8.7 39 248-286 497-535 (1621)
32 PF14874 PapD-like: Flagellar- 43.8 1.1E+02 0.0023 25.4 6.9 64 254-329 10-73 (102)
33 PF05688 DUF824: Salmonella re 43.0 39 0.00084 25.9 3.7 29 261-289 10-38 (47)
34 PF14796 AP3B1_C: Clathrin-ada 40.0 1.1E+02 0.0023 28.7 6.8 74 244-327 64-138 (145)
35 PF07703 A2M_N_2: Alpha-2-macr 39.4 29 0.00063 30.1 3.0 29 248-276 94-122 (136)
36 PF09624 DUF2393: Protein of u 37.3 88 0.0019 28.2 5.8 40 248-288 47-86 (149)
37 PF00963 Cohesin: Cohesin doma 37.1 1.1E+02 0.0023 27.1 6.3 35 251-286 1-35 (141)
38 PF02014 Reeler: Reeler domain 36.3 68 0.0015 28.4 4.8 32 253-286 23-54 (132)
39 PF05753 TRAP_beta: Translocon 36.0 2.8E+02 0.0061 26.6 9.2 69 254-330 28-98 (181)
40 KOG3063|consensus 35.4 5.1E+02 0.011 26.6 19.5 97 34-143 39-139 (301)
41 PF12584 TRAPPC10: Trafficking 34.3 2.3E+02 0.005 25.7 8.1 64 260-332 27-100 (147)
42 PF02883 Alpha_adaptinC2: Adap 33.5 3E+02 0.0064 23.3 9.8 75 242-328 4-78 (115)
43 COG4326 Spo0M Sporulation cont 32.6 82 0.0018 31.5 5.1 42 246-287 30-72 (270)
44 KOG3865|consensus 32.4 5.1E+02 0.011 27.6 10.9 59 117-187 200-259 (402)
45 PF05326 SVA: Seminal vesicle 29.9 95 0.002 28.4 4.6 60 245-306 30-90 (124)
46 PF12690 BsuPI: Intracellular 29.6 1.3E+02 0.0028 25.0 5.2 30 266-296 2-31 (82)
47 PF07703 A2M_N_2: Alpha-2-macr 28.9 67 0.0015 27.8 3.5 25 251-275 1-25 (136)
48 PF04314 DUF461: Protein of un 28.4 98 0.0021 26.8 4.4 58 263-321 13-71 (110)
49 cd08544 Reeler Reeler, the N-t 28.4 1.2E+02 0.0025 26.9 5.0 37 251-289 21-57 (135)
50 KOG2717|consensus 27.8 6.9E+02 0.015 25.7 16.7 42 250-292 180-221 (313)
51 PF08626 TRAPPC9-Trs120: Trans 25.2 3.3E+02 0.0071 33.2 9.4 29 260-288 795-823 (1185)
52 TIGR03358 VI_chp_5 type VI sec 23.4 63 0.0014 30.6 2.4 23 371-399 11-33 (159)
53 PF06299 DUF1045: Protein of u 23.1 73 0.0016 30.2 2.8 33 83-115 84-120 (160)
54 KOG2540|consensus 23.0 2.5E+02 0.0054 28.4 6.5 69 257-331 155-227 (269)
55 PF05591 DUF770: Protein of un 22.8 59 0.0013 30.6 2.1 23 371-399 10-32 (157)
56 PTZ00128 cytochrome c oxidase 21.4 3.4E+02 0.0073 27.4 7.1 66 259-330 133-201 (232)
57 PF04314 DUF461: Protein of un 20.9 1.3E+02 0.0028 26.1 3.7 41 241-281 70-110 (110)
58 PF06988 NifT: NifT/FixU prote 20.9 60 0.0013 26.5 1.5 16 4-19 9-24 (64)
No 1
>KOG3865|consensus
Probab=100.00 E-value=9.7e-144 Score=1061.15 Aligned_cols=377 Identities=52% Similarity=0.872 Sum_probs=362.6
Q ss_pred CCCCceEEEEecceeeeecCCCceeeeeEEEEcceeeeceeEEEEEEEEEeccccCccccCcccchheeeeeeEEeeCCC
Q psy16524 2 TSFPGKVTVYLGKRDFIDHLEEVDPIDGVIVVENEYLKGRKVFGQIITTYRYGREEDEVMGVKFSKEMIVDRGQIVPSTN 81 (453)
Q Consensus 2 ~spn~klt~YlgkRd~vd~~~~vd~v~Gvv~vd~~~l~~rkV~~ql~~tfRYGred~eVmgl~F~ke~~~~~~qi~P~~~ 81 (453)
+|||||||+||||||||||++.||||||||+|||||||+||||+||+|+|||||||+|||||+|+||||+++.|+|||.+
T Consensus 11 ~SpNgkiT~YLgkRDFvDhvd~vdPvDGvVlvDpeYlK~RKvfv~L~caFRYGREDldVlGLtFrKdL~~~~~Qv~Pp~~ 90 (402)
T KOG3865|consen 11 ASPNGKITVYLGKRDFVDHVDQVDPVDGVVLVDPEYLKDRKVFVQLTCAFRYGREDLDVLGLTFRKDLYLATVQVYPPPE 90 (402)
T ss_pred cCCCCcEEEEecccccccccccccccceeEEEChHHhccceEEEEEEeeeecccccceeeeeEEEeeeEEEEEEeeCCCc
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred CCCCCcHHHHHHhhccCCCeeeeEeeCCCCCCceEEecCCCCCCCCcceeEEEEEEEEcCCCcccCcccceeEEeEEEee
Q psy16524 82 EKPELTVIQEKLLKKLGPNAYPFTFHFPSGAPSSVTLQPGDEDTGKPLGVEHAIKTFVGDSIDEKGHKRSSVALAIKKCY 161 (453)
Q Consensus 82 ~~~~lt~lQe~L~kklG~~a~PF~f~lp~~~P~Sv~Lqp~~~~~G~p~gv~Y~Vka~iad~~~ek~~kr~sv~~~Irk~~ 161 (453)
...+||+|||||+||||.|||||+|++|+++||||+|||+|+|+||||||+|+||||+||+.+||+|||++|||+|||
T Consensus 91 ~~~plT~lQErLlkKLG~nAyPF~f~~pp~~P~SVtLQp~p~D~gKpcGVdyevkaF~~~s~edk~hKr~sVrL~IRK-- 168 (402)
T KOG3865|consen 91 DSRPLTRLQERLLKKLGSNAYPFTFEFPPNLPCSVTLQPGPEDTGKPCGVDYEVKAFVADSEEDKIHKRNSVRLVIRK-- 168 (402)
T ss_pred CCCcccHHHHHHHHHhCCCCCceEEeCCCCCCceEEeccCCccCCCcccceEEEEEEecCCcccccccccceeeeeee--
Confidence 788899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEeeeeeeeecccchhhhcccchhhhhccccchhhhcccccccccccccccccCCCCCcccccCCCCCCCCCCceeeeee
Q psy16524 162 VVQHCEVTMVNSQFSRYVASLETREVLADKDKTNALKKSKSIDRARYENSCYATDDDDNILQYAPPSRGRRLPSSLVSKG 241 (453)
Q Consensus 162 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~aP~~~~~~~p~~e~~K~ 241 (453)
+||||...|+| |+++++|.
T Consensus 169 ------------------------------------------------------------vqyAP~~~Gpq-P~~~v~k~ 187 (402)
T KOG3865|consen 169 ------------------------------------------------------------VQYAPLEPGPQ-PSAEVSKQ 187 (402)
T ss_pred ------------------------------------------------------------eeecCCCCCCC-chhHhhHh
Confidence 99999999999 99999999
Q ss_pred eeeecCceEEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEE-cceEEEEEEeeeeccCCcCCCCCe
Q psy16524 242 FTFSQGKINLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMV-NSQFSRYVASLETREGCPVTPGAA 320 (453)
Q Consensus 242 F~~ssGpl~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf-~g~yk~~Va~~E~~eG~pV~pgst 320 (453)
|+||+|+|||+|||||++|||||+|.|||+|+|||+|+||+||+.++|++||||| ++||+++||.+|+.|||||+||+|
T Consensus 188 FlmS~~~lhLevsLDkEiYyHGE~isvnV~V~NNsnKtVKkIK~~V~Q~adi~Lfs~aqy~~~VA~~E~~eGc~v~Pgst 267 (402)
T KOG3865|consen 188 FLMSDGPLHLEVSLDKEIYYHGEPISVNVHVTNNSNKTVKKIKISVRQVADICLFSTAQYKKPVAMEETDEGCPVAPGST 267 (402)
T ss_pred hccCCCceEEEEEecchheecCCceeEEEEEecCCcceeeeeEEEeEeeceEEEEecccccceeeeeecccCCccCCCCe
Confidence 9999999999999999999999999999999999999999999999999999999 999999999999999999999999
Q ss_pred EEEEEEEeeccCCCCccceeeecCcccCCCCcCCCceeecCCCCCCCceeeEEEEEEEEEEEEcC-CCcceeEEeeEEee
Q psy16524 321 FTKTFYLVPLASSNKDRRGIALDGHLKDDDVNLASSTLIGEGKCPSEAMGIVISYSLRVKLSCGT-LGGELQTDVPFKLM 399 (453)
Q Consensus 321 ~~k~~~L~Pll~~nr~krglALdG~Lk~edtnLASSTil~~~~~~ke~~gI~VSY~VKVkL~vsg-~gsdv~veLPf~L~ 399 (453)
++|+|+|+|+|++|++||||||||+|||||||||||||+.++. ++|.+||.|||+|||||.+|+ .+|++.+||||+||
T Consensus 268 l~Kvf~l~PllanN~dkrGlALDG~lKhEDtnLASSTii~~~~-~re~lGI~VsY~VkVkL~vs~ll~ge~~~ElPF~Lm 346 (402)
T KOG3865|consen 268 LSKVFTLTPLLANNKDKRGLALDGKLKHEDTNLASSTIIREGA-DREALGILVSYKVKVKLVVSRLLGGEVAAELPFTLM 346 (402)
T ss_pred eeeeEEechhhhcCcccccccccccccccccccchhheecCCC-CcceeEEEEEEEEEEEEEEecccCCceeeecceEEe
Confidence 9999999999999999999999999999999999999999999 999999999999999999994 78999999999999
Q ss_pred CCCCCCcCccc-ccccccCCccccccccccCCCCCCCCCeEeeeccccccCCC
Q psy16524 400 NPDPLLADKDK-TNALKKSKSIDRARYENSCYATDDDDNIVFEDFARLRLNEP 451 (453)
Q Consensus 400 hp~P~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~f~~~~~~~~ 451 (453)
||+|.+.+... .++....++|+++++ |||||||||||+||++-
T Consensus 347 hPkP~~~p~~~a~~~~~~i~li~~~~~---------dddivfEdFar~rl~~~ 390 (402)
T KOG3865|consen 347 HPKPGEEPRSEAPESETSINLIELDTN---------DDDIVFEDFARMRLKGM 390 (402)
T ss_pred cCCCCCCccchhccccCchhhhhccCC---------CCceehHHHHHhhhccC
Confidence 99998875532 223344677887775 79999999999999754
No 2
>KOG3780|consensus
Probab=99.88 E-value=9.6e-20 Score=187.03 Aligned_cols=284 Identities=21% Similarity=0.324 Sum_probs=186.1
Q ss_pred eEEEEecceeeeecCCCceeeeeEEEE-cceeeeceeEEEEEEEEEeccccCcccc---------------Ccccc--hh
Q psy16524 7 KVTVYLGKRDFIDHLEEVDPIDGVIVV-ENEYLKGRKVFGQIITTYRYGREEDEVM---------------GVKFS--KE 68 (453)
Q Consensus 7 klt~YlgkRd~vd~~~~vd~v~Gvv~v-d~~~l~~rkV~~ql~~tfRYGred~eVm---------------gl~F~--ke 68 (453)
.+-++|..++-|-.-+ ++|.|=|++ -.+.++-|.|.+++.+..+= .|.+.-- ...|. .+
T Consensus 6 ~~~i~~d~~~~iy~~G--~~vsG~v~l~~~~~~~~~~i~l~~~G~~~t-~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (427)
T KOG3780|consen 6 SFEIVLDNPEAIYFPG--EPVSGSVVLSTKEPIKVRAIKLQLKGRART-SWSESERGTKLNSKSEGSIKSSTVNYTAKET 82 (427)
T ss_pred eEEEEeCCCccccCCC--CeEEEEEEEEeCCccceeEEEEEEEEeEEE-eecccccccccccccccccccceEEeeceEE
Confidence 3455666666333333 789998888 66777889999999887762 1111111 12233 23
Q ss_pred eeeeeeEEeeCCCCCCC--CcHHHHHHhhccCCCeeeeEeeCCCCCCceEEecCCCCCCCCcceeEEEEEEEEcCCCccc
Q psy16524 69 MIVDRGQIVPSTNEKPE--LTVIQEKLLKKLGPNAYPFTFHFPSGAPSSVTLQPGDEDTGKPLGVEHAIKTFVGDSIDEK 146 (453)
Q Consensus 69 ~~~~~~qi~P~~~~~~~--lt~lQe~L~kklG~~a~PF~f~lp~~~P~Sv~Lqp~~~~~G~p~gv~Y~Vka~iad~~~ek 146 (453)
.+-....+|-..++... +. -|.+.|||.|.||.++|+|| +|+.+.|+|.|||.+ || .|+
T Consensus 83 y~~~~~~~~~~~~g~~~~~l~---------~G~~~~pF~~~LP~~~P~Sf--------eg~~G~irY~vk~~i-dr-~~~ 143 (427)
T KOG3780|consen 83 YLDSKTILWTSSNGSNSRVLP---------PGNYEFPFSFTLPLNLPPSF--------EGKFGHVRYFVKAEI-DR-PWK 143 (427)
T ss_pred EeeeeeEEeeccCCCCceecC---------CCceEEeEeccCCCCCCCce--------eeCCceEEEEEEEEE-ec-CCC
Confidence 33344556664444443 44 79999999999999999999 999999999999998 44 355
Q ss_pred CcccceeEEeEEEeeEEeeeeeeeecccchhhhcccchhhhhccccchhhhcccccccccccccccccCCCCCcccccCC
Q psy16524 147 GHKRSSVALAIKKCYVVQHCEVTMVNSQFSRYVASLETREVLADKDKTNALKKSKSIDRARYENSCYATDDDDNILQYAP 226 (453)
Q Consensus 147 ~~kr~sv~~~Irk~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~aP 226 (453)
..+ ..+..|.+ ++..+ .| ..|
T Consensus 144 ~~~--~~~~~~~V---~~~~~---------------------------------------------------ln---~~p 164 (427)
T KOG3780|consen 144 LNK--KNRKPFTV---IETVD---------------------------------------------------LN---SSP 164 (427)
T ss_pred CCc--cceeeEEE---ecccc---------------------------------------------------cc---cCc
Confidence 544 33344433 22222 11 112
Q ss_pred CCCCCCCCce-eeeeeeeeecCceEEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEE-cc---eEE
Q psy16524 227 PSRGRRLPSS-LVSKGFTFSQGKINLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMV-NS---QFS 301 (453)
Q Consensus 227 ~~~~~~~p~~-e~~K~F~~ssGpl~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf-~g---~yk 301 (453)
....+..-.. +....++|..|++.++++|++.+|++||.|.+++.|.|.|++.++++++++.|.+.+..+ .+ +.+
T Consensus 165 ~~~~~~~~~~~k~~~~~~~~~g~v~~~~~ip~~~~~~ge~i~~~~~i~n~ss~~~~~~~~~l~q~~~~~~~~~~~~~~~~ 244 (427)
T KOG3780|consen 165 SLLEPIISKASKKLGCVCFSSGPVSLELTIPKTGYVPGETIPVTLEIENKSSRTIKKVKAKLIQKISYLAFSYGEHTKTK 244 (427)
T ss_pred cccCcchhhhhheeeEEEecCCcEEEEEEcccccCcCCccEEEEEEEecCCCCcceeeEEEEEEEEEEEeecCCccccce
Confidence 2211100011 111226789999999999999999999999999999999999999999999999997777 43 222
Q ss_pred E-EEEeeeeccCCcCCCCCe--EEEEEEEeeccCCCCccceeeecCcccCCCCcCCCceeecCCCCCCCceeeEEEEEEE
Q psy16524 302 R-YVASLETREGCPVTPGAA--FTKTFYLVPLASSNKDRRGIALDGHLKDDDVNLASSTLIGEGKCPSEAMGIVISYSLR 378 (453)
Q Consensus 302 ~-~Va~~E~~eG~pV~pgst--~~k~~~L~Pll~~nr~krglALdG~Lk~edtnLASSTil~~~~~~ke~~gI~VSY~VK 378 (453)
. ..........+.|.++.+ +...|.| | ..+| ++.. ....|.|+|.++
T Consensus 245 ~~~~~~~~~~~~~~v~~~~~~~~~~~~~i-P----------------------~~~P-s~~~------~~~~i~v~y~l~ 294 (427)
T KOG3780|consen 245 KSEKTLIKSRGSLEVAPRSEDKFEKELRI-P----------------------PVPP-SILP------DTPIIRVEYELK 294 (427)
T ss_pred eeeeEEeeeccccccCCCCccccceEEEc-C----------------------CCCC-ccCC------CCceEEEEEEEE
Confidence 1 111112222356777655 5555554 3 1223 2221 123599999999
Q ss_pred EEEEEcCC-CcceeEEeeEEeeCC
Q psy16524 379 VKLSCGTL-GGELQTDVPFKLMNP 401 (453)
Q Consensus 379 VkL~vsg~-gsdv~veLPf~L~hp 401 (453)
|.+.++++ ++++.+++|++|++-
T Consensus 295 v~~~~~~~~~~~~~l~~pi~igt~ 318 (427)
T KOG3780|consen 295 VTLKTSSLRHSELALELPIIIGTI 318 (427)
T ss_pred EEEecCcccccceeeeeceEEecc
Confidence 99999853 789999999999963
No 3
>PF02752 Arrestin_C: Arrestin (or S-antigen), C-terminal domain; InterPro: IPR011022 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The C-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=99.71 E-value=3.1e-16 Score=134.60 Aligned_cols=129 Identities=25% Similarity=0.389 Sum_probs=85.0
Q ss_pred cCceEEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEEcc--e---EEEEEEeeeeccCCcCCCCCe
Q psy16524 246 QGKINLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMVNS--Q---FSRYVASLETREGCPVTPGAA 320 (453)
Q Consensus 246 sGpl~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf~g--~---yk~~Va~~E~~eG~pV~pgst 320 (453)
+|++++++++||.+|.+||.|+|++.|+|.|++.|++|++.|.|..++....+ . +.+.++... ..+.....+.+
T Consensus 2 ~g~i~~~~~i~~~~~~~Ge~i~v~v~i~n~s~~~i~~I~v~L~~~~~~~~~~~~~~~~~~~~~v~~~~-~~~~~~~~~~~ 80 (136)
T PF02752_consen 2 SGKISLSISIPRTAYVPGETIPVNVEIDNQSKKKIKKIKVSLVERITYKAKGGKDESKSEKRVVAKSK-NCGVDPGSSGS 80 (136)
T ss_dssp TEEEEEEEEES-SEEETT--EEEEEEEEE-SSSEEEEEEEEEEEEEEE-SS----S-EEEEEEEEEEE-CCEB-B-TTEE
T ss_pred CCEEEEEEEECCCEECCCCEEEEEEEEEECCCCEEEEEEEEEEEEEEEEEeeccccceEEEEEEEEEe-cCCccCCCCce
Confidence 68999999999999999999999999999999999999999999977443322 2 234555532 22122233445
Q ss_pred EEEEEEE-eeccCCCCccceeeecCcccCCCCcCCCceeecCCCCCCCceeeEEEEEEEEEEEEcCCCcceeEEeeEEee
Q psy16524 321 FTKTFYL-VPLASSNKDRRGIALDGHLKDDDVNLASSTLIGEGKCPSEAMGIVISYSLRVKLSCGTLGGELQTDVPFKLM 399 (453)
Q Consensus 321 ~~k~~~L-~Pll~~nr~krglALdG~Lk~edtnLASSTil~~~~~~ke~~gI~VSY~VKVkL~vsg~gsdv~veLPf~L~ 399 (453)
|.....+ .| .++.||+...+ -.|.|+|.|+|++.++++..++.+++|++|+
T Consensus 81 ~~~~~~l~lP---------------------~~~~~s~~~~~-------~~i~v~Y~l~v~~~~~~~~~~~~~~~PI~I~ 132 (136)
T PF02752_consen 81 FEFNIQLQLP---------------------SNLPPSTSTNS-------RLIQVEYQLEVTVKLSGCTSDLRLELPITIG 132 (136)
T ss_dssp EEEEEEE--------------------------B-----CGG-------GSEEEEEEEEEEEEEETTSEEEEEEEEEEEE
T ss_pred EEEEEEEcCC---------------------CccCcccccCC-------cEEEEEEEEEEEEEECCceeEEEEEccEEEE
Confidence 7744433 13 24556553222 2399999999999999878899999999999
Q ss_pred CCCC
Q psy16524 400 NPDP 403 (453)
Q Consensus 400 hp~P 403 (453)
++++
T Consensus 133 ~~p~ 136 (136)
T PF02752_consen 133 SSPC 136 (136)
T ss_dssp B-SS
T ss_pred ecCC
Confidence 8753
No 4
>PF00339 Arrestin_N: Arrestin (or S-antigen), N-terminal domain; InterPro: IPR011021 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The N-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=99.20 E-value=3.9e-10 Score=98.66 Aligned_cols=123 Identities=24% Similarity=0.342 Sum_probs=85.7
Q ss_pred EEEecceeeeecCCCceeeeeEEEE-cceeeeceeEEEEEEEEEeccccCccccCcccchheeeeeeEEeeCC--CCCCC
Q psy16524 9 TVYLGKRDFIDHLEEVDPIDGVIVV-ENEYLKGRKVFGQIITTYRYGREEDEVMGVKFSKEMIVDRGQIVPST--NEKPE 85 (453)
Q Consensus 9 t~YlgkRd~vd~~~~vd~v~Gvv~v-d~~~l~~rkV~~ql~~tfRYGred~eVmgl~F~ke~~~~~~qi~P~~--~~~~~ 85 (453)
+++|-+..-+-+-+ |.|.|.|.+ -.+.++.+.|.++|.+..++.-.+....+..+.+ +.++.. .....
T Consensus 2 ~I~ld~~~~~y~~G--e~I~G~V~l~~~~~~~i~~i~v~l~G~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~ 72 (149)
T PF00339_consen 2 EIELDNPKPVYFPG--EVISGKVVLELSKPIKIKSIKVRLKGRAKTKWSESKSSGSTFRK-------QTTPKVQYSEKKE 72 (149)
T ss_dssp EEEES-SEEEEESS----EEEEEEECTTT-TTTSEEEEEEEEEEEESSSSTTSTTCEEEE-------EEESTSSS-SSSS
T ss_pred EEEECCCCCEECCC--CEEEEEEEEEECCccceeEEEEEEEEEEEEEecCCCcceeeeee-------EEeccccccccee
Confidence 56777777777777 999999999 5677899999999999999877766677777655 444444 23556
Q ss_pred CcHHHHHHhhc--------cCCCeeeeEeeCCCCCCceEEecCCCCCCCCcceeEEEEEEEEcCCCcccCcc
Q psy16524 86 LTVIQEKLLKK--------LGPNAYPFTFHFPSGAPSSVTLQPGDEDTGKPLGVEHAIKTFVGDSIDEKGHK 149 (453)
Q Consensus 86 lt~lQe~L~kk--------lG~~a~PF~f~lp~~~P~Sv~Lqp~~~~~G~p~gv~Y~Vka~iad~~~ek~~k 149 (453)
+...+..|+.. .|.+.|||.|.||.++|+|+ +|..+.|+|.|+|.+ +++..+.++
T Consensus 73 ~~~~~~~l~~~~~~~~~l~~G~~~fpF~f~LP~~lP~S~--------~~~~g~I~Y~l~a~l-~~~~~~~~~ 135 (149)
T PF00339_consen 73 YFDHESQLWGSEDGPNILPPGEYEFPFEFQLPSNLPSSF--------EGSHGSIRYKLKATL-DRPGKKDHK 135 (149)
T ss_dssp SSHHHHHHHHH--------C-TTEEEEEE---TTS--SE--------EEE-SEEEEEEEEEE-SSTTSE--C
T ss_pred eccceeEeeeeccceecccCCCEEEEEEEECCCCCCceE--------eccCcCEEEEEEEEE-ECCCCCCcE
Confidence 77777777777 79999999999999999999 566669999999999 665444443
No 5
>PF03643 Vps26: Vacuolar protein sorting-associated protein 26 ; InterPro: IPR005377 The movement of lipid and protein components between intracellular organelles requires the regulated interactions of many molecules. Vacuolar protein sorting-associated protein (Vps)5 is a yeast protein that is a subunit of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. Sorting nexin (SNX) 1 and SNX2 are its mammalian orthologs []. To carry out its biological functions, Vps5 forms the retromer complex with at least four other proteins: Vps17, Vps26, Vps29, and Vps35 []. This family of Vps26-proteins also contains Down syndrome critical region 3/A.; GO: 0007034 vacuolar transport, 0030904 retromer complex; PDB: 3LHA_A 3LH9_A 2R51_A 3LH8_B 2FAU_A.
Probab=97.85 E-value=0.011 Score=59.58 Aligned_cols=206 Identities=14% Similarity=0.210 Sum_probs=106.9
Q ss_pred eecCCCceeeeeEEEEccee---eeceeEEEEEEEEEeccccCccccCcccchheeeeeeEEeeCCCCCCCCcHHHHHHh
Q psy16524 18 IDHLEEVDPIDGVIVVENEY---LKGRKVFGQIITTYRYGREEDEVMGVKFSKEMIVDRGQIVPSTNEKPELTVIQEKLL 94 (453)
Q Consensus 18 vd~~~~vd~v~Gvv~vd~~~---l~~rkV~~ql~~tfRYGred~eVmgl~F~ke~~~~~~qi~P~~~~~~~lt~lQe~L~ 94 (453)
+-+-+ |.|.|+|.|.... ++-.-|.+++.+.+.--.+.... -+++-.+.++-|+. .|+
T Consensus 34 iY~~g--E~V~G~V~I~~~~gk~~~H~GI~l~lvG~ie~~~~~~k~------~~f~~~~~eL~~~G----~l~------- 94 (275)
T PF03643_consen 34 IYSDG--ETVSGKVVITSKPGKSLEHQGIKLELVGQIEAFYDSGKP------IEFLSLSIELAPPG----KLP------- 94 (275)
T ss_dssp EEETC----EEEEEEEEESSTS-EEES-EEEEEEEEEEEGCCTT-E------EEEEEEEEEEE-SE----EE--------
T ss_pred eEcCC--CEEEEEEEEEECCCCceEEeeEEEEEEEeEeEeccCCCc------eEeEEeeEEEcCCc----ccC-------
Confidence 33444 8899999995444 66667888888877411111111 12344455665654 244
Q ss_pred hccCCCeeeeEeeCCCCCCceEEecCCCCCCCCcceeEEEEEEEEcCCCcccCcccceeEEeEEEeeEEeeeeeeeeccc
Q psy16524 95 KKLGPNAYPFTFHFPSGAPSSVTLQPGDEDTGKPLGVEHAIKTFVGDSIDEKGHKRSSVALAIKKCYVVQHCEVTMVNSQ 174 (453)
Q Consensus 95 kklG~~a~PF~f~lp~~~P~Sv~Lqp~~~~~G~p~gv~Y~Vka~iad~~~ek~~kr~sv~~~Irk~~~~q~~~~~~~~~~ 174 (453)
-|.. |||.|.+-+. |-..|+|....++|.+||-+..+- ..-..+..+.|..
T Consensus 95 --~~~t-~pFeF~~~~k--------~yETY~G~~v~i~Y~lrv~v~R~~---~~i~k~~ef~V~~--------------- 145 (275)
T PF03643_consen 95 --EGKT-FPFEFPLVEK--------PYETYHGVNVNIRYFLRVTVKRSY---KDISKEQEFWVQN--------------- 145 (275)
T ss_dssp --S-EE-EEEEE-SB-----------S--EE-SSEEEEEEEEEEE--SS---S-EEEEEEEEEE----------------
T ss_pred --CCcE-EeeEeCCCCC--------CCccEeeeEEEEEEEEEEEEEccC---CCcceEEEEEEEe---------------
Confidence 3344 9999965322 145679999999999999983322 0001122222221
Q ss_pred chhhhcccchhhhhccccchhhhcccccccccccccccccCCCCCcccccCCCCCCCCCCceeeeeeeeeecCceEEEEE
Q psy16524 175 FSRYVASLETREVLADKDKTNALKKSKSIDRARYENSCYATDDDDNILQYAPPSRGRRLPSSLVSKGFTFSQGKINLEVT 254 (453)
Q Consensus 175 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~aP~~~~~~~p~~e~~K~F~~ssGpl~Leas 254 (453)
....|....+ =+.++ =-.+-+|++..
T Consensus 146 -----------------------------------------------~~~~p~~~~~--ik~ev-----gie~~lhief~ 171 (275)
T PF03643_consen 146 -----------------------------------------------FSITPESNQP--IKMEV-----GIEDCLHIEFE 171 (275)
T ss_dssp -----------------------------------------------EB----------EEEEE-----CETTTEEEEEE
T ss_pred -----------------------------------------------ccCCCCCCCC--ccccc-----CCCccEEEEEE
Confidence 1122222110 01111 12457899999
Q ss_pred eccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEEcceEE--EEEEeeeeccCCcCCCCCeEEEEEEE
Q psy16524 255 LDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMVNSQFS--RYVASLETREGCPVTPGAAFTKTFYL 327 (453)
Q Consensus 255 LdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf~g~yk--~~Va~~E~~eG~pV~pgst~~k~~~L 327 (453)
++|..|.=.+.|.=.+.+.-.. ..|+.|.+.|++.-.+-.-.+..+ ..++..|..||.|+. |.+.-=.+.|
T Consensus 172 ~~k~~~~l~d~i~G~i~f~lv~-~kIk~~elqLiR~Et~g~~~~~~~e~t~i~~~eImDG~p~r-ge~IPirl~l 244 (275)
T PF03643_consen 172 YDKSKYHLKDVITGKIYFLLVR-IKIKSMELQLIRVETCGCGENYAKESTEIQKIEIMDGAPCR-GESIPIRLFL 244 (275)
T ss_dssp ES-SEEETT-EEEEEEEEEEES-S-EEEEEEEEEEEEEECECCCEEEEEEEEEEEEEESS---T-T-EEEEEEEC
T ss_pred EcccceECCCCEEEEEEEEEEe-ecceEEEEEEEEEEEEecCCcccccceEEEEEEeecCCccc-cceeeEEEEc
Confidence 9999999999888776664333 679999999998876321123333 488999999998776 6555444444
No 6
>PF13002 LDB19: Arrestin_N terminal like; InterPro: IPR024391 This entry represents a predicted Ig-like beta sandwich domain found towards the N terminus of protein LDB19 []. It is also found in other sequences and is related to the arrestin N-terminal fold [].
Probab=96.63 E-value=0.048 Score=52.54 Aligned_cols=40 Identities=25% Similarity=0.527 Sum_probs=34.1
Q ss_pred cCCCeeeeEeeCCCCCCceEEecCCCCCCCCcceeEEEEEEEEcC
Q psy16524 97 LGPNAYPFTFHFPSGAPSSVTLQPGDEDTGKPLGVEHAIKTFVGD 141 (453)
Q Consensus 97 lG~~a~PF~f~lp~~~P~Sv~Lqp~~~~~G~p~gv~Y~Vka~iad 141 (453)
.|.|+|||++-||-++|+|..| | .+.-..|.|+++|.+..
T Consensus 49 ~G~h~fPFS~LiPG~LPaS~~l--g---s~~l~~I~Yel~A~a~~ 88 (191)
T PF13002_consen 49 KGSHAFPFSYLIPGHLPASMDL--G---STPLVSIKYELKAEATY 88 (191)
T ss_pred CCcccCCeeEECCCCCcccccc--C---CCCcEEEEEEEEEEEEE
Confidence 8999999999999999999955 2 25678899999998744
No 7
>PF08737 Rgp1: Rgp1; InterPro: IPR014848 Rgp1 forms heterodimer with Ric1 (IPR009771 from INTERPRO) which associates with Golgi membranes and functions as a guanyl-nucleotide exchange factor [].
Probab=96.18 E-value=1.1 Score=47.71 Aligned_cols=54 Identities=17% Similarity=0.269 Sum_probs=42.5
Q ss_pred eeeee-eecCceEEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEE
Q psy16524 239 SKGFT-FSQGKINLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCE 292 (453)
Q Consensus 239 ~K~F~-~ssGpl~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~ 292 (453)
.+.|- -.+|..-..++|.|..|.-||.|...+..++.....+.++.+.|.-...
T Consensus 293 ~~~y~I~~n~~~va~~~LsK~~yrlGE~I~g~idf~~~~~~~c~~v~~~LEs~E~ 347 (415)
T PF08737_consen 293 PNSYNIRRNGQRVARLSLSKPAYRLGEDIVGTIDFNDASTIPCYQVSASLESEET 347 (415)
T ss_pred CcEEEEEECCeEEEEEEecCCCcccCCeEEEEEEcCCCCcceeEEEEEEEEEEEE
Confidence 45664 4578888999999999999999999999999985566666666655433
No 8
>PF00339 Arrestin_N: Arrestin (or S-antigen), N-terminal domain; InterPro: IPR011021 G protein-coupled receptors are a large family of signalling molecules that respond to a wide variety of extracellular stimuli. The receptors relay the information encoded by the ligand through the activation of heterotrimeric G proteins and intracellular effector molecules. To ensure the appropriate regulation of the signalling cascade, it is vital to properly inactivate the receptor. This inactivation is achieved, in part, by the binding of a soluble protein, arrestin, which uncouples the receptor from the downstream G protein after the receptors are phosphorylated by G protein-coupled receptor kinases. In addition to the inactivation of G protein-coupled receptors, arrestins have also been implicated in the endocytosis of receptors and cross talk with other signalling pathways. Arrestin (retinal S-antigen) is a major protein of the retinal rod outer segments. It interacts with photo-activated phosphorylated rhodopsin, inhibiting or 'arresting' its ability to interact with transducin []. The protein binds calcium, and shows similarity in its C terminus to alpha-transducin and other purine nucleotide-binding proteins. In mammals, arrestin is associated with autoimmune uveitis. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X) [], which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction [, , ]. The crystal structure of bovine retinal arrestin comprises two domains of antiparallel beta-sheets connected through a hinge region and one short alpha-helix on the back of the amino-terminal fold []. The binding region for phosphorylated light-activated rhodopsin is located at the N-terminal domain, as indicated by the docking of the photoreceptor to the three-dimensional structure of arrestin. The N-terminal domain consists of an immunoglobulin-like beta-sandwich structure. This entry represents proteins with immunoglobulin-like domains that are similar to those found in arrestin.; PDB: 1SUJ_A 3UGX_A 1CF1_B 1AYR_A 3UGU_A 3P2D_B 1ZSH_A 2WTR_B 3GC3_A 1G4R_A ....
Probab=95.53 E-value=0.031 Score=48.77 Aligned_cols=42 Identities=24% Similarity=0.513 Sum_probs=33.3
Q ss_pred EEEec--cccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEE
Q psy16524 252 EVTLD--REIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEV 293 (453)
Q Consensus 252 easLd--K~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v 293 (453)
++.|| +..|.+||.|.=+|.+...+...++.|++.+.=.+.+
T Consensus 2 ~I~ld~~~~~y~~Ge~I~G~V~l~~~~~~~i~~i~v~l~G~~~~ 45 (149)
T PF00339_consen 2 EIELDNPKPVYFPGEVISGKVVLELSKPIKIKSIKVRLKGRAKT 45 (149)
T ss_dssp EEEES-SEEEEESS--EEEEEEECTTT-TTTSEEEEEEEEEEEE
T ss_pred EEEECCCCCEECCCCEEEEEEEEEECCccceeEEEEEEEEEEEE
Confidence 44555 9999999999999999888889999999998877654
No 9
>PF00927 Transglut_C: Transglutaminase family, C-terminal ig like domain; InterPro: IPR008958 Synonym(s): Protein-glutamine gamma-glutamyltransferase, Fibrinoligase, TGase Transglutaminases catalyse the post-translational modification of proteins at glutamine residues, with formation of isopeptide bonds. Members of the transglutaminase family usually have three domains: N-terminal (IPR001102 from INTERPRO), middle (IPR013808 from INTERPRO) and C-terminal. The middle domain is usually well conserved, but family members can display major differences in their N- and C-terminal domains, although their overall structure is conserved []. This entry represents the C-terminal domain found in transglutaminases, which consists of an immunoglobulin-like beta-sandwich consisting of seven strands in two sheets with a Greek key topology. The best known transglutaminase is blood coagulation factor XIII, a plasma tetrameric protein composed of two catalytic A subunits and two non-catalytic B subunits. Factor XIII is responsible for cross-linking fibrin chains, thus stabilising the fibrin clot. Protein-glutamine gamma-glutamyltransferases (2.3.2.13 from EC) are calcium-dependent enzymes that catalyse the cross-linking of proteins by promoting the formation of isopeptide bonds between the gamma-carboxyl group of a glutamine in one polypeptide chain and the epsilon-amino group of a lysine in a second polypeptide chain. TGases also catalyse the conjugation of polyamines to proteins [, ].; GO: 0003810 protein-glutamine gamma-glutamyltransferase activity, 0018149 peptide cross-linking; PDB: 2XZZ_A 1GGY_B 1FIE_B 1GGU_B 1GGT_B 1F13_A 1QRK_B 1EVU_A 1EX0_B 1L9N_B ....
Probab=94.02 E-value=0.64 Score=39.58 Aligned_cols=75 Identities=11% Similarity=0.210 Sum_probs=51.1
Q ss_pred EEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEEcceEEEEEEeeeeccCCcCCCCCeEEEEEEEee
Q psy16524 250 NLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMVNSQFSRYVASLETREGCPVTPGAAFTKTFYLVP 329 (453)
Q Consensus 250 ~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf~g~yk~~Va~~E~~eG~pV~pgst~~k~~~L~P 329 (453)
++++.++.... -|+.+.+.+.+.|.|+..++.+++.+.-. -..|+|-.+.........- .|.||++..-.+.+.|
T Consensus 2 ~~~i~~~~~~~-vG~d~~v~v~~~N~~~~~l~~v~~~l~~~--~v~ytG~~~~~~~~~~~~~--~l~p~~~~~~~~~i~p 76 (107)
T PF00927_consen 2 EIKIKLPGDPV-VGQDFTVSVSFTNPSSEPLRNVSLNLCAF--TVEYTGLTRDQFKKEKFEV--TLKPGETKSVEVTITP 76 (107)
T ss_dssp EEEEEEESEEB-TTSEEEEEEEEEE-SSS-EECEEEEEEEE--EEECTTTEEEEEEEEEEEE--EE-TTEEEEEEEEE-H
T ss_pred eEEEEECCCcc-CCCCEEEEEEEEeCCcCccccceeEEEEE--EEEECCcccccEeEEEcce--eeCCCCEEEEEEEEEc
Confidence 56677766665 79999999999999999999988776543 2334787543232222221 6899999999999988
No 10
>PF07070 Spo0M: SpoOM protein; InterPro: IPR009776 This family consists of several bacterial SpoOM proteins which are thought to control sporulation in Bacillus subtilis.Spo0M exerts certain negative effects on sporulation and its gene expression is controlled by sigmaH [].
Probab=93.00 E-value=5.5 Score=39.27 Aligned_cols=125 Identities=18% Similarity=0.292 Sum_probs=85.0
Q ss_pred ecCceEEEEEeccccccCCCeEEEEEEEeCCC-CceeEeEEEEEEEEEEEEEEcceEE--EEEEeeeeccCCcCCCCCeE
Q psy16524 245 SQGKINLEVTLDREIYYHGEKVAATIVVNNTS-RKSVKNIKCYVVQHCEVTMVNSQFS--RYVASLETREGCPVTPGAAF 321 (453)
Q Consensus 245 ssGpl~LeasLdK~~Y~pGE~I~V~v~I~N~S-sk~VkkIKv~l~Q~~~v~lf~g~yk--~~Va~~E~~eG~pV~pgst~ 321 (453)
.-|..++..-|++.-|.|||+|.=.|.|.-.+ ...|.+|.+.|.-.+..--=...|+ ..++...-.+++.|.||.+.
T Consensus 9 GiG~akVDT~L~~~~~~pGe~v~G~V~i~GG~v~Q~I~~I~l~L~t~~~~e~~d~~~~~~~~~~~~~v~~~f~I~~ge~~ 88 (218)
T PF07070_consen 9 GIGGAKVDTVLEKPSVRPGETVRGEVHIKGGSVDQEIDRIYLELVTRYEVESDDKEYTQEVELARVRVSGPFTIEPGEEK 88 (218)
T ss_pred CCCCceEEEEECCCCccCCCEEEEEEEEEeCCcceEEeEEEEEEEEEEEEecCCCeEEEEEEEEEEEeCCCEEECCCCEE
Confidence 35778899999999999999999999999985 4899998888877654211122333 35667676777899999987
Q ss_pred EEEEEEeeccCCCCccceeeecCcccCCCCcCCCceeecCCCCCCCceeeEEEEEEEEEEEEcCCCcceeEEeeEEeeCC
Q psy16524 322 TKTFYLVPLASSNKDRRGIALDGHLKDDDVNLASSTLIGEGKCPSEAMGIVISYSLRVKLSCGTLGGELQTDVPFKLMNP 401 (453)
Q Consensus 322 ~k~~~L~Pll~~nr~krglALdG~Lk~edtnLASSTil~~~~~~ke~~gI~VSY~VKVkL~vsg~gsdv~veLPf~L~hp 401 (453)
+--|.+ ++. -+ |++ |+ +. ..|.|+-.|++.+ +-|..=.=|+.| +|
T Consensus 89 ~iPF~~-~lP----------------~e-tPi--T~----~~---------~~v~l~T~LdI~~-avD~~D~D~i~V-~P 133 (218)
T PF07070_consen 89 EIPFSF-PLP----------------WE-TPI--TE----GG---------MRVWLRTGLDIAG-AVDPGDLDPIEV-EP 133 (218)
T ss_pred EEeEEE-ECC----------------CC-CCc--cC----CC---------cEEEEEEEEEeCC-CCCCCCceeEEE-eC
Confidence 666665 211 11 122 22 11 5677888888875 555555556666 55
Q ss_pred CCC
Q psy16524 402 DPL 404 (453)
Q Consensus 402 ~P~ 404 (453)
.|.
T Consensus 134 ~p~ 136 (218)
T PF07070_consen 134 LPA 136 (218)
T ss_pred CHH
Confidence 553
No 11
>PF07070 Spo0M: SpoOM protein; InterPro: IPR009776 This family consists of several bacterial SpoOM proteins which are thought to control sporulation in Bacillus subtilis.Spo0M exerts certain negative effects on sporulation and its gene expression is controlled by sigmaH [].
Probab=88.57 E-value=3.6 Score=40.57 Aligned_cols=95 Identities=17% Similarity=0.363 Sum_probs=58.5
Q ss_pred eeeecCCCc---eeeeeEEEEcceee--eceeEEEEEEEEEeccccCccccCcccchheeeeeeEEeeCCCCCCCCcHHH
Q psy16524 16 DFIDHLEEV---DPIDGVIVVENEYL--KGRKVFGQIITTYRYGREEDEVMGVKFSKEMIVDRGQIVPSTNEKPELTVIQ 90 (453)
Q Consensus 16 d~vd~~~~v---d~v~Gvv~vd~~~l--~~rkV~~ql~~tfRYGred~eVmgl~F~ke~~~~~~qi~P~~~~~~~lt~lQ 90 (453)
|-+-+.+++ +.|.|.|.|.--.. +=.+|++.|.+.|....+|.+ +..+..+...++ . .+.+
T Consensus 16 DT~L~~~~~~pGe~v~G~V~i~GG~v~Q~I~~I~l~L~t~~~~e~~d~~-----~~~~~~~~~~~v---~---~~f~--- 81 (218)
T PF07070_consen 16 DTVLEKPSVRPGETVRGEVHIKGGSVDQEIDRIYLELVTRYEVESDDKE-----YTQEVELARVRV---S---GPFT--- 81 (218)
T ss_pred EEEECCCCccCCCEEEEEEEEEeCCcceEEeEEEEEEEEEEEEecCCCe-----EEEEEEEEEEEe---C---CCEE---
Confidence 445555555 78999999832222 336788888888876665655 333444444443 1 1222
Q ss_pred HHHhhccCCCeeeeEeeCCCCCCceEEecCCCCCCCCcceeEEEEEEEE
Q psy16524 91 EKLLKKLGPNAYPFTFHFPSGAPSSVTLQPGDEDTGKPLGVEHAIKTFV 139 (453)
Q Consensus 91 e~L~kklG~~a~PF~f~lp~~~P~Sv~Lqp~~~~~G~p~gv~Y~Vka~i 139 (453)
|+.-....+||+|.||-+.|-|. .|+.|.+++-+
T Consensus 82 ---I~~ge~~~iPF~~~lP~etPiT~------------~~~~v~l~T~L 115 (218)
T PF07070_consen 82 ---IEPGEEKEIPFSFPLPWETPITE------------GGMRVWLRTGL 115 (218)
T ss_pred ---ECCCCEEEEeEEEECCCCCCccC------------CCcEEEEEEEE
Confidence 11122478999999999999886 35666666554
No 12
>KOG3780|consensus
Probab=87.53 E-value=20 Score=37.31 Aligned_cols=45 Identities=27% Similarity=0.498 Sum_probs=37.8
Q ss_pred EEEEeccc--cccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEE
Q psy16524 251 LEVTLDRE--IYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTM 295 (453)
Q Consensus 251 LeasLdK~--~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~l 295 (453)
+++.+|+. +|.+||+|.=.+.+.+.....++.|++.+.=.+++..
T Consensus 7 ~~i~~d~~~~iy~~G~~vsG~v~l~~~~~~~~~~i~l~~~G~~~t~w 53 (427)
T KOG3780|consen 7 FEIVLDNPEAIYFPGEPVSGSVVLSTKEPIKVRAIKLQLKGRARTSW 53 (427)
T ss_pred EEEEeCCCccccCCCCeEEEEEEEEeCCccceeEEEEEEEEeEEEee
Confidence 45556655 7999999999999999999999999999987776543
No 13
>smart00809 Alpha_adaptinC2 Adaptin C-terminal domain. Adaptins are components of the adaptor complexes which link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. Gamma-adaptin is a subunit of the golgi adaptor. Alpha adaptin is a heterotetramer that regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This Ig-fold domain is found in alpha, beta and gamma adaptins and consists of a beta-sandwich containing 7 strands in 2 beta-sheets in a greek-key topology PUBMED:10430869, PUBMED:12176391. The adaptor appendage contains an additional N-terminal strand.
Probab=81.20 E-value=31 Score=28.78 Aligned_cols=71 Identities=13% Similarity=0.259 Sum_probs=46.2
Q ss_pred eecCceEEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEEcceEEEEEEeeeeccCCcCCCCCeEEE
Q psy16524 244 FSQGKINLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMVNSQFSRYVASLETREGCPVTPGAAFTK 323 (453)
Q Consensus 244 ~ssGpl~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf~g~yk~~Va~~E~~eG~pV~pgst~~k 323 (453)
+.+.-|++.+.+.+. +..+.+.+...|.|..++.++.+.+.- -++ ....+....+..++||++.++
T Consensus 2 ~~~~~l~I~~~~~~~----~~~~~i~~~~~N~s~~~it~f~~~~av--------pk~--~~l~l~~~s~~~l~p~~~i~q 67 (104)
T smart00809 2 YEKNGLQIGFKFERR----PGLIRITLTFTNKSPSPITNFSFQAAV--------PKS--LKLQLQPPSSPTLPPGGQITQ 67 (104)
T ss_pred ccCCCEEEEEEEEcC----CCeEEEEEEEEeCCCCeeeeEEEEEEc--------ccc--eEEEEcCCCCCccCCCCCEEE
Confidence 345567888877664 456899999999999999987765331 111 112223333446888887777
Q ss_pred EEEEe
Q psy16524 324 TFYLV 328 (453)
Q Consensus 324 ~~~L~ 328 (453)
.+.+.
T Consensus 68 ~~~i~ 72 (104)
T smart00809 68 VLKVE 72 (104)
T ss_pred EEEEE
Confidence 77663
No 14
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=81.11 E-value=3.3 Score=34.41 Aligned_cols=26 Identities=31% Similarity=0.466 Sum_probs=21.8
Q ss_pred EEEEeccccccCCCeEEEEEEEeCCC
Q psy16524 251 LEVTLDREIYYHGEKVAATIVVNNTS 276 (453)
Q Consensus 251 LeasLdK~~Y~pGE~I~V~v~I~N~S 276 (453)
+-+..||.+|.|||+|.+.+-+.+..
T Consensus 2 ~~i~TDr~iYrPGetV~~~~~~~~~~ 27 (99)
T PF01835_consen 2 IFIQTDRPIYRPGETVHFRAIVRDLD 27 (99)
T ss_dssp EEEEESSSEE-TTSEEEEEEEEEEEC
T ss_pred EEEECCccCcCCCCEEEEEEEEeccc
Confidence 34678999999999999999988887
No 15
>PF03643 Vps26: Vacuolar protein sorting-associated protein 26 ; InterPro: IPR005377 The movement of lipid and protein components between intracellular organelles requires the regulated interactions of many molecules. Vacuolar protein sorting-associated protein (Vps)5 is a yeast protein that is a subunit of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. Sorting nexin (SNX) 1 and SNX2 are its mammalian orthologs []. To carry out its biological functions, Vps5 forms the retromer complex with at least four other proteins: Vps17, Vps26, Vps29, and Vps35 []. This family of Vps26-proteins also contains Down syndrome critical region 3/A.; GO: 0007034 vacuolar transport, 0030904 retromer complex; PDB: 3LHA_A 3LH9_A 2R51_A 3LH8_B 2FAU_A.
Probab=80.84 E-value=27 Score=35.60 Aligned_cols=103 Identities=25% Similarity=0.387 Sum_probs=51.5
Q ss_pred cccCCCeEEEEEEEeCCCCcee--EeEEEEEEEEEEEEEE--cceEEE---EEEeeeeccCCcCCCCCeEEEEEEEeecc
Q psy16524 259 IYYHGEKVAATIVVNNTSRKSV--KNIKCYVVQHCEVTMV--NSQFSR---YVASLETREGCPVTPGAAFTKTFYLVPLA 331 (453)
Q Consensus 259 ~Y~pGE~I~V~v~I~N~Ssk~V--kkIKv~l~Q~~~v~lf--~g~yk~---~Va~~E~~eG~pV~pgst~~k~~~L~Pll 331 (453)
+|.+||+|.=.|.|+-..+|.+ .+|++.+.=. +-+| .++-.. ...++. ..| .+..|.|+.-.|.+.+
T Consensus 34 iY~~gE~V~G~V~I~~~~gk~~~H~GI~l~lvG~--ie~~~~~~k~~~f~~~~~eL~-~~G-~l~~~~t~pFeF~~~~-- 107 (275)
T PF03643_consen 34 IYSDGETVSGKVVITSKPGKSLEHQGIKLELVGQ--IEAFYDSGKPIEFLSLSIELA-PPG-KLPEGKTFPFEFPLVE-- 107 (275)
T ss_dssp EEETC--EEEEEEEEESSTS-EEES-EEEEEEEE--EEEGCCTT-EEEEEEEEEEEE--SE-EE-S-EEEEEEE-SB---
T ss_pred eEcCCCEEEEEEEEEECCCCceEEeeEEEEEEEe--EeEeccCCCceEeEEeeEEEc-CCc-ccCCCcEEeeEeCCCC--
Confidence 8999999999999988776655 4566665433 4344 443211 111221 111 2333333322222111
Q ss_pred CCCCccceeeecCcccCCCCcCCCceeecCCCCCCCcee--eEEEEEEEEEEEEcCCCcceeEEeeEEeeC
Q psy16524 332 SSNKDRRGIALDGHLKDDDVNLASSTLIGEGKCPSEAMG--IVISYSLRVKLSCGTLGGELQTDVPFKLMN 400 (453)
Q Consensus 332 ~~nr~krglALdG~Lk~edtnLASSTil~~~~~~ke~~g--I~VSY~VKVkL~vsg~gsdv~veLPf~L~h 400 (453)
|. . ....| +.+.|.|+|.+.-+. .+++-+.+|.+-.
T Consensus 108 -----k~---------y-----------------ETY~G~~v~i~Y~lrv~v~R~~--~~i~k~~ef~V~~ 145 (275)
T PF03643_consen 108 -----KP---------Y-----------------ETYHGVNVNIRYFLRVTVKRSY--KDISKEQEFWVQN 145 (275)
T ss_dssp ----------------S-------------------EE-SSEEEEEEEEEEE--SS--S-EEEEEEEEEE-
T ss_pred -----CC---------C-----------------ccEeeeEEEEEEEEEEEEEccC--CCcceEEEEEEEe
Confidence 00 1 11334 899999999887775 8999999999763
No 16
>PF04744 Monooxygenase_B: Monooxygenase subunit B protein; InterPro: IPR006833 Ammonia monooxygenase and the particulate methane monooxygenase are both integral membrane proteins, occurring in ammonia oxidisers and methanotrophs respectively, which are thought to be evolutionarily related []. These enzymes have a relatively wide substrate specificity and can catalyse the oxidation of a range of substrates including ammonia, methane, halogenated hydrocarbons and aromatic molecules []. These enzymes are composed of 3 subunits - A (IPR003393 from INTERPRO), B (IPR006833 from INTERPRO) and C (IPR006980 from INTERPRO) - and contain various metal centres, including copper. Particulate methane monooxygenase from Methylococcus capsulatus str. Bath is an ABC homotrimer, which contains mononuclear and dinuclear copper metal centres, and a third metal centre containing a metal ion whose identity in vivo is not certain[]. The soluble regions of these enzymes derive primarily from the B subunit. This subunit forms two antiparallel beta-barrel-like structures and contains the mono- and di- nuclear copper metal centres [].; PDB: 3CHX_E 3RFR_A 3RGB_A 1YEW_A.
Probab=77.45 E-value=6.3 Score=41.79 Aligned_cols=74 Identities=22% Similarity=0.393 Sum_probs=45.2
Q ss_pred EEEEeccccc-cCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEEcce-------EEE-EEEe--eeeccCCcCCCCC
Q psy16524 251 LEVTLDREIY-YHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMVNSQ-------FSR-YVAS--LETREGCPVTPGA 319 (453)
Q Consensus 251 LeasLdK~~Y-~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf~g~-------yk~-~Va~--~E~~eG~pV~pgs 319 (453)
+++.+.+..| +||-++.++++|+|+|++.|+ +.=.+.+.+.+-+.. |.. .+|. +..++..||+||.
T Consensus 249 V~~~v~~A~Y~vpgR~l~~~l~VtN~g~~pv~---LgeF~tA~vrFln~~v~~~~~~~P~~l~A~~gL~vs~~~pI~PGE 325 (381)
T PF04744_consen 249 VKVKVTDATYRVPGRTLTMTLTVTNNGDSPVR---LGEFNTANVRFLNPDVPTDDPDYPDELLAERGLSVSDNSPIAPGE 325 (381)
T ss_dssp EEEEEEEEEEESSSSEEEEEEEEEEESSS-BE---EEEEESSS-EEE-TTT-SS-S---TTTEETT-EEES--S-B-TT-
T ss_pred eEEEEeccEEecCCcEEEEEEEEEcCCCCceE---eeeEEeccEEEeCcccccCCCCCchhhhccCcceeCCCCCcCCCc
Confidence 7777888877 899999999999999999986 666677777764221 221 2332 3334446999999
Q ss_pred eEEEEEEE
Q psy16524 320 AFTKTFYL 327 (453)
Q Consensus 320 t~~k~~~L 327 (453)
|-+-.+.+
T Consensus 326 Trtl~V~a 333 (381)
T PF04744_consen 326 TRTLTVEA 333 (381)
T ss_dssp EEEEEEEE
T ss_pred eEEEEEEe
Confidence 86444443
No 17
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=76.60 E-value=8.3 Score=30.75 Aligned_cols=41 Identities=22% Similarity=0.271 Sum_probs=35.6
Q ss_pred cCceEEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEE
Q psy16524 246 QGKINLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCY 286 (453)
Q Consensus 246 sGpl~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~ 286 (453)
...+.+.-+.++....+||.|..++.+.|.++.....+++.
T Consensus 23 ~~~~~~~k~~~~~~~~~Gd~v~ytitvtN~G~~~a~nv~v~ 63 (76)
T PF01345_consen 23 IPDLSITKTVNPSTANPGDTVTYTITVTNTGPAPATNVVVT 63 (76)
T ss_pred CCCEEEEEecCCCcccCCCEEEEEEEEEECCCCeeEeEEEE
Confidence 45677888899999999999999999999999998876554
No 18
>PF00207 A2M: Alpha-2-macroglobulin family; InterPro: IPR001599 This entry contains serum complement C3 and C4 precursors and alpha-macrogrobulins. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; GO: 0004866 endopeptidase inhibitor activity; PDB: 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 2PN5_A 3FRP_G 3HRZ_B ....
Probab=76.23 E-value=8.1 Score=32.17 Aligned_cols=40 Identities=15% Similarity=0.280 Sum_probs=28.6
Q ss_pred ecCceEEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEE
Q psy16524 245 SQGKINLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCY 286 (453)
Q Consensus 245 ssGpl~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~ 286 (453)
...|+.++.+||+.+ ..||.+.+.+.|.|+..+.++ +++.
T Consensus 52 v~~p~~i~~~lP~~l-~~GD~~~i~v~v~N~~~~~~~-v~V~ 91 (92)
T PF00207_consen 52 VFKPFFIQLNLPRSL-RRGDQIQIPVTVFNYTDKDQE-VTVT 91 (92)
T ss_dssp EB-SEEEEEE--SEE-ETTSEEEEEEEEEE-SSS-EE-EEEE
T ss_pred EEeeEEEEcCCCcEE-ecCCEEEEEEEEEeCCCCCEE-EEEE
Confidence 346788999999854 689999999999999998876 4554
No 19
>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; InterPro: IPR018905 This domain has been named NEW3, but its function is not known. It is found on proteins which are bacterial galactosidases [].; PDB: 1EUT_A 2BZD_A 1WCQ_C 2BER_A 1W8O_A 1EUU_A 1W8N_A.
Probab=71.43 E-value=13 Score=29.88 Aligned_cols=59 Identities=22% Similarity=0.335 Sum_probs=33.8
Q ss_pred cCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEEcceEEEEEEeeeeccCCcCCCCCeEEEEEEEee
Q psy16524 261 YHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMVNSQFSRYVASLETREGCPVTPGAAFTKTFYLVP 329 (453)
Q Consensus 261 ~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf~g~yk~~Va~~E~~eG~pV~pgst~~k~~~L~P 329 (453)
.+||++.+++.|.|.....+..+++.+.-= .| +.......... .++||.+..-.+.|.|
T Consensus 2 ~~G~~~~~~~tv~N~g~~~~~~v~~~l~~P------~G-W~~~~~~~~~~---~l~pG~s~~~~~~V~v 60 (78)
T PF10633_consen 2 TPGETVTVTLTVTNTGTAPLTNVSLSLSLP------EG-WTVSASPASVP---SLPPGESVTVTFTVTV 60 (78)
T ss_dssp -TTEEEEEEEEEE--SSS-BSS-EEEEE--------TT-SE---EEEEE-----B-TTSEEEEEEEEEE
T ss_pred CCCCEEEEEEEEEECCCCceeeEEEEEeCC------CC-ccccCCccccc---cCCCCCEEEEEEEEEC
Confidence 489999999999999998888877775432 11 11001111111 6899999888888877
No 20
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=70.53 E-value=8.7 Score=29.37 Aligned_cols=32 Identities=22% Similarity=0.360 Sum_probs=27.3
Q ss_pred eccccccCCCeEEEEEEEeCCCCceeEeEEEE
Q psy16524 255 LDREIYYHGEKVAATIVVNNTSRKSVKNIKCY 286 (453)
Q Consensus 255 LdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~ 286 (453)
.++....+||.|..++.|.|........+.+.
T Consensus 3 ~d~~~~~~Gd~v~Yti~v~N~g~~~a~~v~v~ 34 (53)
T TIGR01451 3 VDKTVATIGDTITYTITVTNNGNVPATNVVVT 34 (53)
T ss_pred cCccccCCCCEEEEEEEEEECCCCceEeEEEE
Confidence 47788899999999999999999888765544
No 21
>PF07705 CARDB: CARDB; InterPro: IPR011635 The APHP (acidic peptide-dependent hydrolases/peptidase) domain is found in a variety of different proteins.; PDB: 2KUT_A 2L0D_A 3IDU_A 2KL6_A.
Probab=70.25 E-value=55 Score=26.29 Aligned_cols=68 Identities=21% Similarity=0.339 Sum_probs=41.5
Q ss_pred eEEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEEcceEEEEEEeeeeccCCcCCCCCeEEEEEEEe
Q psy16524 249 INLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMVNSQFSRYVASLETREGCPVTPGAAFTKTFYLV 328 (453)
Q Consensus 249 l~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf~g~yk~~Va~~E~~eG~pV~pgst~~k~~~L~ 328 (453)
|.+.......-...|+.+.|++.|.|.-......+.+.+.. .|... ..... ..++||.+..-.+.+.
T Consensus 4 L~v~~~~~~~~~~~g~~~~i~~~V~N~G~~~~~~~~v~~~~-------~~~~~---~~~~i---~~L~~g~~~~v~~~~~ 70 (101)
T PF07705_consen 4 LTVSITVSPSNVVPGEPVTITVTVKNNGTADAENVTVRLYL-------DGNSV---STVTI---PSLAPGESETVTFTWT 70 (101)
T ss_dssp EEE-EEEC-SEEETTSEEEEEEEEEE-SSS-BEEEEEEEEE-------TTEEE---EEEEE---SEB-TTEEEEEEEEEE
T ss_pred EEEEEeeCCCcccCCCEEEEEEEEEECCCCCCCCEEEEEEE-------CCcee---ccEEE---CCcCCCcEEEEEEEEE
Confidence 44455666777789999999999999988888776666322 44432 11111 2578888877777775
Q ss_pred e
Q psy16524 329 P 329 (453)
Q Consensus 329 P 329 (453)
+
T Consensus 71 ~ 71 (101)
T PF07705_consen 71 P 71 (101)
T ss_dssp -
T ss_pred e
Confidence 5
No 22
>PF07919 Gryzun: Gryzun, putative trafficking through Golgi; InterPro: IPR012880 The proteins featured in this family are all hypothetical eukaryotic proteins of unknown function. The region in question is approximately 150 residues long.
Probab=65.89 E-value=29 Score=37.39 Aligned_cols=77 Identities=12% Similarity=0.177 Sum_probs=56.0
Q ss_pred eecCceEEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEEcceEEEEEEeeeeccCCcCCCCCeEEE
Q psy16524 244 FSQGKINLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMVNSQFSRYVASLETREGCPVTPGAAFTK 323 (453)
Q Consensus 244 ~ssGpl~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf~g~yk~~Va~~E~~eG~pV~pgst~~k 323 (453)
.-+.++.+.+.++..+.. |+++.+.+.|.|.|+.... +.+.+.---+ .+|.|.....+ +|.|++.-.-
T Consensus 466 v~~~~~~v~~~~p~~~~~-~~~~~l~~~I~N~T~~~~~-~~~~me~s~~-F~fsG~k~~~~---------~llP~s~~~~ 533 (554)
T PF07919_consen 466 VPSSPLRVLASVPPSAIV-GEPFTLSYTIENPTNHFQT-FELSMEPSDD-FMFSGPKQTTF---------SLLPFSRHTV 533 (554)
T ss_pred ccCCCcEEEEecCCcccc-CcEEEEEEEEECCCCccEE-EEEEEccCCC-EEEECCCcCce---------EECCCCcEEE
Confidence 456788888888766654 8899999999999987776 6666643333 45555533233 7889999888
Q ss_pred EEEEeeccC
Q psy16524 324 TFYLVPLAS 332 (453)
Q Consensus 324 ~~~L~Pll~ 332 (453)
.|.|.|+.+
T Consensus 534 ~y~l~pl~~ 542 (554)
T PF07919_consen 534 RYNLLPLVA 542 (554)
T ss_pred EEEEEEccC
Confidence 999999643
No 23
>TIGR03079 CH4_NH3mon_ox_B methane monooxygenase/ammonia monooxygenase, subunit B. Both ammonia oxidizers such as Nitrosomonas europaea and methanotrophs (obligate methane oxidizers) such as Methylococcus capsulatus each can grow only on their own characteristic substrate. However, both groups have the ability to oxidize both substrates, and so the relevant enzymes must be named here according to their ability to oxidze both. The protein family represented here reflects subunit B of both the particulate methane monooxygenase of methylotrophs and the ammonia monooxygenase of nitrifying bacteria.
Probab=61.60 E-value=37 Score=36.26 Aligned_cols=72 Identities=15% Similarity=0.317 Sum_probs=48.2
Q ss_pred EEEEEeccccc-cCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEEcc--eEE------E-EEE-eeeeccCCcCCCC
Q psy16524 250 NLEVTLDREIY-YHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMVNS--QFS------R-YVA-SLETREGCPVTPG 318 (453)
Q Consensus 250 ~LeasLdK~~Y-~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf~g--~yk------~-~Va-~~E~~eG~pV~pg 318 (453)
.+++.+.+..| +||-.+.++++|+|+++..|+ +.=.+.+.+.+-|. .++ . .+| .+..++..||.||
T Consensus 267 ~V~~kv~~a~Y~VPGR~l~~~~~VTN~g~~~vr---lgEF~TA~vRFlN~~~v~~~~~~yP~~lla~GL~v~d~~pI~PG 343 (399)
T TIGR03079 267 PVSINVTKANYDVPGRALRVTMEITNNGDQVIS---IGEFTTAGIRFMNANGVRVLDPDYPRELLAEGLEVDDQSAIAPG 343 (399)
T ss_pred ceEEEEeccEEecCCcEEEEEEEEEcCCCCceE---EEeEeecceEeeCcccccccCCCChHHHhhccceeCCCCCcCCC
Confidence 45556666666 999999999999999999876 55566777665543 332 1 122 2333455789999
Q ss_pred CeEEEE
Q psy16524 319 AAFTKT 324 (453)
Q Consensus 319 st~~k~ 324 (453)
.|-+-.
T Consensus 344 ETr~v~ 349 (399)
T TIGR03079 344 ETVEVK 349 (399)
T ss_pred cceEEE
Confidence 885433
No 24
>PF07919 Gryzun: Gryzun, putative trafficking through Golgi; InterPro: IPR012880 The proteins featured in this family are all hypothetical eukaryotic proteins of unknown function. The region in question is approximately 150 residues long.
Probab=59.06 E-value=1.5e+02 Score=31.88 Aligned_cols=39 Identities=13% Similarity=0.187 Sum_probs=31.5
Q ss_pred eecCceEEEEEe--ccccccCCCeEEEEEEEeCCCCceeEe
Q psy16524 244 FSQGKINLEVTL--DREIYYHGEKVAATIVVNNTSRKSVKN 282 (453)
Q Consensus 244 ~ssGpl~LeasL--dK~~Y~pGE~I~V~v~I~N~Ssk~Vkk 282 (453)
....|-+|++++ .+.-|+-||.+.+.+.|.|+.......
T Consensus 168 I~p~pp~v~I~~~~~~~~~l~gE~~~i~i~I~n~e~~~~~~ 208 (554)
T PF07919_consen 168 ILPRPPKVSIKLPNHKPPALTGEFYPIPITISNNEDEEASG 208 (554)
T ss_pred EECCCCCeEEEeCCCCCCeEcCCEEEEEEEEEcCCCcccee
Confidence 445566777777 677899999999999999999876663
No 25
>PF06159 DUF974: Protein of unknown function (DUF974); InterPro: IPR010378 This is a family of uncharacterised eukaryotic proteins.
Probab=58.12 E-value=24 Score=35.10 Aligned_cols=31 Identities=35% Similarity=0.521 Sum_probs=27.2
Q ss_pred ccCCCeEEEEEEEeCCCCceeEeEEEEEEEE
Q psy16524 260 YYHGEKVAATIVVNNTSRKSVKNIKCYVVQH 290 (453)
Q Consensus 260 Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~ 290 (453)
.|-||+-...+++.|+|+..|+.+.+++.-.
T Consensus 10 iylGEtF~~~l~~~N~s~~~v~~v~ikvemq 40 (249)
T PF06159_consen 10 IYLGETFSCYLSVNNDSNKPVRNVRIKVEMQ 40 (249)
T ss_pred EeecCCEEEEEEeecCCCCceEEeEEEEEEe
Confidence 3779999999999999999999998886544
No 26
>KOG0452|consensus
Probab=57.61 E-value=10 Score=42.60 Aligned_cols=151 Identities=23% Similarity=0.342 Sum_probs=89.9
Q ss_pred CccccCcccchheeeeeeEEeeCCCCCCCCcHHHHHHhhccCCCeeeeEeeCCCCCC---------------ceEEecCC
Q psy16524 57 EDEVMGVKFSKEMIVDRGQIVPSTNEKPELTVIQEKLLKKLGPNAYPFTFHFPSGAP---------------SSVTLQPG 121 (453)
Q Consensus 57 d~eVmgl~F~ke~~~~~~qi~P~~~~~~~lt~lQe~L~kklG~~a~PF~f~lp~~~P---------------~Sv~Lqp~ 121 (453)
|-+--|-+=-||.+|+..-. ..-+|=.+|++|.| |=+.++|+.-- |.+.|. +
T Consensus 708 dFNsYGsRRGND~vMaRGTF--------ANIrlvNkl~~k~g----P~TvHiPsge~ldvFdAA~~Y~~~g~p~iila-G 774 (892)
T KOG0452|consen 708 DFNSYGSRRGNDAVMARGTF--------ANIRLVNKLLSKVG----PKTVHIPSGEELDVFDAAERYKSEGIPLIILA-G 774 (892)
T ss_pred hccccccccCchhhhhcccc--------hhhHHHHHHhcccC----CceEecCCCCeecHhhHHHHHHhcCCceEEEe-c
Confidence 33444444445555543321 23556666777777 55778876532 223332 3
Q ss_pred CCCCCCcceeEE--------EEEEEEcCCCcccCcccceeEEeEEEeeEEeeeeeeeecccchhhhcccchhhhhccccc
Q psy16524 122 DEDTGKPLGVEH--------AIKTFVGDSIDEKGHKRSSVALAIKKCYVVQHCEVTMVNSQFSRYVASLETREVLADKDK 193 (453)
Q Consensus 122 ~~~~G~p~gv~Y--------~Vka~iad~~~ek~~kr~sv~~~Irk~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 193 (453)
++ +|.--.-+| -|||.||++- |++||.|-|-|||--
T Consensus 775 ke-YGsGsSRDWAAKGP~LlGvKAViaeS~-ErIHrsnLvGmGIiP---------------------------------- 818 (892)
T KOG0452|consen 775 KE-YGSGSSRDWAAKGPFLLGVKAVIAESY-ERIHRSNLVGMGIIP---------------------------------- 818 (892)
T ss_pred cc-cCCCCccchhhcCchhhhhHHHHHHHH-HHHHhhccccceeee----------------------------------
Confidence 32 232222222 3688898887 999999999999977
Q ss_pred hhhhcccccccccccccccccCCCCCcccccCCCCCCCCCCceeeeeeeeeecCceEEEEEeccccccCCCeEEEEEEEe
Q psy16524 194 TNALKKSKSIDRARYENSCYATDDDDNILQYAPPSRGRRLPSSLVSKGFTFSQGKINLEVTLDREIYYHGEKVAATIVVN 273 (453)
Q Consensus 194 ~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~aP~~~~~~~p~~e~~K~F~~ssGpl~LeasLdK~~Y~pGE~I~V~v~I~ 273 (453)
+||-|-... ++ +=-.|.=...+.||..+..||+.|.|+. +
T Consensus 819 ----------------------------l~f~~Ge~A------dt----LgLtG~E~yti~lP~~~lkPgq~i~v~~--d 858 (892)
T KOG0452|consen 819 ----------------------------LQFLPGEDA------DT----LGLTGRERYTIHLPENILKPGQDITVTT--D 858 (892)
T ss_pred ----------------------------eeecCCCCh------hh----cCcccceeEEEECCcccCCCCceEEEEe--c
Confidence 777664332 11 1113556678899999999999987753 4
Q ss_pred CCCCceeEeEEEEEEEEEEEEEE-cce
Q psy16524 274 NTSRKSVKNIKCYVVQHCEVTMV-NSQ 299 (453)
Q Consensus 274 N~Ssk~VkkIKv~l~Q~~~v~lf-~g~ 299 (453)
|...-. .-+++.--+++++| +|-
T Consensus 859 tGk~F~---~~~rFdteVeltyy~~GG 882 (892)
T KOG0452|consen 859 TGKVFV---CTLRFDTEVELTYYKNGG 882 (892)
T ss_pred CCcEEE---EEEEecceEEEEEEecCC
Confidence 443322 23555566677777 664
No 27
>PF13199 Glyco_hydro_66: Glycosyl hydrolase family 66; PDB: 3VMO_A 3VMN_A 3VMP_A.
Probab=57.21 E-value=24 Score=39.41 Aligned_cols=28 Identities=36% Similarity=0.456 Sum_probs=17.6
Q ss_pred EeccccccCCCeEEEEEEEeCCCCceeE
Q psy16524 254 TLDREIYYHGEKVAATIVVNNTSRKSVK 281 (453)
Q Consensus 254 sLdK~~Y~pGE~I~V~v~I~N~Ssk~Vk 281 (453)
+.||..|.|||+|.++++..|.......
T Consensus 1 ~tDKA~Y~PGe~V~l~~~~~~~~~~~~~ 28 (559)
T PF13199_consen 1 TTDKARYRPGEKVTLTASLKNTTGSDFS 28 (559)
T ss_dssp EES-SSB-TTS-EEEE-EEE--SSS-EE
T ss_pred CCCcceeCCCCeEEEEEEeccCcccccc
Confidence 4689999999999999999998665433
No 28
>PF11355 DUF3157: Protein of unknown function (DUF3157); InterPro: IPR021501 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=47.14 E-value=54 Score=32.20 Aligned_cols=42 Identities=26% Similarity=0.393 Sum_probs=33.8
Q ss_pred EEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEE--cce
Q psy16524 251 LEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMV--NSQ 299 (453)
Q Consensus 251 LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf--~g~ 299 (453)
+++.|...-|-.| .+-+...|+|+|+..|.-|.+. |.+| +|+
T Consensus 100 VdV~l~~~~y~~~-~L~l~~~ltnqSsqsVv~Vel~------v~l~d~~G~ 143 (199)
T PF11355_consen 100 VDVSLGASQYEDG-QLGLPFSLTNQSSQSVVLVELE------VTLFDDSGQ 143 (199)
T ss_pred eeEEEeccceeCC-eEEEEEEEecCCCceEEEEEEE------EEEEcCCCC
Confidence 6777777667666 9999999999999999887776 5667 555
No 29
>PF09478 CBM49: Carbohydrate binding domain CBM49; InterPro: IPR019028 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This domain is found at the C-terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose []. ; GO: 0030246 carbohydrate binding, 0005576 extracellular region
Probab=47.02 E-value=50 Score=27.03 Aligned_cols=39 Identities=18% Similarity=0.255 Sum_probs=30.5
Q ss_pred EEEEEeccccccCCC-eEEEEEEEeCCCCceeEeEEEEEE
Q psy16524 250 NLEVTLDREIYYHGE-KVAATIVVNNTSRKSVKNIKCYVV 288 (453)
Q Consensus 250 ~LeasLdK~~Y~pGE-~I~V~v~I~N~Ssk~VkkIKv~l~ 288 (453)
.++-++..+....|. -..+.+.|.|+++++|+.+++.+.
T Consensus 2 ~i~q~~~~sW~~~g~~y~qy~v~I~N~~~~~I~~~~i~~~ 41 (80)
T PF09478_consen 2 TITQTLVNSWTENGQTYTQYDVTITNNGSKPIKSLKISID 41 (80)
T ss_pred EEEEEEEeEEEeCCEEEEEEEEEEEECCCCeEEEEEEEEC
Confidence 455566666666665 578999999999999999888866
No 30
>PF06030 DUF916: Bacterial protein of unknown function (DUF916); InterPro: IPR010317 This family consists of putative cell surface proteins, from Firmicutes, of unknown function.
Probab=47.00 E-value=42 Score=29.94 Aligned_cols=29 Identities=21% Similarity=0.290 Sum_probs=24.1
Q ss_pred cCCCeEEEEEEEeCCCCceeEeEEEEEEEE
Q psy16524 261 YHGEKVAATIVVNNTSRKSVKNIKCYVVQH 290 (453)
Q Consensus 261 ~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~ 290 (453)
-|||...+.+.|.|+|++.++ +++.+..-
T Consensus 24 ~P~q~~~l~v~i~N~s~~~~t-v~v~~~~A 52 (121)
T PF06030_consen 24 KPGQKQTLEVRITNNSDKEIT-VKVSANTA 52 (121)
T ss_pred CCCCEEEEEEEEEeCCCCCEE-EEEEEeee
Confidence 689999999999999999887 66665543
No 31
>COG2373 Large extracellular alpha-helical protein [General function prediction only]
Probab=45.90 E-value=77 Score=39.90 Aligned_cols=39 Identities=13% Similarity=0.272 Sum_probs=35.2
Q ss_pred ceEEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEE
Q psy16524 248 KINLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCY 286 (453)
Q Consensus 248 pl~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~ 286 (453)
.+.+.++++|+.+.+|+.+.+++...|-+..++..-++.
T Consensus 497 r~~i~l~~~k~~~~~g~~v~~~v~~~yL~GaPa~g~~~~ 535 (1621)
T COG2373 497 RFKINLTLDKTEWVPGKDVKIKVDLRYLYGAPAAGLTVQ 535 (1621)
T ss_pred eEEEecccccccccCCCcEEEEEEEEecCCCcccCceee
Confidence 377889999999999999999999999999998887766
No 32
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=43.78 E-value=1.1e+02 Score=25.42 Aligned_cols=64 Identities=25% Similarity=0.321 Sum_probs=41.9
Q ss_pred EeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEEcceEEEEEEeeeeccCCcCCCCCeEEEEEEEee
Q psy16524 254 TLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMVNSQFSRYVASLETREGCPVTPGAAFTKTFYLVP 329 (453)
Q Consensus 254 sLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf~g~yk~~Va~~E~~eG~pV~pgst~~k~~~L~P 329 (453)
.||-..+..|+.....+.|.|.|....+ +++.+-.+ ... ...++...| .++||.+..-.+.+.|
T Consensus 10 ~ldFG~v~~g~~~~~~v~l~N~s~~p~~---f~v~~~~~---~~~-----~~~v~~~~g-~l~PG~~~~~~V~~~~ 73 (102)
T PF14874_consen 10 ELDFGNVFVGQTYSRTVTLTNTSSIPAR---FRVRQPES---LSS-----FFSVEPPSG-FLAPGESVELEVTFSP 73 (102)
T ss_pred EEEeeEEccCCEEEEEEEEEECCCCCEE---EEEEeCCc---CCC-----CEEEECCCC-EECCCCEEEEEEEEEe
Confidence 4566677899999999999999998865 34333221 011 123333344 4899998776677764
No 33
>PF05688 DUF824: Salmonella repeat of unknown function (DUF824); InterPro: IPR008542 This family consists of a series of repeated sequences (of around 180 residues) which are found in Salmonella typhimurium, Salmonella typhi and Escherichia coli. These repeats are almost always found with this entry. The repeats are associated with RatA and RatB, the coding sequences of which are found in the pathogeneicity island of Salmonella. The sequences may be determinants of pathogenicity [, ].
Probab=43.00 E-value=39 Score=25.88 Aligned_cols=29 Identities=21% Similarity=0.322 Sum_probs=23.7
Q ss_pred cCCCeEEEEEEEeCCCCceeEeEEEEEEE
Q psy16524 261 YHGEKVAATIVVNNTSRKSVKNIKCYVVQ 289 (453)
Q Consensus 261 ~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q 289 (453)
.-||+|+++|.+.|....+|-..-+.|..
T Consensus 10 K~Ge~I~ltVt~kda~G~pv~n~~f~l~r 38 (47)
T PF05688_consen 10 KVGETIPLTVTVKDANGNPVPNAPFTLTR 38 (47)
T ss_pred ecCCeEEEEEEEECCCCCCcCCceEEEEe
Confidence 45999999999999999998876665443
No 34
>PF14796 AP3B1_C: Clathrin-adaptor complex-3 beta-1 subunit C-terminal
Probab=39.99 E-value=1.1e+02 Score=28.67 Aligned_cols=74 Identities=20% Similarity=0.212 Sum_probs=50.4
Q ss_pred eecCceEEEEEeccccc-cCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEEcceEEEEEEeeeeccCCcCCCCCeEE
Q psy16524 244 FSQGKINLEVTLDREIY-YHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMVNSQFSRYVASLETREGCPVTPGAAFT 322 (453)
Q Consensus 244 ~ssGpl~LeasLdK~~Y-~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf~g~yk~~Va~~E~~eG~pV~pgst~~ 322 (453)
+..+=|.++-...|+-+ +....+.|.+.++|+|...++.|++.-.... .|- ...++.+=..+.||++++
T Consensus 64 v~G~GL~v~Y~F~RqP~~~s~~mvsIql~ftN~s~~~i~~I~i~~k~l~-----~g~-----~i~~F~~I~~L~pg~s~t 133 (145)
T PF14796_consen 64 VNGKGLSVEYRFSRQPSLYSPSMVSIQLTFTNNSDEPIKNIHIGEKKLP-----AGM-----RIHEFPEIESLEPGASVT 133 (145)
T ss_pred cCCCceeEEEEEccCCcCCCCCcEEEEEEEEecCCCeecceEECCCCCC-----CCc-----EeeccCcccccCCCCeEE
Confidence 45566899999999888 5667999999999999999999887633310 011 111222112467888887
Q ss_pred EEEEE
Q psy16524 323 KTFYL 327 (453)
Q Consensus 323 k~~~L 327 (453)
..+-|
T Consensus 134 ~~lgI 138 (145)
T PF14796_consen 134 VSLGI 138 (145)
T ss_pred EEEEE
Confidence 76655
No 35
>PF07703 A2M_N_2: Alpha-2-macroglobulin family N-terminal region; InterPro: IPR011625 This is a domain of the alpha-2-macroglobulin family. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; PDB: 2QKI_D 3L3O_D 3NMS_A 2ICF_A 2A73_A 2ICE_D 2HR0_A 2A74_A 2XWJ_G 3OHX_A ....
Probab=39.42 E-value=29 Score=30.09 Aligned_cols=29 Identities=28% Similarity=0.401 Sum_probs=24.3
Q ss_pred ceEEEEEeccccccCCCeEEEEEEEeCCC
Q psy16524 248 KINLEVTLDREIYYHGEKVAATIVVNNTS 276 (453)
Q Consensus 248 pl~LeasLdK~~Y~pGE~I~V~v~I~N~S 276 (453)
.++++++.+++.|.|||++.++++...+|
T Consensus 94 ~~~v~l~~~~~~~~Pg~~~~~~i~~~~~s 122 (136)
T PF07703_consen 94 ELKVELTASPDEYKPGEEVTLRIKAPPNS 122 (136)
T ss_dssp SSSEEEEESSSSBTTTSEEEEEEEESTTE
T ss_pred cceEEEEEecceeCCCCEEEEEEEeCCCC
Confidence 36688888999999999999999995554
No 36
>PF09624 DUF2393: Protein of unknown function (DUF2393); InterPro: IPR013417 The function of this protein is unknown. It is always found as part of a two-gene operon with IPR013416 from INTERPRO, a protein that appears to span the membrane seven times. It has so far been found in the bacteria Anabaena sp. (strain PCC 7120), Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus.
Probab=37.28 E-value=88 Score=28.23 Aligned_cols=40 Identities=28% Similarity=0.262 Sum_probs=29.8
Q ss_pred ceEEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEEEE
Q psy16524 248 KINLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVV 288 (453)
Q Consensus 248 pl~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~ 288 (453)
+..+++.-.+. .--+|.+-|...|+|.+++++++.++.+.
T Consensus 47 ~~~~~~~~~~~-l~~~~~~~v~g~V~N~g~~~i~~c~i~~~ 86 (149)
T PF09624_consen 47 KIELTLTSQKR-LQYSESFYVDGTVTNTGKFTIKKCKITVK 86 (149)
T ss_pred CceEEEeeeee-eeeccEEEEEEEEEECCCCEeeEEEEEEE
Confidence 34444444444 44589999999999999999998877743
No 37
>PF00963 Cohesin: Cohesin domain; InterPro: IPR002102 Cohesin domains interact with a complementary domain, termed the dockerin domain (see IPR002105 from INTERPRO). The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome []. The scaffoldin component of the cellulolytic bacterium Clostridium thermocellum is a non-hydrolytic protein which organises the hydrolytic enzymes in a large complex, called the cellulosome. Scaffoldin comprises a series of functional domains, amongst which is a single cellulose-binding domain and nine cohesin domains which are responsible for integrating the individual enzymatic subunits into the complex.; GO: 0030246 carbohydrate binding, 0000272 polysaccharide catabolic process; PDB: 2BM3_A 3P0D_I 3KCP_A 2B59_A 3L8Q_B 3FNK_C 3GHP_B 2CCL_A 1ANU_A 1OHZ_A ....
Probab=37.11 E-value=1.1e+02 Score=27.13 Aligned_cols=35 Identities=20% Similarity=0.313 Sum_probs=26.6
Q ss_pred EEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEE
Q psy16524 251 LEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCY 286 (453)
Q Consensus 251 LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~ 286 (453)
+++++++.--.+||++.|.+.++|.++. |..+.+.
T Consensus 1 v~l~~~~~~a~~G~tv~V~V~v~~~~~~-i~~~~~~ 35 (141)
T PF00963_consen 1 VTLSVDSVSAKPGETVTVPVNVSNVSNS-IAGMQFT 35 (141)
T ss_dssp EEEEESECEE-TTSEEEEEEEEESCTTT-EEEEEEE
T ss_pred CEEEeCCceECCCCEEEEEEEEEcCCCc-EEEEEEE
Confidence 4677787777999999999999999775 5554443
No 38
>PF02014 Reeler: Reeler domain Schematic picture including Reeler domain; InterPro: IPR002861 Extracellular matrix (ECM) proteins play an important role in early cortical development, specifically in the formation of neural connections and in controlling the cyto-architecture of the central nervous system. The product of the reeler gene in mouse is reelin,a large extracellular protein secreted by pioneer neurons that coordinates cell positioning during neurodevelopment []. F-spondin and mindin are a family of matrix-attached adhesion molecules that share structural similarities and overlapping domains of expression. Both F-spondin and mindin promote adhesion and outgrowth of hippocampal embryonic neurons and bind to a putative receptor(s) expressed on both hippocampal and sensory neurons []. This domain of unknown function is found at the N terminus of reelin and F-spondin.; PDB: 2ZOT_B 2ZOU_B 3COO_A.
Probab=36.32 E-value=68 Score=28.37 Aligned_cols=32 Identities=13% Similarity=0.277 Sum_probs=21.8
Q ss_pred EEeccccccCCCeEEEEEEEeCCCCceeEeEEEE
Q psy16524 253 VTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCY 286 (453)
Q Consensus 253 asLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~ 286 (453)
++++.+.|.+|+.+.|++ .+.++...+.+-+.
T Consensus 23 i~~~~~~y~pg~~~~Vtl--~~~~~~~F~GFllq 54 (132)
T PF02014_consen 23 ISVSPSSYEPGQTYTVTL--SSSGSSSFRGFLLQ 54 (132)
T ss_dssp EEET-SSB-TTBEEEEEE--EETTTEEBSEEEEE
T ss_pred EEeCCCeEcCCCEEEEEE--ECCCCCceeEEEEE
Confidence 344499999999999999 66666676664444
No 39
>PF05753 TRAP_beta: Translocon-associated protein beta (TRAPB); InterPro: IPR008856 This family consists of several eukaryotic translocon-associated protein beta (TRAPB) or signal sequence receptor beta subunit (SSR-beta) proteins. The normal translocation of nascent polypeptides into the lumen of the endoplasmic reticulum (ER) is thought to be aided in part by a translocon-associated protein (TRAP) complex consisting of 4 protein subunits. The association of mature proteins with the ER and Golgi, or other intracellular locales, such as lysosomes, depends on the initial targeting of the nascent polypeptide to the ER membrane. A similar scenario must also exist for proteins destined for secretion [].; GO: 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=36.04 E-value=2.8e+02 Score=26.56 Aligned_cols=69 Identities=20% Similarity=0.330 Sum_probs=46.2
Q ss_pred EeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEE--EEEEEEcceEEEEEEeeeeccCCcCCCCCeEEEEEEEeec
Q psy16524 254 TLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQH--CEVTMVNSQFSRYVASLETREGCPVTPGAAFTKTFYLVPL 330 (453)
Q Consensus 254 sLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~--~~v~lf~g~yk~~Va~~E~~eG~pV~pgst~~k~~~L~Pl 330 (453)
++..+.-..|+.|.|+++|-|.-+.+...+++.=... .++.+-.|.-. +..+ .|+||++.+.+|.|+|.
T Consensus 28 ~il~~~~v~g~~v~V~~~iyN~G~~~A~dV~l~D~~fp~~~F~lvsG~~s---~~~~-----~i~pg~~vsh~~vv~p~ 98 (181)
T PF05753_consen 28 QILNKYLVEGEDVTVTYTIYNVGSSAAYDVKLTDDSFPPEDFELVSGSLS---ASWE-----RIPPGENVSHSYVVRPK 98 (181)
T ss_pred eeccccccCCcEEEEEEEEEECCCCeEEEEEEECCCCCccccEeccCceE---EEEE-----EECCCCeEEEEEEEeee
Confidence 3344455779999999999999999888766653111 11222244322 2223 58899999999999993
No 40
>KOG3063|consensus
Probab=35.44 E-value=5.1e+02 Score=26.62 Aligned_cols=97 Identities=23% Similarity=0.371 Sum_probs=52.0
Q ss_pred cceeeeceeEEEEEEEEEeccccCccccCcccchheeeeeeEEeeCCCCCCCCcHHHHHHhhccC----CCeeeeEeeCC
Q psy16524 34 ENEYLKGRKVFGQIITTYRYGREEDEVMGVKFSKEMIVDRGQIVPSTNEKPELTVIQEKLLKKLG----PNAYPFTFHFP 109 (453)
Q Consensus 34 d~~~l~~rkV~~ql~~tfRYGred~eVmgl~F~ke~~~~~~qi~P~~~~~~~lt~lQe~L~kklG----~~a~PF~f~lp 109 (453)
.|=|-.|..|-+.++++++=|+ -.|=-|++- |++=+....|-.. ...+.+.+-..|. +.| ..+|||-| +
T Consensus 39 ~~lf~dgEtv~G~V~l~lk~gk-kleH~Giki--efiGqIe~~~drg-n~~eF~~lv~eLa-~pGel~~~~~fpFeF--~ 111 (301)
T KOG3063|consen 39 HPLFYDGETVSGKVNLRLKDGK-KLEHQGIKI--EFIGQIEMYYDRG-NFHEFTSLVRELA-RPGELTQSQSFPFEF--P 111 (301)
T ss_pred eeeEecCCeeeeEEEEEEcCCc-ccccCceEE--EEEEEEEEEecCC-cHHHHHHHHHhhc-CCcceeecccCCccc--c
Confidence 3334445556666777776543 334445443 2333333333222 2223333322232 244 36788766 3
Q ss_pred CCCCceEEecCCCCCCCCcceeEEEEEEEEcCCC
Q psy16524 110 SGAPSSVTLQPGDEDTGKPLGVEHAIKTFVGDSI 143 (453)
Q Consensus 110 ~~~P~Sv~Lqp~~~~~G~p~gv~Y~Vka~iad~~ 143 (453)
+-- .|-..|.|+...++|-+|+.|..+.
T Consensus 112 ~ve------kpyEsY~G~NV~lrY~lkvTv~Rr~ 139 (301)
T KOG3063|consen 112 HVE------KPYESYIGKNVRLRYFLKVTVSRRL 139 (301)
T ss_pred ccc------cchhhhcCcceEEEEEEEEEEEech
Confidence 221 3556789999999999999985543
No 41
>PF12584 TRAPPC10: Trafficking protein particle complex subunit 10, TRAPPC10; InterPro: IPR022233 The trafficking protein particle complex TRAPP is a multi-protein complex needed in the early stages of the secretory pathway. To date, two kinds of TRAPP complexes have been studied, TRAPPI and TRAPP II. These complexes differ in subunit composition []. TRAPP I binds vesicles derived from the endoplasmic reticulum bringing them closer to the acceptor membrane. This entry represents a domain which forms part of the TRAPP complex for mediating vesicle docking and fusion in the Golgi apparatus. The fungal version is referred to as Trs130, and an alternative vertebrate alias is TMEM1 [, ].
Probab=34.27 E-value=2.3e+02 Score=25.73 Aligned_cols=64 Identities=14% Similarity=0.242 Sum_probs=38.0
Q ss_pred ccCCCeEEEEEEEeCCC----------CceeEeEEEEEEEEEEEEEEcceEEEEEEeeeeccCCcCCCCCeEEEEEEEee
Q psy16524 260 YYHGEKVAATIVVNNTS----------RKSVKNIKCYVVQHCEVTMVNSQFSRYVASLETREGCPVTPGAAFTKTFYLVP 329 (453)
Q Consensus 260 Y~pGE~I~V~v~I~N~S----------sk~VkkIKv~l~Q~~~v~lf~g~yk~~Va~~E~~eG~pV~pgst~~k~~~L~P 329 (453)
.+-||.|.+++.|.|.. +.........+.+..+.=+-.|+.+..+.. ..|+..+-.+.|.|
T Consensus 27 ~~vGqpi~~~l~I~~~~~W~~~~~~~~~~~~~~~~yei~a~~~~WlV~Grrrg~f~~---------~~~~~~~~~l~LIP 97 (147)
T PF12584_consen 27 CRVGQPIPAELRIKNSRKWSSEDQEESSNEDTEFMYEIVADSDNWLVSGRRRGVFSL---------SDGSEHEIPLTLIP 97 (147)
T ss_pred eEeCCeEEEEEEEEEcccCCccccccccCCCccEEEEEecCCCcEEEeccCcceEEe---------cCCCeEEEEEEEEe
Confidence 36899999999999951 122234455554444433336664434422 33556667888889
Q ss_pred ccC
Q psy16524 330 LAS 332 (453)
Q Consensus 330 ll~ 332 (453)
+.+
T Consensus 98 L~~ 100 (147)
T PF12584_consen 98 LRA 100 (147)
T ss_pred ccc
Confidence 643
No 42
>PF02883 Alpha_adaptinC2: Adaptin C-terminal domain; InterPro: IPR008152 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. GGAs (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) are a family of monomeric clathrin adaptor proteins that are conserved from yeasts to humans. GGAs regulate clathrin-mediated the transport of proteins (such as mannose 6-phosphate receptors) from the TGN to endosomes and lysosomes through interactions with TGN-sorting receptors, sometimes in conjunction with AP-1 [, ]. GGAs bind cargo, membranes, clathrin and accessory factors. GGA1, GGA2 and GGA3 all contain a domain homologous to the ear domain of gamma-adaptin. GGAs are composed of a single polypeptide with four domains: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The VHS domain is responsible for endocytosis and signal transduction, recognising transmembrane cargo through the ACLL sequence in the cytoplasmic domains of sorting receptors []. The GAT domain (also found in Tom1 proteins) interacts with ARF (ADP-ribosylation factor) to regulate membrane trafficking [], and with ubiquitin for receptor sorting []. The hinge region contains a clathrin box for recognition and binding to clathrin, similar to that found in AP adaptins. The GAE domain is similar to the AP gamma-adaptin ear domain, and is responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. This entry represents a beta-sandwich structural motif found in the appendage (ear) domain of alpha-, beta- and gamma-adaptin from AP clathrin adaptor complexes, and the GAE (gamma-adaptin ear) domain of GGA adaptor proteins. These domains have an immunoglobulin-like beta-sandwich fold containing 7 or 8 strands in 2 beta-sheets in a Greek key topology [, ]. Although these domains share a similar fold, there is little sequence identity between the alpha/beta-adaptins and gamma-adaptin/GAE. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 3MNM_B 3ZY7_B 1GYU_A 1GYW_B 2A7B_A 1GYV_A 2E9G_A 1E42_B 2G30_A 2IV9_B ....
Probab=33.51 E-value=3e+02 Score=23.32 Aligned_cols=75 Identities=11% Similarity=0.224 Sum_probs=49.8
Q ss_pred eeeecCceEEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEEcceEEEEEEeeeeccCCcCCCCCeE
Q psy16524 242 FTFSQGKINLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMVNSQFSRYVASLETREGCPVTPGAAF 321 (453)
Q Consensus 242 F~~ssGpl~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf~g~yk~~Va~~E~~eG~pV~pgst~ 321 (453)
.++.+.-|++.+...+ -.++..+.+.+...|.|+..+.++.+.+- ....++-.+... .+-.|+|+...
T Consensus 4 ~~ye~~~l~I~~~~~~--~~~~~~~~i~~~f~N~s~~~it~f~~q~a-------vpk~~~l~l~~~---s~~~i~p~~~i 71 (115)
T PF02883_consen 4 VLYEDNGLQIGFKSEK--SPNPNQGRIKLTFGNKSSQPITNFSFQAA-------VPKSFKLQLQPP---SSSTIPPGQQI 71 (115)
T ss_dssp EEEEETTEEEEEEEEE--CCETTEEEEEEEEEE-SSS-BEEEEEEEE-------EBTTSEEEEEES---S-SSB-TTTEE
T ss_pred EEEeCCCEEEEEEEEe--cCCCCEEEEEEEEEECCCCCcceEEEEEE-------eccccEEEEeCC---CCCeeCCCCeE
Confidence 4577788888888887 56788999999999999999998776621 111122222222 23468888888
Q ss_pred EEEEEEe
Q psy16524 322 TKTFYLV 328 (453)
Q Consensus 322 ~k~~~L~ 328 (453)
++.+.+.
T Consensus 72 ~Q~~~v~ 78 (115)
T PF02883_consen 72 TQVIKVE 78 (115)
T ss_dssp EEEEEEE
T ss_pred EEEEEEE
Confidence 8888774
No 43
>COG4326 Spo0M Sporulation control protein [General function prediction only]
Probab=32.63 E-value=82 Score=31.52 Aligned_cols=42 Identities=21% Similarity=0.445 Sum_probs=32.2
Q ss_pred cCceEEEEEeccccccCCCeEEEEEEEeCCCC-ceeEeEEEEE
Q psy16524 246 QGKINLEVTLDREIYYHGEKVAATIVVNNTSR-KSVKNIKCYV 287 (453)
Q Consensus 246 sGpl~LeasLdK~~Y~pGE~I~V~v~I~N~Ss-k~VkkIKv~l 287 (453)
=|.-++.--|.++.|+|||.+...|.|.-.-. ..|..|..+|
T Consensus 30 IGaAKVDt~L~~~~~~PG~~v~g~vhv~GG~~AQdI~~I~LkL 72 (270)
T COG4326 30 IGAAKVDTVLQQEVLYPGQSVKGIVHVYGGATAQDIDNIELKL 72 (270)
T ss_pred cchhhhhhhhhhccccCCceEEEEEEEecCchHhhhhhhhhhh
Confidence 35566777899999999999999999987643 5666665554
No 44
>KOG3865|consensus
Probab=32.37 E-value=5.1e+02 Score=27.64 Aligned_cols=59 Identities=27% Similarity=0.309 Sum_probs=40.9
Q ss_pred EecCCCCCCCCcceeEEEEEEEEcCCCcccCcccceeEEeEEEeeEEeeeeeeee-cccchhhhcccchhhh
Q psy16524 117 TLQPGDEDTGKPLGVEHAIKTFVGDSIDEKGHKRSSVALAIKKCYVVQHCEVTMV-NSQFSRYVASLETREV 187 (453)
Q Consensus 117 ~Lqp~~~~~G~p~gv~Y~Vka~iad~~~ek~~kr~sv~~~Irk~~~~q~~~~~~~-~~~~~~~~~~~~~~~~ 187 (453)
+|--.-.|+|.|+.|.-.| .++. .|.-| + | ||||.|+.+..++ .-||...||.+|+-++
T Consensus 200 sLDkEiYyHGE~isvnV~V----~NNs-nKtVK----k--I-K~~V~Q~adi~Lfs~aqy~~~VA~~E~~eG 259 (402)
T KOG3865|consen 200 SLDKEIYYHGEPISVNVHV----TNNS-NKTVK----K--I-KISVRQVADICLFSTAQYKKPVAMEETDEG 259 (402)
T ss_pred EecchheecCCceeEEEEE----ecCC-cceee----e--e-EEEeEeeceEEEEecccccceeeeeecccC
Confidence 3444456889999876554 3433 22222 1 3 6789999999999 6699999999997665
No 45
>PF05326 SVA: Seminal vesicle autoantigen (SVA); InterPro: IPR007990 This family consists of seminal vesicle autoantigen and prolactin-inducible (PIP) proteins. Seminal vesicle autoantigen (SVA) is specifically present in the seminal plasma of mice. This 19 kDa secretory glycoprotein suppresses the motility of spermatozoa by interacting with phospholipid. PIP has several known functions. In saliva, this protein plays a role in host defence by binding to microorganisms such as Streptococcus. PIP is an aspartyl proteinase and it acts as a factor capable of suppressing T-cell apoptosis through its interaction with CD4 [].; GO: 0005576 extracellular region; PDB: 3ES6_B.
Probab=29.88 E-value=95 Score=28.42 Aligned_cols=60 Identities=17% Similarity=0.306 Sum_probs=30.7
Q ss_pred ecCceEEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEE-cceEEEEEEe
Q psy16524 245 SQGKINLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMV-NSQFSRYVAS 306 (453)
Q Consensus 245 ssGpl~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf-~g~yk~~Va~ 306 (453)
+..+|.|+..+++.. .+||.+.|.+.|.|+=..-+. ||+.+.-...+-.+ +-.|+.+++.
T Consensus 30 ~~k~l~l~l~~~~~~-~~~eev~v~l~V~t~~~eCmv-Vk~yl~sn~~i~~~fny~YTaCLC~ 90 (124)
T PF05326_consen 30 SRKPLSLNLQVPQTA-KANEEVTVTLTVTTELRECMV-VKIYLESNPPIDGSFNYKYTACLCD 90 (124)
T ss_dssp -----EE-----SEE--SS--EEEEEEEEE--SS-EE-EEEEEEESS---SGGG-EEEEEE-S
T ss_pred cCccEEEEeecCCCC-CCCCEEEEEEEEEcchheeEE-EEEEeccCCCccccccceEEEEeCC
Confidence 567899999999887 899999999999998776665 77887777666654 6677766644
No 46
>PF12690 BsuPI: Intracellular proteinase inhibitor; InterPro: IPR020481 BsuPI is a intracellular proteinase inhibitor that directly regulates the major intracellular proteinase (ISP-1) activity in vivo. It inhibits ISP-1 in the early stages of sporulation and then may be inactivated by a membrane-bound proteinase [].; PDB: 3ISY_A.
Probab=29.56 E-value=1.3e+02 Score=25.03 Aligned_cols=30 Identities=23% Similarity=0.259 Sum_probs=21.4
Q ss_pred EEEEEEEeCCCCceeEeEEEEEEEEEEEEEE
Q psy16524 266 VAATIVVNNTSRKSVKNIKCYVVQHCEVTMV 296 (453)
Q Consensus 266 I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf 296 (453)
+.+.+.|.|+|++.|. +...=-|..|+.+.
T Consensus 2 v~~~l~v~N~s~~~v~-l~f~sgq~~D~~v~ 31 (82)
T PF12690_consen 2 VEFTLTVTNNSDEPVT-LQFPSGQRYDFVVK 31 (82)
T ss_dssp EEEEEEEEE-SSS-EE-EEESSS--EEEEEE
T ss_pred EEEEEEEEeCCCCeEE-EEeCCCCEEEEEEE
Confidence 6789999999999987 66666788887776
No 47
>PF07703 A2M_N_2: Alpha-2-macroglobulin family N-terminal region; InterPro: IPR011625 This is a domain of the alpha-2-macroglobulin family. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; PDB: 2QKI_D 3L3O_D 3NMS_A 2ICF_A 2A73_A 2ICE_D 2HR0_A 2A74_A 2XWJ_G 3OHX_A ....
Probab=28.87 E-value=67 Score=27.80 Aligned_cols=25 Identities=24% Similarity=0.417 Sum_probs=20.7
Q ss_pred EEEEeccccccCCCeEEEEEEEeCC
Q psy16524 251 LEVTLDREIYYHGEKVAATIVVNNT 275 (453)
Q Consensus 251 LeasLdK~~Y~pGE~I~V~v~I~N~ 275 (453)
|++.+||..|.+||++.+.+.-.-.
T Consensus 1 l~i~~~~~~~~~Ge~~~v~v~~~~~ 25 (136)
T PF07703_consen 1 LQISTDKDSYKPGETAKVTVQSPFP 25 (136)
T ss_dssp EEEEE-SSSB-TTSEEEEEEEEESC
T ss_pred CEEEcCCCCcCCCCEEEEEEEcCCC
Confidence 6789999999999999999988776
No 48
>PF04314 DUF461: Protein of unknown function (DUF461); InterPro: IPR007410 This entry represents a domain found in of proteins of unknown function, including DR1885 from Deinococcus radiodurans and CC3502 from Caulobacter crescentus (Caulobacter vibrioides), which share a potential metal binding motif H(M)X10MX21HXM. DR1885 was found to bind copper(I) through a histidine and three Mets in a cupredoxin-like fold []. The surface location of the copper-binding site as well as the type of coordination are well poised for metal transfer chemistry, suggesting that DR1885 might transfer copper, taking the role of Cox17 in bacteria (Cox17 being an accessory protein required for correct assembly of eukaryotic cyochrome c oxidase). ; PDB: 2K6W_A 2K6Z_A 2K6Y_A 2K70_A 1X9L_A 2JQA_A.
Probab=28.43 E-value=98 Score=26.80 Aligned_cols=58 Identities=12% Similarity=0.184 Sum_probs=34.3
Q ss_pred CCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEE-cceEEEEEEeeeeccCCcCCCCCeE
Q psy16524 263 GEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMV-NSQFSRYVASLETREGCPVTPGAAF 321 (453)
Q Consensus 263 GE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf-~g~yk~~Va~~E~~eG~pV~pgst~ 321 (453)
+....+-+.|.|+++.+++=+.++.-....+.|. ... ..-+.....-++.+|+||+++
T Consensus 13 ~~~~a~y~ti~N~g~~~~~L~~v~s~~a~~v~lh~~~~-~~g~~~m~~v~~i~ipa~~~v 71 (110)
T PF04314_consen 13 ANVTAAYFTITNNGDQDDRLVGVSSPAAARVELHETVM-EDGVMKMRPVDSIPIPAGSTV 71 (110)
T ss_dssp -SEEEEEEEEE-CSSSEEEEEEEE-TTCCEEEEEEECC-CCCEEEECCSS-EEEETT-EE
T ss_pred CccEEEEEEEEeCCCCCeEEEEEEcCCCceEEEEEEEc-cCCeEEEEECCCEEECCCCeE
Confidence 3578888999999999988767765555555554 222 223333444445678888775
No 49
>cd08544 Reeler Reeler, the N-terminal domain of reelin, F-spondin, and a variety of other proteins. This domain is found at the N-terminus of F-spondin, a protein attached to the extracellular matrix, which plays roles in neuronal development and vascular remodelling. The F-spondin reeler domain has been reported to bind heparin. The reeler domain is also found at the N-terminus of reelin, an extracellular glycoprotein involved in the development of the brain cortex, and in a variety of other eukaryotic proteins with different domain architectures, including the animal ferric-chelate reductase 1 or stromal cell-derived receptor 2, a member of the cytochrome B561 family, which reduces ferric iron before its transport from the endosome to the cytoplasm. Also included is the insect putative defense protein 1, which is expressed upon bacterial infection and appears to contain a single reeler domain.
Probab=28.39 E-value=1.2e+02 Score=26.85 Aligned_cols=37 Identities=14% Similarity=0.218 Sum_probs=25.7
Q ss_pred EEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEE
Q psy16524 251 LEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQ 289 (453)
Q Consensus 251 LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q 289 (453)
..++++...|.|||.+.|++.-.|. ..-+.+-+..+.
T Consensus 21 y~i~~~~~~y~pG~~~~Vtl~~~~~--~~F~GF~lqAr~ 57 (135)
T cd08544 21 YSITISGNSYVPGETYTVTLSGSSP--SPFRGFLLQARD 57 (135)
T ss_pred EEEEeCCCEECCCCEEEEEEECCCC--CceeEEEEEEEc
Confidence 3455666699999999999988776 455554444333
No 50
>KOG2717|consensus
Probab=27.82 E-value=6.9e+02 Score=25.73 Aligned_cols=42 Identities=14% Similarity=0.162 Sum_probs=29.2
Q ss_pred EEEEEeccccccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEE
Q psy16524 250 NLEVTLDREIYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCE 292 (453)
Q Consensus 250 ~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~ 292 (453)
-+.-.||.+-+.--+++.=.+.|. +|+..|+.|.+.|.+..+
T Consensus 180 lvtG~Ld~t~c~~t~PltGeltVe-~seaaI~Sie~qLvRVEt 221 (313)
T KOG2717|consen 180 LVTGKLDATQCSLTDPLTGELTVE-ASEAAITSIEIQLVRVET 221 (313)
T ss_pred EEEeeecceeeEecCCccceEEEE-eeccceeEEEEEEEEEEE
Confidence 344566666666666666555555 467899999999998765
No 51
>PF08626 TRAPPC9-Trs120: Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit; InterPro: IPR013935 The trafficking protein particle complex TRAPP is a multi-protein complex needed in the early stages of the secretory pathway. To date, two kinds of TRAPP complexes have been studied, TRAPPI and TRAPP II. These complexes differ in subunit composition []. TRAPP I binds vesicles derived from the endoplasmic reticulum bringing them closer to the acceptor membrane. Trs120 is a subunit specific to the TRAPP II complex [] along with Trs65p and Trs130p(TRAPPC10). It is suggested that Trs120p is required for the stability of the Trs130p subunit, suggesting that these two proteins might interact in some way []. It is likely that there is a complex function for TRAPP II in multiple pathways [].
Probab=25.19 E-value=3.3e+02 Score=33.23 Aligned_cols=29 Identities=31% Similarity=0.298 Sum_probs=27.1
Q ss_pred ccCCCeEEEEEEEeCCCCceeEeEEEEEE
Q psy16524 260 YYHGEKVAATIVVNNTSRKSVKNIKCYVV 288 (453)
Q Consensus 260 Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~ 288 (453)
.+.||.-.+++++.|.|+.+|..+.+.+.
T Consensus 795 lleGE~~~~~ItL~N~S~~pvd~l~~sf~ 823 (1185)
T PF08626_consen 795 LLEGEKQTFTITLRNTSSVPVDFLSFSFQ 823 (1185)
T ss_pred EECCcEEEEEEEEEECCccccceEEEEEE
Confidence 48999999999999999999999999976
No 52
>TIGR03358 VI_chp_5 type VI secretion protein, VC_A0107 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PubMed:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al.
Probab=23.41 E-value=63 Score=30.62 Aligned_cols=23 Identities=22% Similarity=0.483 Sum_probs=19.1
Q ss_pred eEEEEEEEEEEEEcCCCcceeEEeeEEee
Q psy16524 371 IVISYSLRVKLSCGTLGGELQTDVPFKLM 399 (453)
Q Consensus 371 I~VSY~VKVkL~vsg~gsdv~veLPf~L~ 399 (453)
|.|.|.+.. +|..-.+||||+++
T Consensus 11 V~I~Y~~et------gga~~~vELPf~~~ 33 (159)
T TIGR03358 11 VQITYDVET------GGAEEKVELPLVVG 33 (159)
T ss_pred eeEEEEccC------CCceeeeecCeEEE
Confidence 888898765 56788999999976
No 53
>PF06299 DUF1045: Protein of unknown function (DUF1045); InterPro: IPR009389 This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown.
Probab=23.06 E-value=73 Score=30.18 Aligned_cols=33 Identities=15% Similarity=0.265 Sum_probs=28.2
Q ss_pred CCCCcHHHHHHhhccCC----CeeeeEeeCCCCCCce
Q psy16524 83 KPELTVIQEKLLKKLGP----NAYPFTFHFPSGAPSS 115 (453)
Q Consensus 83 ~~~lt~lQe~L~kklG~----~a~PF~f~lp~~~P~S 115 (453)
+..||+-|+++|.+-|- ..|=|+++|+..+|..
T Consensus 84 ~~~Ls~~Q~~~L~rWGYPYV~deFRFHmTLTg~l~~~ 120 (160)
T PF06299_consen 84 PAGLSPRQRANLERWGYPYVMDEFRFHMTLTGRLDPA 120 (160)
T ss_pred cccCCHHHHHHHHHhCCCceeCcCEeeEEeCCCCCHH
Confidence 46799999999999996 7889999998877643
No 54
>KOG2540|consensus
Probab=23.02 E-value=2.5e+02 Score=28.38 Aligned_cols=69 Identities=26% Similarity=0.393 Sum_probs=45.2
Q ss_pred cccc-cCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEE-cceEEEEEEeeeeccCCcCCCCCeEE--EEEEEeecc
Q psy16524 257 REIY-YHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMV-NSQFSRYVASLETREGCPVTPGAAFT--KTFYLVPLA 331 (453)
Q Consensus 257 K~~Y-~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf-~g~yk~~Va~~E~~eG~pV~pgst~~--k~~~L~Pll 331 (453)
+++| .|||+.-......|-|.++|.+|.-. +|+-+ .|+|-+.++.--++| ..+.||.+.. --|.|-|-.
T Consensus 155 rEiyV~PGEtALaFYta~N~sdkpIiGvstY-----ni~P~~Aa~YFnKiqCFCFEE-Q~L~pgE~vDmPVFFyIDPef 227 (269)
T KOG2540|consen 155 REIYVLPGETALAFYTAENPSDKPIIGVSTY-----NITPGQAAVYFNKIQCFCFEE-QKLNPGEQVDMPVFFYIDPEF 227 (269)
T ss_pred eEEEEcCCcceeeeEeccCCCCCCceeeEee-----ccCccHhhhheeceeEEeehh-hccCCCcccCcceEEEeCccc
Confidence 4566 79999999999999999999876432 34446 667755444433333 2467777642 344666643
No 55
>PF05591 DUF770: Protein of unknown function (DUF770); InterPro: IPR008312 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, these proteins are encoded in type VI secretion loci (including the SCI genomic island in Salmonella enterica and the imp locus in Rhizobium leguminosarum) implicated in pathogenicity and protein secretion [, , [].
Probab=22.79 E-value=59 Score=30.61 Aligned_cols=23 Identities=26% Similarity=0.694 Sum_probs=19.2
Q ss_pred eEEEEEEEEEEEEcCCCcceeEEeeEEee
Q psy16524 371 IVISYSLRVKLSCGTLGGELQTDVPFKLM 399 (453)
Q Consensus 371 I~VSY~VKVkL~vsg~gsdv~veLPf~L~ 399 (453)
|.+.|.+.+ +|..-.+||||.++
T Consensus 10 V~I~Y~~~~------gga~~~~ELPf~~~ 32 (157)
T PF05591_consen 10 VNITYDVET------GGAQEKVELPFKML 32 (157)
T ss_pred eEEEEecCC------CCchhceecCeEEE
Confidence 888898775 57889999999966
No 56
>PTZ00128 cytochrome c oxidase assembly protein-like; Provisional
Probab=21.41 E-value=3.4e+02 Score=27.38 Aligned_cols=66 Identities=18% Similarity=0.216 Sum_probs=39.8
Q ss_pred cccCCCeEEEEEEEeCCCCceeEeEEEEEEEEEEEEEE-cceEEEEEEeeeeccCCcCCCCCeE--EEEEEEeec
Q psy16524 259 IYYHGEKVAATIVVNNTSRKSVKNIKCYVVQHCEVTMV-NSQFSRYVASLETREGCPVTPGAAF--TKTFYLVPL 330 (453)
Q Consensus 259 ~Y~pGE~I~V~v~I~N~Ssk~VkkIKv~l~Q~~~v~lf-~g~yk~~Va~~E~~eG~pV~pgst~--~k~~~L~Pl 330 (453)
-..|||+..+...+.|.|.++|..+-+. - |.=. -|.|=+.+..--+. ..++.||.+. --.|.|-|-
T Consensus 133 ~V~pGE~~lv~Y~a~N~sd~~i~G~A~y--n---V~P~~Ag~YFnKieCFCF~-eQ~L~pgE~~~MPV~F~IDP~ 201 (232)
T PTZ00128 133 EVLPGETALAFYRAKNRSDKPVIGVATY--H---IAPPEAGLYFNKIQCFCFE-EQRLNPHEEVDMPVFFYIDPD 201 (232)
T ss_pred EEcCCCeEEEEEEEECCCCCcEEEEEec--c---cCHHHHhhhccceeeeccc-ccccCCCCeEecCEEEEECCC
Confidence 3489999999999999999999874432 1 1112 34442222221122 1367888874 345667663
No 57
>PF04314 DUF461: Protein of unknown function (DUF461); InterPro: IPR007410 This entry represents a domain found in of proteins of unknown function, including DR1885 from Deinococcus radiodurans and CC3502 from Caulobacter crescentus (Caulobacter vibrioides), which share a potential metal binding motif H(M)X10MX21HXM. DR1885 was found to bind copper(I) through a histidine and three Mets in a cupredoxin-like fold []. The surface location of the copper-binding site as well as the type of coordination are well poised for metal transfer chemistry, suggesting that DR1885 might transfer copper, taking the role of Cox17 in bacteria (Cox17 being an accessory protein required for correct assembly of eukaryotic cyochrome c oxidase). ; PDB: 2K6W_A 2K6Z_A 2K6Y_A 2K70_A 1X9L_A 2JQA_A.
Probab=20.88 E-value=1.3e+02 Score=26.05 Aligned_cols=41 Identities=15% Similarity=0.211 Sum_probs=31.0
Q ss_pred eeeeecCceEEEEEeccccccCCCeEEEEEEEeCCCCceeE
Q psy16524 241 GFTFSQGKINLEVTLDREIYYHGEKVAATIVVNNTSRKSVK 281 (453)
Q Consensus 241 ~F~~ssGpl~LeasLdK~~Y~pGE~I~V~v~I~N~Ssk~Vk 281 (453)
..-|+.|-.||-+.=.+.-..+||.+++++...|....+|+
T Consensus 70 ~v~l~pgg~HlmL~g~~~~l~~G~~v~ltL~f~~gg~v~v~ 110 (110)
T PF04314_consen 70 TVELKPGGYHLMLMGLKRPLKPGDTVPLTLTFEDGGKVTVE 110 (110)
T ss_dssp EEEE-CCCCEEEEECESS-B-TTEEEEEEEEETTTEEEEE-
T ss_pred eEEecCCCEEEEEeCCcccCCCCCEEEEEEEECCCCEEEeC
Confidence 44578888998887778889999999999999998876653
No 58
>PF06988 NifT: NifT/FixU protein; InterPro: IPR009727 This family consists of several NifT and FixU bacterial proteins. The function of NifT is unknown although it is thought that the protein may be involved in biosynthesis of the FeMo cofactor of nitrogenase although perturbation of nifT expression in Klebsiella pneumoniae has only a limited effect on nitrogen fixation [].; GO: 0009399 nitrogen fixation; PDB: 2JN4_A.
Probab=20.87 E-value=60 Score=26.49 Aligned_cols=16 Identities=25% Similarity=0.513 Sum_probs=11.5
Q ss_pred CCceEEEEecceeeee
Q psy16524 4 FPGKVTVYLGKRDFID 19 (453)
Q Consensus 4 pn~klt~YlgkRd~vd 19 (453)
.+|.|++|+.|+|+=.
T Consensus 9 ~~G~ls~YVpKKDLEE 24 (64)
T PF06988_consen 9 GAGGLSAYVPKKDLEE 24 (64)
T ss_dssp SS--EEEEETTTTEEE
T ss_pred CCcCEEEEEeCCcccc
Confidence 5689999999999743
Done!