Query psy4382
Match_columns 258
No_of_seqs 122 out of 194
Neff 4.6
Searched_HMMs 46136
Date Sat Aug 17 00:06:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4382.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4382hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03896 TRAP_alpha: Transloco 100.0 1.2E-58 2.6E-63 426.4 19.7 188 10-248 92-281 (285)
2 KOG1631|consensus 100.0 1.7E-54 3.6E-59 386.5 13.3 186 13-248 72-259 (261)
3 KOG1631|consensus 98.5 7.1E-08 1.5E-12 87.6 3.0 168 64-248 72-254 (261)
4 PF03896 TRAP_alpha: Transloco 97.4 0.001 2.2E-08 62.4 9.6 111 61-181 92-213 (285)
5 PF10633 NPCBM_assoc: NPCBM-as 97.2 0.0022 4.7E-08 47.9 7.8 76 14-95 2-77 (78)
6 PF05753 TRAP_beta: Translocon 95.0 1.2 2.5E-05 39.3 14.2 84 10-99 31-116 (181)
7 PF06030 DUF916: Bacterial pro 92.2 2.4 5.2E-05 34.9 10.4 82 4-85 14-111 (121)
8 PF07705 CARDB: CARDB; InterP 91.1 2 4.4E-05 31.8 8.2 72 11-95 13-85 (101)
9 PF04442 CtaG_Cox11: Cytochrom 89.8 1.3 2.8E-05 38.4 6.9 73 8-82 58-131 (152)
10 PF00927 Transglut_C: Transglu 89.5 2.8 6.1E-05 32.7 8.2 66 12-80 10-78 (107)
11 PF12690 BsuPI: Intracellular 88.8 2.8 6E-05 32.3 7.5 70 19-89 2-80 (82)
12 COG3175 COX11 Cytochrome oxida 88.8 2 4.3E-05 38.6 7.4 95 9-126 85-181 (195)
13 PRK05089 cytochrome C oxidase 88.8 1.4 3E-05 39.4 6.5 90 8-125 85-175 (188)
14 PF07760 DUF1616: Protein of u 84.3 13 0.00027 34.6 10.6 88 6-98 180-271 (287)
15 PTZ00128 cytochrome c oxidase 83.3 4.2 9E-05 37.6 6.9 94 8-124 129-223 (232)
16 PF14874 PapD-like: Flagellar- 82.1 20 0.00044 27.3 9.8 72 12-93 15-86 (102)
17 PF07610 DUF1573: Protein of u 82.0 6.1 0.00013 26.9 5.8 43 23-76 2-45 (45)
18 PF11611 DUF4352: Domain of un 78.6 8.2 0.00018 30.0 6.3 65 14-79 33-102 (123)
19 PF05506 DUF756: Domain of unk 78.5 15 0.00033 27.9 7.6 58 20-93 21-78 (89)
20 PF13473 Cupredoxin_1: Cupredo 78.1 9.7 0.00021 29.6 6.5 45 10-74 36-80 (104)
21 PF06159 DUF974: Protein of un 76.1 21 0.00046 32.7 9.1 84 12-98 9-94 (249)
22 PF09478 CBM49: Carbohydrate b 75.9 14 0.00031 27.8 6.7 55 19-75 19-78 (80)
23 PF00630 Filamin: Filamin/ABP2 69.4 23 0.00051 26.5 6.6 72 13-93 17-90 (101)
24 COG1361 S-layer domain [Cell e 69.3 43 0.00093 33.0 10.1 84 10-99 160-247 (500)
25 KOG3317|consensus 68.4 75 0.0016 28.5 10.3 83 13-100 38-121 (188)
26 PF11906 DUF3426: Protein of u 66.8 47 0.001 27.2 8.4 63 15-77 66-135 (149)
27 PF05568 ASFV_J13L: African sw 65.5 4.7 0.0001 35.3 2.2 31 172-202 30-61 (189)
28 smart00557 IG_FLMN Filamin-typ 65.2 46 0.001 25.3 7.6 52 14-80 15-66 (93)
29 COG1470 Predicted membrane pro 64.6 1.5E+02 0.0033 30.4 12.8 81 7-93 387-467 (513)
30 PF04314 DUF461: Protein of un 61.8 42 0.00092 26.7 7.0 59 14-72 11-73 (110)
31 PF09624 DUF2393: Protein of u 57.9 73 0.0016 26.3 8.1 66 13-78 58-133 (149)
32 PLN02171 endoglucanase 54.1 53 0.0011 34.4 7.9 72 17-95 553-627 (629)
33 COG1470 Predicted membrane pro 54.1 1.2E+02 0.0026 31.2 10.0 102 9-116 276-386 (513)
34 PF07919 Gryzun: Gryzun, putat 51.9 1.2E+02 0.0027 29.8 9.8 69 11-80 21-105 (554)
35 PF06280 DUF1034: Fn3-like dom 51.2 1.2E+02 0.0025 23.8 12.7 67 16-82 7-84 (112)
36 PF14016 DUF4232: Protein of u 46.3 1.3E+02 0.0028 24.3 7.6 68 14-84 16-88 (131)
37 PF04744 Monooxygenase_B: Mono 42.9 47 0.001 32.9 5.2 63 14-76 260-333 (381)
38 TIGR03079 CH4_NH3mon_ox_B meth 42.5 47 0.001 33.0 5.1 61 14-76 279-352 (399)
39 PF11044 TMEMspv1-c74-12: Plec 41.4 18 0.0004 25.7 1.6 22 170-191 7-28 (49)
40 PF12742 Gryzun-like: Gryzun, 40.3 35 0.00076 25.2 3.0 21 60-80 26-46 (57)
41 COG5246 PRP11 Splicing factor 39.0 35 0.00077 31.0 3.4 62 74-135 123-190 (222)
42 COG2847 Copper(I)-binding prot 36.9 1.1E+02 0.0025 26.5 6.1 61 11-72 35-100 (151)
43 PF14851 FAM176: FAM176 family 36.4 51 0.0011 28.7 3.9 25 167-191 18-42 (153)
44 PF07919 Gryzun: Gryzun, putat 35.6 3.6E+02 0.0079 26.5 10.2 80 13-97 186-283 (554)
45 PRK05461 apaG CO2+/MG2+ efflux 35.4 1.5E+02 0.0033 24.8 6.5 54 20-75 32-85 (127)
46 PF13598 DUF4139: Domain of un 33.6 2.1E+02 0.0046 26.2 7.8 58 18-78 243-313 (317)
47 PF15179 Myc_target_1: Myc tar 32.3 36 0.00078 30.8 2.4 43 152-194 2-47 (197)
48 PF02883 Alpha_adaptinC2: Adap 31.0 2.5E+02 0.0054 21.7 9.6 77 15-99 22-102 (115)
49 COG4743 Predicted membrane pro 30.3 2.5E+02 0.0053 26.9 7.5 37 10-46 217-257 (316)
50 PF08626 TRAPPC9-Trs120: Trans 30.0 1.9E+02 0.0042 32.2 7.9 80 7-95 789-895 (1185)
51 PF10622 Ehbp: Energy-converti 28.8 13 0.00027 29.0 -0.9 10 219-228 39-48 (78)
52 PRK10144 formate-dependent nit 28.6 35 0.00075 28.8 1.6 57 117-176 41-107 (126)
53 PF04379 DUF525: Protein of un 28.6 2.5E+02 0.0054 22.0 6.3 55 20-76 15-69 (90)
54 smart00809 Alpha_adaptinC2 Ada 28.1 2.7E+02 0.0058 21.0 10.3 75 16-99 17-91 (104)
55 PF05283 MGC-24: Multi-glycosy 27.8 57 0.0012 29.2 2.8 30 163-192 154-184 (186)
56 PF05545 FixQ: Cbb3-type cytoc 27.1 64 0.0014 22.2 2.5 11 179-189 20-30 (49)
57 PF06679 DUF1180: Protein of u 26.1 1.2E+02 0.0027 26.5 4.6 21 173-193 98-118 (163)
58 PRK11875 psbT photosystem II r 25.7 84 0.0018 20.6 2.6 18 172-189 4-21 (31)
59 PF02221 E1_DerP2_DerF2: ML do 25.0 3.4E+02 0.0073 21.2 8.7 83 11-93 26-117 (134)
60 PHA03105 EEV glycoprotein; Pro 24.4 91 0.002 27.8 3.4 22 167-188 1-23 (188)
61 PF14524 Wzt_C: Wzt C-terminal 24.1 3.4E+02 0.0074 20.9 9.4 81 7-93 25-107 (142)
62 PF14962 AIF-MLS: Mitochondria 23.9 26 0.00056 31.3 0.0 30 167-196 42-71 (180)
63 CHL00031 psbT photosystem II p 23.2 94 0.002 20.7 2.5 18 172-189 4-21 (33)
64 PF00287 Na_K-ATPase: Sodium / 23.1 65 0.0014 30.4 2.5 23 171-193 45-67 (289)
65 PF10883 DUF2681: Protein of u 23.0 59 0.0013 25.8 1.8 23 171-193 2-24 (87)
66 cd00912 ML The ML (MD-2-relate 22.9 3.9E+02 0.0085 21.2 9.1 84 12-95 25-114 (127)
67 PF10342 GPI-anchored: Ser-Thr 22.9 2.7E+02 0.006 20.3 5.5 41 7-47 3-43 (93)
68 COG4454 Uncharacterized copper 22.5 90 0.002 27.4 3.0 31 3-33 108-138 (158)
69 PF01345 DUF11: Domain of unkn 21.3 2.9E+02 0.0063 19.9 5.2 24 11-34 35-58 (76)
70 PF06522 B12D: NADH-ubiquinone 21.2 1.1E+02 0.0024 22.9 3.0 27 166-192 2-28 (73)
71 TIGR02830 spore_III_AG stage I 21.2 1.4E+02 0.003 26.7 4.0 24 171-194 2-25 (186)
72 PF09451 ATG27: Autophagy-rela 20.6 92 0.002 28.7 2.9 26 168-193 199-224 (268)
73 TIGR03147 cyt_nit_nrfF cytochr 20.5 58 0.0012 27.5 1.4 57 117-176 41-107 (126)
74 PF02468 PsbN: Photosystem II 20.3 1.3E+02 0.0029 21.0 2.9 24 170-193 5-28 (43)
75 KOG3620|consensus 20.2 1.1E+02 0.0023 35.0 3.7 55 23-81 871-925 (1626)
76 TIGR01451 B_ant_repeat conserv 20.2 2.6E+02 0.0057 19.4 4.5 26 11-36 6-31 (53)
77 PF10215 Ost4: Oligosaccaryltr 20.1 1.2E+02 0.0026 20.2 2.6 20 176-195 12-31 (35)
No 1
>PF03896 TRAP_alpha: Translocon-associated protein (TRAP), alpha subunit; InterPro: IPR005595 The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane [].; GO: 0005783 endoplasmic reticulum
Probab=100.00 E-value=1.2e-58 Score=426.38 Aligned_cols=188 Identities=49% Similarity=0.820 Sum_probs=174.1
Q ss_pred ceeecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEEEEeeCcccCCcceeE
Q psy4382 10 NMDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAEAVAGRPFGL 89 (258)
Q Consensus 10 ~~~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~~~~~p~~L 89 (258)
..+||||+++++||+|+|+|+.+++|..|+||||+|+||+++|||||+++|++.|+||+++||+|+|.|++.|+||+|+|
T Consensus 92 ~~~l~aG~~~~~LvgftN~g~~~~~V~~i~aSl~~p~d~~~~iqNfTa~~y~~~V~pg~~aT~~YsF~~~~~l~pr~f~L 171 (285)
T PF03896_consen 92 TKKLPAGEPVKFLVGFTNKGSEPFTVESIEASLRYPQDYSYYIQNFTAVRYNREVPPGEEATFPYSFTPSEELAPRPFGL 171 (285)
T ss_pred cccccCCCeEEEEEEEEeCCCCCEEEEEEeeeecCccccceEEEeecccccCcccCCCCeEEEEEEEecchhcCCcceEE
Confidence 68899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEeecCCceeEEEEecceEEEEeecccccccccccCCCCcccccceecccCCceeeeeeeeeeEEEEecCCCcCce
Q psy4382 90 SVNLQYRDEHNNFFYEGIYNETVNIITLGYSFVPAEAVAGRPFGLSVNLQYRDEHNNFFYEGIYNETVNIIEIDEGLDGE 169 (258)
Q Consensus 90 ~l~l~Y~~~~~~~~~~~~~n~~v~~~t~~~~~~p~e~~~g~p~g~~i~~~~~d~~g~~y~~~vfN~TVtVvE~~~sfD~q 169 (258)
+|+++|+|.+ |+.|+.++||+||+|||++++||+|
T Consensus 172 ~i~l~y~d~~---------------------------------------------g~~y~~~~fN~TV~IvE~~~~~D~e 206 (285)
T PF03896_consen 172 VINLIYEDSD---------------------------------------------GNQYQVTVFNGTVTIVEPESGFDPE 206 (285)
T ss_pred EEEEEEEeCC---------------------------------------------CCEEEEEEecceEEEeecCCCcChh
Confidence 9999999887 8899999999999999999999999
Q ss_pred eehhHHHHHHHHHHHHHHhhhhhhhccccccCCCCCCcceeeecCCCCCCCCCCccChhhhhhcccCCC--CCCCCCCCc
Q psy4382 170 TFFLYVFLGACVVLLLVIGQHFLYSVGKKRVGTAQSKKQTVETGTKNSKDIDYDWIPKESLNSLKNLTN--SPKSPSVHK 247 (258)
Q Consensus 170 ~iFLYlfL~a~~gll~y~~y~~~~~~~kK~~~~~~~~~~~Ve~gt~~~~~yD~eWIP~~hL~~~~k~~~--sP~~~~~~~ 247 (258)
+||||+||+|+++|++|++|+++.+..|| |+ +++||+||++.++||+||||+|||++++|.++ ||||||+||
T Consensus 207 ~iFLY~~l~a~~~l~l~~~~~~l~~~~kk-r~-----~~~VE~GT~~~~~~D~eWIp~~~l~~~~k~spk~SPr~r~~~~ 280 (285)
T PF03896_consen 207 TIFLYLFLAALGVLGLYFVYQFLPSSKKK-RK-----AKKVETGTSSTNDVDEEWIPKEHLNRPNKKSPKQSPRKRKQKR 280 (285)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHhcccc-cc-----CCcccCCCCCCCCCCcccCCHHHhhhccCCCCCCChhhhhccc
Confidence 99999999999999999999987644332 22 34799999988899999999999999866665 999999887
Q ss_pred c
Q psy4382 248 I 248 (258)
Q Consensus 248 ~ 248 (258)
-
T Consensus 281 ~ 281 (285)
T PF03896_consen 281 S 281 (285)
T ss_pred c
Confidence 3
No 2
>KOG1631|consensus
Probab=100.00 E-value=1.7e-54 Score=386.47 Aligned_cols=186 Identities=44% Similarity=0.793 Sum_probs=174.0
Q ss_pred ecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEEEEeeCcccCCcceeEEEE
Q psy4382 13 LPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAEAVAGRPFGLSVN 92 (258)
Q Consensus 13 l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~~~~~p~~L~l~ 92 (258)
+|+|+++++||||+|+|+++|.|.++++|||+|+||+++|||||+..||+.|+|++|+||+|.|.|++.|+||||||+++
T Consensus 72 ~pagk~vkfLiGftNkG~edfvV~~~eaSfr~P~D~~~~iQNft~~~~N~~Vpp~~qaT~~Y~F~~se~~~grpFgLv~~ 151 (261)
T KOG1631|consen 72 FPAGKPVKFLIGFTNKGEEDFVVEYAEASFRYPTDHSYHIQNFTALEYNRSVPPSEQATLPYGFAVSETFAGRPFGLVGN 151 (261)
T ss_pred CCCCCceEEEEEeccCCceeEEEEEEeeeeecCccHHHHHhhhhhhhccccCCCcceeeeeeeeeehhhcCCCccceEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeecCCceeEEEEecceEEEEeecccccccccccCCCCcccccceecccCCceeeeeeeeeeEEEEecCCCcCceeeh
Q psy4382 93 LQYRDEHNNFFYEGIYNETVNIITLGYSFVPAEAVAGRPFGLSVNLQYRDEHNNFFYEGIYNETVNIIEIDEGLDGETFF 172 (258)
Q Consensus 93 l~Y~~~~~~~~~~~~~n~~v~~~t~~~~~~p~e~~~g~p~g~~i~~~~~d~~g~~y~~~vfN~TVtVvE~~~sfD~q~iF 172 (258)
+.|+|.+ |+.|+.++||+||+|+|.+.+||+|++|
T Consensus 152 i~Y~D~d---------------------------------------------G~~yq~~vyN~TI~VvE~~~gl~GETvF 186 (261)
T KOG1631|consen 152 IIYQDAD---------------------------------------------GNVYQSAVYNQTIEVVEDDSGLSGETVF 186 (261)
T ss_pred EEEecCC---------------------------------------------CCchhhhhccceEEEEecCCCcccchhH
Confidence 9888777 8999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHhhhhhhhccccccCCCCCCcceeeecCCCCCCCCCCccChhhhhhcccCCC--CCCCCCCCcc
Q psy4382 173 LYVFLGACVVLLLVIGQHFLYSVGKKRVGTAQSKKQTVETGTKNSKDIDYDWIPKESLNSLKNLTN--SPKSPSVHKI 248 (258)
Q Consensus 173 LYlfL~a~~gll~y~~y~~~~~~~kK~~~~~~~~~~~Ve~gt~~~~~yD~eWIP~~hL~~~~k~~~--sP~~~~~~~~ 248 (258)
||++|+|+..++++++++++.+..||+++ +++||+||++.++.|.||||+++|++.+|+|+ |||||++||-
T Consensus 187 L~~lligl~llllv~~~q~L~~~sKk~~~-----~~kVE~GTas~~~vd~eWip~~tl~q~~k~sp~~spkkrK~Kks 259 (261)
T KOG1631|consen 187 LYILLIGLSLLLLVLSQQFLSKLSKKTKK-----RRKVEVGTASKDAVDDEWIPGTTLKQKSKRSPAVSPKKRKSKKS 259 (261)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhcccc-----cceEeecccCcccccccccccHhHHhhccCCcccChhhhhhhcc
Confidence 99999999999999999998755443332 45899999998899999999999999999887 9999999983
No 3
>KOG1631|consensus
Probab=98.49 E-value=7.1e-08 Score=87.64 Aligned_cols=168 Identities=23% Similarity=0.259 Sum_probs=106.5
Q ss_pred ecCCceeEEEEEEeeCcccCCcceeE-EEEEEEeecCC-----ceeEEEEecceEE---EEeecccccccccccCCCCcc
Q psy4382 64 VKPGHEATLGYSFVPAEAVAGRPFGL-SVNLQYRDEHN-----NFFYEGIYNETVN---IITLGYSFVPAEAVAGRPFGL 134 (258)
Q Consensus 64 V~pg~~at~~Y~F~p~~~~~~~p~~L-~l~l~Y~~~~~-----~~~~~~~~n~~v~---~~t~~~~~~p~e~~~g~p~g~ 134 (258)
+|.|+...|---|.-.- ...|.+ .+..++|.-.+ ++|...+||..|. .+||.|.|+|+|.|+||||||
T Consensus 72 ~pagk~vkfLiGftNkG---~edfvV~~~eaSfr~P~D~~~~iQNft~~~~N~~Vpp~~qaT~~Y~F~~se~~~grpFgL 148 (261)
T KOG1631|consen 72 FPAGKPVKFLIGFTNKG---EEDFVVEYAEASFRYPTDHSYHIQNFTALEYNRSVPPSEQATLPYGFAVSETFAGRPFGL 148 (261)
T ss_pred CCCCCceEEEEEeccCC---ceeEEEEEEeeeeecCccHHHHHhhhhhhhccccCCCcceeeeeeeeeehhhcCCCccce
Confidence 77777777766664331 111111 11123332221 3356789998887 899999999999999999999
Q ss_pred cccceecccCCceeeeeeeeeeE--EEEecCCCcCceeehhHH-HHHHHHHHHHHHhhhhhh-hccccccCCCCCCccee
Q psy4382 135 SVNLQYRDEHNNFFYEGIYNETV--NIIEIDEGLDGETFFLYV-FLGACVVLLLVIGQHFLY-SVGKKRVGTAQSKKQTV 210 (258)
Q Consensus 135 ~i~~~~~d~~g~~y~~~vfN~TV--tVvE~~~sfD~q~iFLYl-fL~a~~gll~y~~y~~~~-~~~kK~~~~~~~~~~~V 210 (258)
+++++|+ .-...+|++.| ..+|+-+ |...+-... ||..++++++.+..-... ...+.. + +.+++
T Consensus 149 v~~i~Y~-----D~dG~~yq~~vyN~TI~VvE--~~~gl~GETvFL~~lligl~llllv~~~q~L~~~s--K---k~~~~ 216 (261)
T KOG1631|consen 149 VGNIIYQ-----DADGNVYQSAVYNQTIEVVE--DDSGLSGETVFLYILLIGLSLLLLVLSQQFLSKLS--K---KTKKR 216 (261)
T ss_pred EEEEEEe-----cCCCCchhhhhccceEEEEe--cCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHhh--h---ccccc
Confidence 9999997 78899999999 6888888 777777776 565666665554433322 333322 2 24444
Q ss_pred eecCCCCCCCCCCccChhhhhh--cccCCCCCCCCCCCcc
Q psy4382 211 ETGTKNSKDIDYDWIPKESLNS--LKNLTNSPKSPSVHKI 248 (258)
Q Consensus 211 e~gt~~~~~yD~eWIP~~hL~~--~~k~~~sP~~~~~~~~ 248 (258)
..=-.|. -..+=+-.+.|-+ +++.+++|-+++-||.
T Consensus 217 ~kVE~GT--as~~~vd~eWip~~tl~q~~k~sp~~spkkr 254 (261)
T KOG1631|consen 217 RKVEVGT--ASKDAVDDEWIPGTTLKQKSKRSPAVSPKKR 254 (261)
T ss_pred ceEeecc--cCcccccccccccHhHHhhccCCcccChhhh
Confidence 4434453 2333445555544 4666677777766653
No 4
>PF03896 TRAP_alpha: Translocon-associated protein (TRAP), alpha subunit; InterPro: IPR005595 The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane [].; GO: 0005783 endoplasmic reticulum
Probab=97.40 E-value=0.001 Score=62.37 Aligned_cols=111 Identities=27% Similarity=0.343 Sum_probs=79.8
Q ss_pred ceeecCCceeEEEEEEeeCcccCCcceeEEEE-EEEeecCC-----ceeEEEEecceEE---EEeecccccccccccCCC
Q psy4382 61 NRIVKPGHEATLGYSFVPAEAVAGRPFGLSVN-LQYRDEHN-----NFFYEGIYNETVN---IITLGYSFVPAEAVAGRP 131 (258)
Q Consensus 61 ~~~V~pg~~at~~Y~F~p~~~~~~~p~~L~l~-l~Y~~~~~-----~~~~~~~~n~~v~---~~t~~~~~~p~e~~~g~p 131 (258)
...+++|+...+-=.|.-.. ..|+.+..- ..++.-.+ ++|....||..|. -+||.|+|.|++.|.|||
T Consensus 92 ~~~l~aG~~~~~LvgftN~g---~~~~~V~~i~aSl~~p~d~~~~iqNfTa~~y~~~V~pg~~aT~~YsF~~~~~l~pr~ 168 (285)
T PF03896_consen 92 TKKLPAGEPVKFLVGFTNKG---SEPFTVESIEASLRYPQDYSYYIQNFTAVRYNREVPPGEEATFPYSFTPSEELAPRP 168 (285)
T ss_pred cccccCCCeEEEEEEEEeCC---CCCEEEEEEeeeecCccccceEEEeecccccCcccCCCCeEEEEEEEecchhcCCcc
Confidence 67789999998888887764 244443221 13333332 3455678999888 899999999999999999
Q ss_pred CcccccceecccCCceeeeeeeeeeE--EEEecCCCcCceeehhHHHHHHHH
Q psy4382 132 FGLSVNLQYRDEHNNFFYEGIYNETV--NIIEIDEGLDGETFFLYVFLGACV 181 (258)
Q Consensus 132 ~g~~i~~~~~d~~g~~y~~~vfN~TV--tVvE~~~sfD~q~iFLYlfL~a~~ 181 (258)
|||++++.|+ .-....|-.++ ..|++-+ .+..+=..++++=++
T Consensus 169 f~L~i~l~y~-----d~~g~~y~~~~fN~TV~IvE--~~~~~D~e~iFLY~~ 213 (285)
T PF03896_consen 169 FGLVINLIYE-----DSDGNQYQVTVFNGTVTIVE--PESGFDPETIFLYLF 213 (285)
T ss_pred eEEEEEEEEE-----eCCCCEEEEEEecceEEEee--cCCCcChhhhhHHHH
Confidence 9999999996 44556788887 6888888 455566666555444
No 5
>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=97.21 E-value=0.0022 Score=47.93 Aligned_cols=76 Identities=22% Similarity=0.347 Sum_probs=46.5
Q ss_pred cCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEEEEeeCcccCCcceeEEEEE
Q psy4382 14 PAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAEAVAGRPFGLSVNL 93 (258)
Q Consensus 14 ~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~~~~~p~~L~l~l 93 (258)
.+|+.+++-+.++|.|..++.-..+ ++.-|..+. ......... .|+||++.++.+.+.+.+.-.+..|.|.+.+
T Consensus 2 ~~G~~~~~~~tv~N~g~~~~~~v~~--~l~~P~GW~---~~~~~~~~~-~l~pG~s~~~~~~V~vp~~a~~G~y~v~~~a 75 (78)
T PF10633_consen 2 TPGETVTVTLTVTNTGTAPLTNVSL--SLSLPEGWT---VSASPASVP-SLPPGESVTVTFTVTVPADAAPGTYTVTVTA 75 (78)
T ss_dssp -TTEEEEEEEEEE--SSS-BSS-EE--EEE--TTSE------EEEEE---B-TTSEEEEEEEEEE-TT--SEEEEEEEEE
T ss_pred CCCCEEEEEEEEEECCCCceeeEEE--EEeCCCCcc---ccCCccccc-cCCCCCEEEEEEEEECCCCCCCceEEEEEEE
Confidence 4799999999999999876543333 444588865 122223333 8999999999999998887888889898888
Q ss_pred EE
Q psy4382 94 QY 95 (258)
Q Consensus 94 ~Y 95 (258)
.|
T Consensus 76 ~y 77 (78)
T PF10633_consen 76 RY 77 (78)
T ss_dssp E-
T ss_pred Ee
Confidence 76
No 6
>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=95.03 E-value=1.2 Score=39.29 Aligned_cols=84 Identities=23% Similarity=0.341 Sum_probs=58.8
Q ss_pred ceeecCCceEEEEEEEEeCCCCcE-EEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEEEEeeCcccCCccee
Q psy4382 10 NMDLPAGSVVEFLVGFTNKGKQDF-TLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAEAVAGRPFG 88 (258)
Q Consensus 10 ~~~l~~G~~~~~lv~~~N~g~~~~-tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~~~~~p~~ 88 (258)
+..++.|+.+.+-+.+.|.|+.+- .|...+.+| .|.+| .++.-.+...+ ..++||++.+..|...|-. .+.|.
T Consensus 31 ~~~~v~g~~v~V~~~iyN~G~~~A~dV~l~D~~f-p~~~F-~lvsG~~s~~~-~~i~pg~~vsh~~vv~p~~---~G~f~ 104 (181)
T PF05753_consen 31 NKYLVEGEDVTVTYTIYNVGSSAAYDVKLTDDSF-PPEDF-ELVSGSLSASW-ERIPPGENVSHSYVVRPKK---SGYFN 104 (181)
T ss_pred cccccCCcEEEEEEEEEECCCCeEEEEEEECCCC-Ccccc-EeccCceEEEE-EEECCCCeEEEEEEEeeee---eEEEE
Confidence 456788999999999999998554 587778788 23444 45655555555 5899999999999987763 23333
Q ss_pred EE-EEEEEeecC
Q psy4382 89 LS-VNLQYRDEH 99 (258)
Q Consensus 89 L~-l~l~Y~~~~ 99 (258)
+. ..+.|+++.
T Consensus 105 ~~~a~VtY~~~~ 116 (181)
T PF05753_consen 105 FTPAVVTYRDSE 116 (181)
T ss_pred ccCEEEEEECCC
Confidence 22 234666665
No 7
>PF06030 DUF916: Bacterial protein of unknown function (DUF916); InterPro: IPR010317 This family consists of putative cell surface proteins, from Firmicutes, of unknown function.
Probab=92.17 E-value=2.4 Score=34.88 Aligned_cols=82 Identities=16% Similarity=0.349 Sum_probs=58.2
Q ss_pred ccCCccceeecCCceEEEEEEEEeCCCCcEEEEEEe--------eeeeccccc-------ceEEEecceeeeceeecCCc
Q psy4382 4 EHGVYINMDLPAGSVVEFLVGFTNKGKQDFTLDTLD--------ASLRYPMDF-------NFYIQNFSTIIYNRIVKPGH 68 (258)
Q Consensus 4 ~~~~~~~~~l~~G~~~~~lv~~~N~g~~~~tV~~i~--------gSl~~P~d~-------~~~iqNfTa~~~~~~V~pg~ 68 (258)
...+|....+..|+..++-+.++|.++++++|..-- |.+-|-..- .+-+..+....-...|+|++
T Consensus 14 ~~~~YFdL~~~P~q~~~l~v~i~N~s~~~~tv~v~~~~A~Tn~nG~I~Y~~~~~~~d~sl~~~~~~~v~~~~~Vtl~~~~ 93 (121)
T PF06030_consen 14 KNVSYFDLKVKPGQKQTLEVRITNNSDKEITVKVSANTATTNDNGVIDYSQNNPKKDKSLKYPFSDLVKIPKEVTLPPNE 93 (121)
T ss_pred CCCCeEEEEeCCCCEEEEEEEEEeCCCCCEEEEEEEeeeEecCCEEEEECCCCcccCcccCcchHHhccCCcEEEECCCC
Confidence 346889999999999999999999999999876532 222221110 12333333333448899999
Q ss_pred eeEEEEEE-eeCcccCCc
Q psy4382 69 EATLGYSF-VPAEAVAGR 85 (258)
Q Consensus 69 ~at~~Y~F-~p~~~~~~~ 85 (258)
+.++++.+ +|++.+.|-
T Consensus 94 sk~V~~~i~~P~~~f~G~ 111 (121)
T PF06030_consen 94 SKTVTFTIKMPKKAFDGI 111 (121)
T ss_pred EEEEEEEEEcCCCCcCCE
Confidence 99999999 788777665
No 8
>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=91.08 E-value=2 Score=31.85 Aligned_cols=72 Identities=17% Similarity=0.307 Sum_probs=43.4
Q ss_pred eeecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeec-eeecCCceeEEEEEEeeCcccCCcceeE
Q psy4382 11 MDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYN-RIVKPGHEATLGYSFVPAEAVAGRPFGL 89 (258)
Q Consensus 11 ~~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~-~~V~pg~~at~~Y~F~p~~~~~~~p~~L 89 (258)
.....|+.+++-+.++|.|..+.. .+.-.|..- + ..+ .... ..+.||++.++.+.+.+. .+..+.|
T Consensus 13 ~~~~~g~~~~i~~~V~N~G~~~~~--~~~v~~~~~-~--~~~-----~~~~i~~L~~g~~~~v~~~~~~~---~~G~~~i 79 (101)
T PF07705_consen 13 SNVVPGEPVTITVTVKNNGTADAE--NVTVRLYLD-G--NSV-----STVTIPSLAPGESETVTFTWTPP---SPGSYTI 79 (101)
T ss_dssp SEEETTSEEEEEEEEEE-SSS-BE--EEEEEEEET-T--EEE-----EEEEESEB-TTEEEEEEEEEE-S---S-CEEEE
T ss_pred CcccCCCEEEEEEEEEECCCCCCC--CEEEEEEEC-C--cee-----ccEEECCcCCCcEEEEEEEEEeC---CCCeEEE
Confidence 457789999999999999986521 122222211 1 112 1112 578999999999999887 4567777
Q ss_pred EEEEEE
Q psy4382 90 SVNLQY 95 (258)
Q Consensus 90 ~l~l~Y 95 (258)
.+.+.+
T Consensus 80 ~~~iD~ 85 (101)
T PF07705_consen 80 RVVIDP 85 (101)
T ss_dssp EEEEST
T ss_pred EEEEee
Confidence 766633
No 9
>PF04442 CtaG_Cox11: Cytochrome c oxidase assembly protein CtaG/Cox11; InterPro: IPR007533 Cytochrome c oxidase assembly protein is essential for the assembly of functional cytochrome oxidase protein. In eukaryotes it is an integral protein of the mitochondrial inner membrane. Cox11 is essential for the insertion of Cu(I) ions to form the CuB site. This is essential for the stability of other structures in subunit I, for example haems a and a3, and the magnesium/manganese centre. Cox11 is probably only required in sub-stoichiometric amounts relative to the structural units []. The C-terminal region of the protein is known to form a dimer. Each monomer coordinates one Cu(I) ion via three conserved cysteine residues (111, 208 and 210) in Saccharomyces cerevisiae (P19516 from SWISSPROT). Met 224 is also thought to play a role in copper transfer or stabilising the copper site [].; GO: 0005507 copper ion binding; PDB: 1SO9_A 1SP0_A.
Probab=89.81 E-value=1.3 Score=38.38 Aligned_cols=73 Identities=12% Similarity=0.224 Sum_probs=41.8
Q ss_pred ccceeecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeec-eeecCCceeEEEEEEeeCccc
Q psy4382 8 YINMDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYN-RIVKPGHEATLGYSFVPAEAV 82 (258)
Q Consensus 8 ~~~~~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~-~~V~pg~~at~~Y~F~p~~~~ 82 (258)
...+++.-||...+.+..+|..+++++-..+--- .|.....|..-.-=-=+. ..+.|||+..+|=.|.-+..+
T Consensus 58 q~~v~V~pGe~~~~~y~a~N~s~~~i~g~A~~nV--~P~~a~~YF~KieCFCF~eQ~L~pgE~~~mPv~F~IDp~i 131 (152)
T PF04442_consen 58 QRSVKVHPGETALVFYEATNPSDKPITGQAIPNV--TPGEAGKYFNKIECFCFEEQTLAPGETVDMPVVFYIDPDI 131 (152)
T ss_dssp -SEEEEETT--EEEEEEEEE-SSS-EE---EEEE---SSS-STTECCS-TTS-S--EE-TT-EEEEEEEEEE-GGG
T ss_pred eeeEEeCCCCEEEEEEEEECCCCCcEEEEEeeeE--CHHHhhhhccccceEeccCcCcCCCCeEEEEEEEEECCcc
Confidence 4567889999999999999999999976655432 355444444332222234 789999999999999766644
No 10
>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=89.54 E-value=2.8 Score=32.68 Aligned_cols=66 Identities=20% Similarity=0.323 Sum_probs=46.9
Q ss_pred eecCCceEEEEEEEEeCCCCc---EEEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEEEEeeCc
Q psy4382 12 DLPAGSVVEFLVGFTNKGKQD---FTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAE 80 (258)
Q Consensus 12 ~l~~G~~~~~lv~~~N~g~~~---~tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~ 80 (258)
+..-|+..++.+.|+|..+.+ +++....-+..|+-- ....+........|.||++.+++-.+.|++
T Consensus 10 ~~~vG~d~~v~v~~~N~~~~~l~~v~~~l~~~~v~ytG~---~~~~~~~~~~~~~l~p~~~~~~~~~i~p~~ 78 (107)
T PF00927_consen 10 DPVVGQDFTVSVSFTNPSSEPLRNVSLNLCAFTVEYTGL---TRDQFKKEKFEVTLKPGETKSVEVTITPSQ 78 (107)
T ss_dssp EEBTTSEEEEEEEEEE-SSS-EECEEEEEEEEEEECTTT---EEEEEEEEEEEEEE-TTEEEEEEEEE-HHS
T ss_pred CccCCCCEEEEEEEEeCCcCccccceeEEEEEEEEECCc---ccccEeEEEcceeeCCCCEEEEEEEEEcee
Confidence 567899999999999998755 444445555555422 234666777778999999999999999986
No 11
>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=88.84 E-value=2.8 Score=32.30 Aligned_cols=70 Identities=17% Similarity=0.222 Sum_probs=35.2
Q ss_pred EEEEEEEEeCCCCcEEEEEEeeeeeccc---ccceEE------EecceeeeceeecCCceeEEEEEEeeCcccCCcceeE
Q psy4382 19 VEFLVGFTNKGKQDFTLDTLDASLRYPM---DFNFYI------QNFSTIIYNRIVKPGHEATLGYSFVPAEAVAGRPFGL 89 (258)
Q Consensus 19 ~~~lv~~~N~g~~~~tV~~i~gSl~~P~---d~~~~i------qNfTa~~~~~~V~pg~~at~~Y~F~p~~~~~~~p~~L 89 (258)
+++.+.++|.++.++++..-+|.--+-. .-+..| +=||..--...++||++.++.-.+-... ++|+.|-|
T Consensus 2 v~~~l~v~N~s~~~v~l~f~sgq~~D~~v~d~~g~~vwrwS~~~~FtQal~~~~l~pGe~~~~~~~~~~~~-~~~G~Y~~ 80 (82)
T PF12690_consen 2 VEFTLTVTNNSDEPVTLQFPSGQRYDFVVKDKEGKEVWRWSDGKMFTQALQEETLEPGESLTYEETWDLKD-LSPGEYTL 80 (82)
T ss_dssp EEEEEEEEE-SSS-EEEEESSS--EEEEEE-TT--EEEETTTT-------EEEEE-TT-EEEEEEEESS-----SEEEEE
T ss_pred EEEEEEEEeCCCCeEEEEeCCCCEEEEEEECCCCCEEEEecCCchhhheeeEEEECCCCEEEEEEEECCCC-CCCceEEE
Confidence 5789999999999999987777543321 001111 1244444568899999999888873332 33444443
No 12
>COG3175 COX11 Cytochrome oxidase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=88.77 E-value=2 Score=38.60 Aligned_cols=95 Identities=19% Similarity=0.282 Sum_probs=62.6
Q ss_pred cceeecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeec-eeecCCceeEEEEEEeeCcccCCcce
Q psy4382 9 INMDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYN-RIVKPGHEATLGYSFVPAEAVAGRPF 87 (258)
Q Consensus 9 ~~~~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~-~~V~pg~~at~~Y~F~p~~~~~~~p~ 87 (258)
..+.+.-|+.+.+.+..+|..+.+++=..+-- -.|+....|..-.---=+. ..+.|||+.-+|-.|.-+..++-
T Consensus 85 ~~v~v~pGet~~~~y~a~N~sd~~itg~A~~n--v~P~~Ag~YF~KveCFCFteq~L~pgE~vemPV~FfVDpd~~~--- 159 (195)
T COG3175 85 REVYVRPGETNLIFYEAENLSDKPITGQATYN--VAPGQAGAYFNKVECFCFTEQTLKPGETVEMPVVFFVDPDFAD--- 159 (195)
T ss_pred ceeEeccCceEEEEEEEecCCCCCceeEEecc--cChhHhhhheeeeeEEEeeecccCCCCeEeccEEEEECccccc---
Confidence 45678889999999999999999985433211 1144333444332222233 67999999999999976653322
Q ss_pred eEEEEEEEeecCCceeEEEEecceEEEEeecccccc-ccc
Q psy4382 88 GLSVNLQYRDEHNNFFYEGIYNETVNIITLGYSFVP-AEA 126 (258)
Q Consensus 88 ~L~l~l~Y~~~~~~~~~~~~~n~~v~~~t~~~~~~p-~e~ 126 (258)
+++ =+.|+.|||.|.|.| .|.
T Consensus 160 ----------dPe--------~kdvk~iTLSYTFF~~~~~ 181 (195)
T COG3175 160 ----------DPE--------MKDVKTITLSYTFFPIRED 181 (195)
T ss_pred ----------Ccc--------cCCCCeEEEEEEEEEcccC
Confidence 221 145778999999999 444
No 13
>PRK05089 cytochrome C oxidase assembly protein; Provisional
Probab=88.75 E-value=1.4 Score=39.42 Aligned_cols=90 Identities=16% Similarity=0.287 Sum_probs=62.2
Q ss_pred ccceeecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeec-eeecCCceeEEEEEEeeCcccCCcc
Q psy4382 8 YINMDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYN-RIVKPGHEATLGYSFVPAEAVAGRP 86 (258)
Q Consensus 8 ~~~~~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~-~~V~pg~~at~~Y~F~p~~~~~~~p 86 (258)
...+++.-||...+-+..+|..+++++-..+--- .|.....|..-+-=-=+. ..+.|||+..+|=.|.-+..+
T Consensus 85 q~~v~V~pGE~~~~~y~a~N~sd~~i~g~A~~nV--~P~~a~~YF~KieCFCF~eQ~L~pgE~~~mPV~F~IDP~i---- 158 (188)
T PRK05089 85 QRSVDVHPGELNLVFYEAENLSDRPIVGQAIPSV--TPGQAGAYFNKIECFCFTQQTLQPGETREMPVVFYVDPDL---- 158 (188)
T ss_pred eeEEEEcCCCeEEEEEEEECCCCCcEEEEEeccc--CHHHHhhhccceeeecccCcccCCCCeEecCEEEEECCCc----
Confidence 4567899999999999999999999966554321 244434444332222344 789999999999999666522
Q ss_pred eeEEEEEEEeecCCceeEEEEecceEEEEeecccccccc
Q psy4382 87 FGLSVNLQYRDEHNNFFYEGIYNETVNIITLGYSFVPAE 125 (258)
Q Consensus 87 ~~L~l~l~Y~~~~~~~~~~~~~n~~v~~~t~~~~~~p~e 125 (258)
-+.|+-|||.|.|.+..
T Consensus 159 ----------------------~~dv~~iTLSYTff~~~ 175 (188)
T PRK05089 159 ----------------------PKDVKTITLSYTFFDVT 175 (188)
T ss_pred ----------------------ccccCEEEEEEEEEecC
Confidence 22367788888888743
No 14
>PF07760 DUF1616: Protein of unknown function (DUF1616); InterPro: IPR011674 This is a group of sequences from hypothetical archaeal proteins. The region in question is approximately 330 amino acid residues long.
Probab=84.26 E-value=13 Score=34.61 Aligned_cols=88 Identities=15% Similarity=0.216 Sum_probs=55.5
Q ss_pred CCccceeecCCceEEEEEEEEeCCC--CcEEEEEE-eeeeecccccceEEEecceee-eceeecCCceeEEEEEEeeCcc
Q psy4382 6 GVYINMDLPAGSVVEFLVGFTNKGK--QDFTLDTL-DASLRYPMDFNFYIQNFSTII-YNRIVKPGHEATLGYSFVPAEA 81 (258)
Q Consensus 6 ~~~~~~~l~~G~~~~~lv~~~N~g~--~~~tV~~i-~gSl~~P~d~~~~iqNfTa~~-~~~~V~pg~~at~~Y~F~p~~~ 81 (258)
+++-..++..|++.++.|++.|+|. ..++++.. ..+..+|.+ ..+.+-+... ....+..|++.+.+|+|.|.
T Consensus 180 a~~Ypt~l~~ge~~~v~vgI~NhE~~~~~Ytv~v~l~~~~~~~~~--~~~~~~~~l~~~~~~L~~n~t~~~~~~~~~~-- 255 (287)
T PF07760_consen 180 AGDYPTNLTSGEPGTVIVGIENHEGRPENYTVVVVLQNVTWNPNN--YNVMESTVLDRPIVTLADNETWEQPYKFTPF-- 255 (287)
T ss_pred cccCCeeEEcCCcEEEEEEEEcCCCCcEEEEEEEEEecccccccc--ccccchhcccceEEEeCCCCeEEEEEEEEEe--
Confidence 3444567899999999999999994 66666554 444444432 2232222222 23488999999999999993
Q ss_pred cCCcceeEEEEEEEeec
Q psy4382 82 VAGRPFGLSVNLQYRDE 98 (258)
Q Consensus 82 ~~~~p~~L~l~l~Y~~~ 98 (258)
..|....+..- -|+++
T Consensus 256 ~~~~~~~l~~l-LY~~~ 271 (287)
T PF07760_consen 256 ITGENPRLEYL-LYKGG 271 (287)
T ss_pred cCCCceEEEEE-EEcCC
Confidence 33444444443 35543
No 15
>PTZ00128 cytochrome c oxidase assembly protein-like; Provisional
Probab=83.31 E-value=4.2 Score=37.57 Aligned_cols=94 Identities=16% Similarity=0.223 Sum_probs=62.3
Q ss_pred ccceeecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeec-eeecCCceeEEEEEEeeCcccCCcc
Q psy4382 8 YINMDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYN-RIVKPGHEATLGYSFVPAEAVAGRP 86 (258)
Q Consensus 8 ~~~~~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~-~~V~pg~~at~~Y~F~p~~~~~~~p 86 (258)
-..+++.-||...+.+..+|..+++++-..+--- .|.....|..-+-=-=+. ..+.|||+..+|=.|.-+..+...|
T Consensus 129 q~~v~V~pGE~~lv~Y~a~N~sd~~i~G~A~ynV--~P~~Ag~YFnKieCFCF~eQ~L~pgE~~~MPV~F~IDP~i~~D~ 206 (232)
T PTZ00128 129 QKEVEVLPGETALAFYRAKNRSDKPVIGVATYHI--APPEAGLYFNKIQCFCFEEQRLNPHEEVDMPVFFYIDPDILNDP 206 (232)
T ss_pred eeEEEEcCCCeEEEEEEEECCCCCcEEEEEeccc--CHHHHhhhccceeeecccccccCCCCeEecCEEEEECCCCCCCc
Confidence 3467889999999999999999999965544221 243333333322222233 7899999999999997665332211
Q ss_pred eeEEEEEEEeecCCceeEEEEecceEEEEeeccccccc
Q psy4382 87 FGLSVNLQYRDEHNNFFYEGIYNETVNIITLGYSFVPA 124 (258)
Q Consensus 87 ~~L~l~l~Y~~~~~~~~~~~~~n~~v~~~t~~~~~~p~ 124 (258)
- -+.|+-|||.|-|.+.
T Consensus 207 ~---------------------~~~v~~ITLSYTFF~~ 223 (232)
T PTZ00128 207 R---------------------LKWVDEITLSYTFFEA 223 (232)
T ss_pred c---------------------cCCcCEEEEEEEEEec
Confidence 1 1346778888888873
No 16
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=82.08 E-value=20 Score=27.26 Aligned_cols=72 Identities=19% Similarity=0.267 Sum_probs=47.7
Q ss_pred eecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEEEEeeCcccCCcceeEEE
Q psy4382 12 DLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAEAVAGRPFGLSV 91 (258)
Q Consensus 12 ~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~~~~~p~~L~l 91 (258)
++.-|+....-+.++|.+..+..... +.|.+... .|+...-...|.||++.++.-.|.|.... +.+.-.|
T Consensus 15 ~v~~g~~~~~~v~l~N~s~~p~~f~v-----~~~~~~~~---~~~v~~~~g~l~PG~~~~~~V~~~~~~~~--g~~~~~l 84 (102)
T PF14874_consen 15 NVFVGQTYSRTVTLTNTSSIPARFRV-----RQPESLSS---FFSVEPPSGFLAPGESVELEVTFSPTKPL--GDYEGSL 84 (102)
T ss_pred EEccCCEEEEEEEEEECCCCCEEEEE-----EeCCcCCC---CEEEECCCCEECCCCEEEEEEEEEeCCCC--ceEEEEE
Confidence 46789999999999999998865543 22332221 23333334689999999999999976533 3344444
Q ss_pred EE
Q psy4382 92 NL 93 (258)
Q Consensus 92 ~l 93 (258)
.+
T Consensus 85 ~i 86 (102)
T PF14874_consen 85 VI 86 (102)
T ss_pred EE
Confidence 44
No 17
>PF07610 DUF1573: Protein of unknown function (DUF1573); InterPro: IPR011467 These hypothetical proteins from bacteria, such as Rhodopirellula baltica, Bacteroides thetaiotaomicron and Porphyromonas gingivalis, share a region of conserved sequence towards their N termini.
Probab=82.02 E-value=6.1 Score=26.86 Aligned_cols=43 Identities=21% Similarity=0.475 Sum_probs=32.3
Q ss_pred EEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeec-eeecCCceeEEEEEE
Q psy4382 23 VGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYN-RIVKPGHEATLGYSF 76 (258)
Q Consensus 23 v~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~-~~V~pg~~at~~Y~F 76 (258)
+.|+|.|++++.|..|..|=-- |+..+. ..|+||++..+..+|
T Consensus 2 F~~~N~g~~~L~I~~v~tsCgC-----------t~~~~~~~~i~PGes~~i~v~y 45 (45)
T PF07610_consen 2 FEFTNTGDSPLVITDVQTSCGC-----------TTAEYSKKPIAPGESGKIKVTY 45 (45)
T ss_pred EEEEECCCCcEEEEEeeEccCC-----------EEeeCCcceECCCCEEEEEEEC
Confidence 5799999999999988876532 233333 569999999887665
No 18
>PF11611 DUF4352: Domain of unknown function (DUF4352); InterPro: IPR021652 This entry is represented by Bacteriophage A118, Gp32. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a group of putative lipoproteins of unknown function.; PDB: 3CFU_A.
Probab=78.65 E-value=8.2 Score=30.00 Aligned_cols=65 Identities=22% Similarity=0.270 Sum_probs=39.6
Q ss_pred cCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEeccee-----eeceeecCCceeEEEEEEeeC
Q psy4382 14 PAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTI-----IYNRIVKPGHEATLGYSFVPA 79 (258)
Q Consensus 14 ~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~-----~~~~~V~pg~~at~~Y~F~p~ 79 (258)
..++-+.+-+.+.|.+++++.+....-.|.+..+. .+=..++.. .....|.||++.+....|.-.
T Consensus 33 ~g~~fv~v~v~v~N~~~~~~~~~~~~f~l~d~~g~-~~~~~~~~~~~~~~~~~~~i~pG~~~~g~l~F~vp 102 (123)
T PF11611_consen 33 EGNKFVVVDVTVKNNGDEPLDFSPSDFKLYDSDGN-KYDPDFSASSNDNDLFSETIKPGESVTGKLVFEVP 102 (123)
T ss_dssp --SEEEEEEEEEEE-SSS-EEEEGGGEEEE-TT---B--EEE-CCCTTTB--EEEE-TT-EEEEEEEEEES
T ss_pred CCCEEEEEEEEEEECCCCcEEecccceEEEeCCCC-EEcccccchhccccccccEECCCCEEEEEEEEEEC
Confidence 34677889999999999999998887788766542 222333332 245899999999988888433
No 19
>PF05506 DUF756: Domain of unknown function (DUF756); InterPro: IPR008475 This domain is found, normally as a tandem repeat, at the C terminus of bacterial phospholipase C proteins.; GO: 0004629 phospholipase C activity, 0016042 lipid catabolic process
Probab=78.50 E-value=15 Score=27.94 Aligned_cols=58 Identities=17% Similarity=0.277 Sum_probs=42.7
Q ss_pred EEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEEEEeeCcccCCcceeEEEEE
Q psy4382 20 EFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAEAVAGRPFGLSVNL 93 (258)
Q Consensus 20 ~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~~~~~p~~L~l~l 93 (258)
.+.+.|.|.|....++..-+... .+.......|+||++.++......+ +.-|||.|..
T Consensus 21 ~l~l~l~N~g~~~~~~~v~~~~y------------~~~~~~~~~v~ag~~~~~~w~l~~s----~gwYDl~v~~ 78 (89)
T PF05506_consen 21 NLRLTLSNPGSAAVTFTVYDNAY------------GGGGPWTYTVAAGQTVSLTWPLAAS----GGWYDLTVTG 78 (89)
T ss_pred EEEEEEEeCCCCcEEEEEEeCCc------------CCCCCEEEEECCCCEEEEEEeecCC----CCcEEEEEEc
Confidence 88999999999988777665221 1123345689999999988887444 4889988876
No 20
>PF13473 Cupredoxin_1: Cupredoxin-like domain; PDB: 1IBZ_D 1IC0_E 1IBY_D.
Probab=78.10 E-value=9.7 Score=29.56 Aligned_cols=45 Identities=24% Similarity=0.462 Sum_probs=26.5
Q ss_pred ceeecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEE
Q psy4382 10 NMDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGY 74 (258)
Q Consensus 10 ~~~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y 74 (258)
..++++|+++++ .|+|++.....+..-+ ......++||++.++..
T Consensus 36 ~i~v~~G~~v~l--~~~N~~~~~h~~~i~~------------------~~~~~~l~~g~~~~~~f 80 (104)
T PF13473_consen 36 TITVKAGQPVTL--TFTNNDSRPHEFVIPD------------------LGISKVLPPGETATVTF 80 (104)
T ss_dssp EEEEETTCEEEE--EEEE-SSS-EEEEEGG------------------GTEEEEE-TT-EEEEEE
T ss_pred EEEEcCCCeEEE--EEEECCCCcEEEEECC------------------CceEEEECCCCEEEEEE
Confidence 567899999884 4789988754332222 22336788998776654
No 21
>PF06159 DUF974: Protein of unknown function (DUF974); InterPro: IPR010378 This is a family of uncharacterised eukaryotic proteins.
Probab=76.12 E-value=21 Score=32.65 Aligned_cols=84 Identities=13% Similarity=0.088 Sum_probs=65.0
Q ss_pred eecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccc--cceEEEecceeeeceeecCCceeEEEEEEeeCcccCCcceeE
Q psy4382 12 DLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMD--FNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAEAVAGRPFGL 89 (258)
Q Consensus 12 ~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d--~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~~~~~p~~L 89 (258)
.+.-||.-.+.+.+.|....+++-+.|.+.+..|.. --.+..|-....-...+.||+...+--+|--.| ...+-|
T Consensus 9 ~iylGEtF~~~l~~~N~s~~~v~~v~ikvemqT~s~~~r~~L~~~~~~~~~~~~L~p~~~l~~iv~~~lkE---~G~h~L 85 (249)
T PF06159_consen 9 SIYLGETFSCYLSVNNDSNKPVRNVRIKVEMQTPSQSLRLPLSDNENSDSPVASLAPGESLDFIVSHELKE---LGNHTL 85 (249)
T ss_pred CEeecCCEEEEEEeecCCCCceEEeEEEEEEeCCCCCccccCCCCccccccccccCCCCeEeEEEEEEeee---cCceEE
Confidence 467799999999999999999999999999999976 222333322221224689999998888885443 577999
Q ss_pred EEEEEEeec
Q psy4382 90 SVNLQYRDE 98 (258)
Q Consensus 90 ~l~l~Y~~~ 98 (258)
++.+.|.+.
T Consensus 86 ~c~VsY~~~ 94 (249)
T PF06159_consen 86 VCTVSYTDP 94 (249)
T ss_pred EEEEEEecC
Confidence 999999988
No 22
>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=75.93 E-value=14 Score=27.78 Aligned_cols=55 Identities=22% Similarity=0.323 Sum_probs=36.1
Q ss_pred EEEEEEEEeCCCCcEEEEEEeee-eecccccceEEE----ecceeeeceeecCCceeEEEEE
Q psy4382 19 VEFLVGFTNKGKQDFTLDTLDAS-LRYPMDFNFYIQ----NFSTIIYNRIVKPGHEATLGYS 75 (258)
Q Consensus 19 ~~~lv~~~N~g~~~~tV~~i~gS-l~~P~d~~~~iq----NfTa~~~~~~V~pg~~at~~Y~ 75 (258)
...-+.++|++..++.=..+... |. .+.+.+.+ .++--.+...++||++.+|.|-
T Consensus 19 ~qy~v~I~N~~~~~I~~~~i~~~~l~--~~iW~l~~~~~~~y~lPs~~~~i~pg~s~~FGYI 78 (80)
T PF09478_consen 19 TQYDVTITNNGSKPIKSLKISIDNLY--GSIWGLDKVSGNTYTLPSYQPTIKPGQSFTFGYI 78 (80)
T ss_pred EEEEEEEEECCCCeEEEEEEEECccc--hhheeEEeccCCEEECCccccccCCCCEEEEEEE
Confidence 57889999999988865555544 33 44444443 1122233458999999999884
No 23
>PF00630 Filamin: Filamin/ABP280 repeat; InterPro: IPR017868 The many different actin cross-linking proteins share a common architecture, consisting of a globular actin-binding domain and an extended rod. Whereas their actin-binding domains consist of two calponin homology domains (see IPR001715 from INTERPRO), their rods fall into three families. The rod domain of the family including the Dictyostelium discoideum (Slime mould) gelation factor (ABP120) and human filamin (ABP280) is constructed from tandem repeats of a 100-residue motif that is glycine and proline rich []. The gelation factor's rod contains 6 copies of the repeat, whereas filamin has a rod constructed from 24 repeats. The resolution of the 3D structure of rod repeats from the gelation factor has shown that they consist of a beta-sandwich, formed by two beta-sheets arranged in an immunoglobulin-like fold [, ]. Because conserved residues that form the core of the repeats are preserved in filamin, the repeat structure should be common to the members of the gelation factor/filamin family. The head to tail homodimerisation is crucial to the function of the ABP120 and ABP280 proteins. This interaction involves a small portion at the distal end of the rod domains. For the gelation factor it has been shown that the carboxy-terminal repeat 6 dimerises through a double edge-to-edge extension of the beta-sheet and that repeat 5 contributes to dimerisation to some extent [, , ].; PDB: 2DI9_A 2EEC_A 2DIC_A 2EEA_A 2DMC_A 2EE9_A 2D7O_A 2D7N_A 2K7P_A 2NQC_A ....
Probab=69.45 E-value=23 Score=26.54 Aligned_cols=72 Identities=18% Similarity=0.231 Sum_probs=41.9
Q ss_pred ecCCceEEEEEEEEeCCCCcEEE--EEEeeeeecccccceEEEecceeeeceeecCCceeEEEEEEeeCcccCCcceeEE
Q psy4382 13 LPAGSVVEFLVGFTNKGKQDFTL--DTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAEAVAGRPFGLS 90 (258)
Q Consensus 13 l~~G~~~~~lv~~~N~g~~~~tV--~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~~~~~p~~L~ 90 (258)
...|++.+|.|...+.+..++.. +.+.-.+..|....... .....+.....-++..+|.|.+ +..+.|.
T Consensus 17 ~~~g~~~~F~V~~~d~~g~~~~~~~~~~~v~i~~p~~~~~~~------~~~~~v~~~~~G~y~v~y~p~~---~G~y~i~ 87 (101)
T PF00630_consen 17 AVVGEPATFTVDTRDAGGNPVSSGGDEFQVTITSPDGKEEPV------PVPVEVIDNGDGTYTVSYTPTE---PGKYKIS 87 (101)
T ss_dssp EETTSEEEEEEEETTTTSSBEESTSSEEEEEEESSSSESS--------EEEEEEEEESSSEEEEEEEESS---SEEEEEE
T ss_pred eECCCcEEEEEEEccCCCCccccCCceeEEEEeCCCCCcccc------ccceEEEECCCCEEEEEEEeCc---cEeEEEE
Confidence 48899999999999997776543 22233345554421110 2222333445558888888885 3556555
Q ss_pred EEE
Q psy4382 91 VNL 93 (258)
Q Consensus 91 l~l 93 (258)
|.+
T Consensus 88 V~~ 90 (101)
T PF00630_consen 88 VKI 90 (101)
T ss_dssp EEE
T ss_pred EEE
Confidence 444
No 24
>COG1361 S-layer domain [Cell envelope biogenesis, outer membrane]
Probab=69.25 E-value=43 Score=33.00 Aligned_cols=84 Identities=15% Similarity=0.249 Sum_probs=59.2
Q ss_pred ceeecCCceEEEEEEEEeCCCCcE---EEEEEe-eeeecccccceEEEecceeeeceeecCCceeEEEEEEeeCcccCCc
Q psy4382 10 NMDLPAGSVVEFLVGFTNKGKQDF---TLDTLD-ASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAEAVAGR 85 (258)
Q Consensus 10 ~~~l~~G~~~~~lv~~~N~g~~~~---tV~~i~-gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~~~~~ 85 (258)
...+..|+...+.+.+.|.|..+. .+.... .+...|...... ..|-..+.||+...+.+++....-...+
T Consensus 160 ~~~i~~G~~~~l~~~I~N~G~~~~~~v~l~~~~~~~~~~~i~~~~~------~~~i~~l~p~es~~v~f~v~~~~~a~~g 233 (500)
T COG1361 160 PEAIIPGETNTLTLTIKNPGEGPAKNVSLSLESPTSYLGPIYSAND------TPYIGALGPGESVNVTFSVYAGSNAEPG 233 (500)
T ss_pred ccccCCCCccEEEEEEEeCCcccccceEEEEeCCcceecccccccc------ceeeeeeCCCceEEEEEEEEeecCCCCc
Confidence 456788999999999999997443 333322 112222211111 3456789999999999999888655788
Q ss_pred ceeEEEEEEEeecC
Q psy4382 86 PFGLSVNLQYRDEH 99 (258)
Q Consensus 86 p~~L~l~l~Y~~~~ 99 (258)
.+-+.+.+.|++.+
T Consensus 234 ~y~i~i~i~~~~~~ 247 (500)
T COG1361 234 TYTINLEITYKDEE 247 (500)
T ss_pred cEEEEEEEEEecCC
Confidence 89999999999943
No 25
>KOG3317|consensus
Probab=68.45 E-value=75 Score=28.54 Aligned_cols=83 Identities=17% Similarity=0.130 Sum_probs=49.3
Q ss_pred ecCCceEEEEEEEEeCCCCc-EEEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEEEEeeCcccCCcceeEEE
Q psy4382 13 LPAGSVVEFLVGFTNKGKQD-FTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAEAVAGRPFGLSV 91 (258)
Q Consensus 13 l~~G~~~~~lv~~~N~g~~~-~tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~~~~~p~~L~l 91 (258)
=+.++.+.+-+++-|-|..+ +.|..-+-|| ++.+| .++ |......=-.++||... ..+.+-.....|-=.+-..
T Consensus 38 ~v~~rd~~leY~IyNvGsspAldVtLsD~Sf-pt~~F-eIv-kG~~~~swerIpags~v--sHsivl~prv~g~f~~t~a 112 (188)
T KOG3317|consen 38 AVEARDVSLEYDIYNVGSSPALDVTLSDNSF-PTKTF-EIV-KGNLSVSWERIPAGSNV--SHSIVLRPRVKGVFNGTPA 112 (188)
T ss_pred cccceeeEEEEeeEEcCCCcceeEEecCCCC-Cccce-eee-ccccccceeecCCCCce--EEEEEEeecccceeccCce
Confidence 36788999999999999854 4555555555 34454 333 44444444567888744 4444433323333333455
Q ss_pred EEEEeecCC
Q psy4382 92 NLQYRDEHN 100 (258)
Q Consensus 92 ~l~Y~~~~~ 100 (258)
.+.|++..+
T Consensus 113 tVty~~~e~ 121 (188)
T KOG3317|consen 113 TVTYRIPEK 121 (188)
T ss_pred EEEEEcCCC
Confidence 667777764
No 26
>PF11906 DUF3426: Protein of unknown function (DUF3426); InterPro: IPR021834 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 262 to 463 amino acids in length.
Probab=66.76 E-value=47 Score=27.24 Aligned_cols=63 Identities=16% Similarity=0.144 Sum_probs=49.8
Q ss_pred CCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeee-------ceeecCCceeEEEEEEe
Q psy4382 15 AGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIY-------NRIVKPGHEATLGYSFV 77 (258)
Q Consensus 15 ~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~-------~~~V~pg~~at~~Y~F~ 77 (258)
.+....+-..+.|..+.+..+=.|..+|++.++.--.=+.++...| ...++||++.+|.-.|.
T Consensus 66 ~~~~l~v~g~i~N~~~~~~~~P~l~l~L~D~~g~~l~~r~~~P~~yl~~~~~~~~~l~pg~~~~~~~~~~ 135 (149)
T PF11906_consen 66 GPGVLVVSGTIRNRADFPQALPALELSLLDAQGQPLARRVFTPADYLPPGLAAQAGLPPGESVPFRLRLE 135 (149)
T ss_pred CCCEEEEEEEEEeCCCCcccCceEEEEEECCCCCEEEEEEEChHHhcccccccccccCCCCeEEEEEEee
Confidence 4666778889999999999999999999998875444456655333 45799999999988885
No 27
>PF05568 ASFV_J13L: African swine fever virus J13L protein; InterPro: IPR008385 This family consists of several African swine fever virus (ASFV) j13L proteins [, , ].
Probab=65.50 E-value=4.7 Score=35.34 Aligned_cols=31 Identities=35% Similarity=0.462 Sum_probs=20.7
Q ss_pred hhHHHHHHHHHHHHHHhhhh-hhhccccccCC
Q psy4382 172 FLYVFLGACVVLLLVIGQHF-LYSVGKKRVGT 202 (258)
Q Consensus 172 FLYlfL~a~~gll~y~~y~~-~~~~~kK~~~~ 202 (258)
-||.+|+|++.+++.|...+ |.+.||||+.+
T Consensus 30 hm~tILiaIvVliiiiivli~lcssRKkKaaA 61 (189)
T PF05568_consen 30 HMYTILIAIVVLIIIIIVLIYLCSSRKKKAAA 61 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHh
Confidence 47889999888766655544 55566665543
No 28
>smart00557 IG_FLMN Filamin-type immunoglobulin domains. These form a rod-like structure in the actin-binding cytoskeleton protein, filamin. The C-terminal repeats of filamin bind beta1-integrin (CD29).
Probab=65.25 E-value=46 Score=25.34 Aligned_cols=52 Identities=21% Similarity=0.314 Sum_probs=36.4
Q ss_pred cCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEEEEeeCc
Q psy4382 14 PAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAE 80 (258)
Q Consensus 14 ~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~ 80 (258)
..|++.+|.|.-.+.|..++.|.. ..|.. . .....|.....-++.-+|+|.+
T Consensus 15 ~vg~~~~f~v~~~d~G~~~~~v~i-----~~p~g-~---------~~~~~v~d~~dGty~v~y~P~~ 66 (93)
T smart00557 15 VVGEPAEFTIDTRGAGGGELEVEV-----TGPSG-K---------KVPVEVKDNGDGTYTVSYTPTE 66 (93)
T ss_pred ecCCCEEEEEEcCCCCCCcEEEEE-----ECCCC-C---------eeEeEEEeCCCCEEEEEEEeCC
Confidence 788999999999999888886654 44432 1 1223344455568888998885
No 29
>COG1470 Predicted membrane protein [Function unknown]
Probab=64.61 E-value=1.5e+02 Score=30.41 Aligned_cols=81 Identities=11% Similarity=0.282 Sum_probs=58.2
Q ss_pred CccceeecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEEEEeeCcccCCcc
Q psy4382 7 VYINMDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAEAVAGRP 86 (258)
Q Consensus 7 ~~~~~~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~~~~~p 86 (258)
+-...++.+|+...+-+.+.|-|..++ .-|.=++..||++.--++=.|- -.++||+..++.-.....+.-.+..
T Consensus 387 g~~~lt~taGee~~i~i~I~NsGna~L--tdIkl~v~~PqgWei~Vd~~~I----~sL~pge~~tV~ltI~vP~~a~aGd 460 (513)
T COG1470 387 GPYRLTITAGEEKTIRISIENSGNAPL--TDIKLTVNGPQGWEIEVDESTI----PSLEPGESKTVSLTITVPEDAGAGD 460 (513)
T ss_pred CcEEEEecCCccceEEEEEEecCCCcc--ceeeEEecCCccceEEECcccc----cccCCCCcceEEEEEEcCCCCCCCc
Confidence 345678899999999999999995544 4555578899997666665422 3689999999999885444345555
Q ss_pred eeEEEEE
Q psy4382 87 FGLSVNL 93 (258)
Q Consensus 87 ~~L~l~l 93 (258)
+...+..
T Consensus 461 Y~i~i~~ 467 (513)
T COG1470 461 YRITITA 467 (513)
T ss_pred EEEEEEE
Confidence 6554444
No 30
>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=61.75 E-value=42 Score=26.69 Aligned_cols=59 Identities=17% Similarity=0.178 Sum_probs=34.3
Q ss_pred cCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEE-Eecc--eeee-ceeecCCceeEE
Q psy4382 14 PAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYI-QNFS--TIIY-NRIVKPGHEATL 72 (258)
Q Consensus 14 ~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~i-qNfT--a~~~-~~~V~pg~~at~ 72 (258)
+.+...-+-..+.|+++++.+|.+++...-.-....... ++-. ..+. +..|+||++..|
T Consensus 11 ~~~~~~a~y~ti~N~g~~~~~L~~v~s~~a~~v~lh~~~~~~g~~~m~~v~~i~ipa~~~v~l 73 (110)
T PF04314_consen 11 PGANVTAAYFTITNNGDQDDRLVGVSSPAAARVELHETVMEDGVMKMRPVDSIPIPAGSTVEL 73 (110)
T ss_dssp TT-SEEEEEEEEE-CSSSEEEEEEEE-TTCCEEEEEEECCCCCEEEECCSS-EEEETT-EEEE
T ss_pred CCCccEEEEEEEEeCCCCCeEEEEEEcCCCceEEEEEEEccCCeEEEEECCCEEECCCCeEEe
Confidence 344678888999999999999999987632222211111 1111 1122 588999999888
No 31
>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=57.95 E-value=73 Score=26.31 Aligned_cols=66 Identities=21% Similarity=0.223 Sum_probs=44.6
Q ss_pred ecCCceEEEEEEEEeCCCCcEEEEEEeeeeec---ccc--cce-EEEe--c--ceeeeceeecCCceeEEEEEEee
Q psy4382 13 LPAGSVVEFLVGFTNKGKQDFTLDTLDASLRY---PMD--FNF-YIQN--F--STIIYNRIVKPGHEATLGYSFVP 78 (258)
Q Consensus 13 l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~---P~d--~~~-~iqN--f--Ta~~~~~~V~pg~~at~~Y~F~p 78 (258)
+--++..-+-..++|.|+.++.-..+.++|.+ ..+ ... .-+. | +...+...++||+...|...|..
T Consensus 58 l~~~~~~~v~g~V~N~g~~~i~~c~i~~~l~~~~~~~~n~~~~~~~~~~~f~~~~~~i~~~L~~~e~~~f~~~~~~ 133 (149)
T PF09624_consen 58 LQYSESFYVDGTVTNTGKFTIKKCKITVKLYNDKQVSGNKFKEIFYQQIPFVKKSIPIADNLKPGESKEFRFIFPY 133 (149)
T ss_pred eeeccEEEEEEEEEECCCCEeeEEEEEEEEEeCCCccCchhhhhhccccchhccceeHHhhcCcccceeEEEEecC
Confidence 44567777889999999999999999999976 221 000 1111 1 12233444999999999888743
No 32
>PLN02171 endoglucanase
Probab=54.14 E-value=53 Score=34.44 Aligned_cols=72 Identities=10% Similarity=0.029 Sum_probs=52.1
Q ss_pred ceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEE--e-cceeeeceeecCCceeEEEEEEeeCcccCCcceeEEEEE
Q psy4382 17 SVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQ--N-FSTIIYNRIVKPGHEATLGYSFVPAEAVAGRPFGLSVNL 93 (258)
Q Consensus 17 ~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iq--N-fTa~~~~~~V~pg~~at~~Y~F~p~~~~~~~p~~L~l~l 93 (258)
.-++..|.++|++..++....| ++.++..+.+.+.. | +|--.+-..+++|++.+|.|--. +.|.++.++.
T Consensus 553 ~y~qy~v~I~N~s~~~ik~i~i-~~~~~~~~iW~v~~~~ngytlPs~~~sL~aG~s~tFgyI~~------~~pA~~~v~~ 625 (629)
T PLN02171 553 TYYRYSTTVTNRSAKTLKELHL-GISKLYGPLWGLTKAGYGYVLPSWMPSLPAGKSLEFVYVHS------ASPADVWVSG 625 (629)
T ss_pred eEEEEEEEEEECCCCceeeeee-eeccccccchheeecCCcccCchhhcccCCCCeeEEEeecC------CCCceEEEEE
Confidence 4567889999999999988888 77788887766654 2 12222235899999999988832 3666777776
Q ss_pred EE
Q psy4382 94 QY 95 (258)
Q Consensus 94 ~Y 95 (258)
.|
T Consensus 626 y~ 627 (629)
T PLN02171 626 YK 627 (629)
T ss_pred EE
Confidence 54
No 33
>COG1470 Predicted membrane protein [Function unknown]
Probab=54.11 E-value=1.2e+02 Score=31.19 Aligned_cols=102 Identities=21% Similarity=0.345 Sum_probs=73.1
Q ss_pred cceeecCCceEEEEEEEEeCCCCcEEEEEEeeeee-cccccceEEEecceeeec---eeecCCceeEEEEEEeeCcccCC
Q psy4382 9 INMDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLR-YPMDFNFYIQNFSTIIYN---RIVKPGHEATLGYSFVPAEAVAG 84 (258)
Q Consensus 9 ~~~~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~-~P~d~~~~iqNfTa~~~~---~~V~pg~~at~~Y~F~p~~~~~~ 84 (258)
....+..|....+-|.+.|+|+++-++.. ++. -|.+|++ +||...+- ..|.|||+..+.-...|+.--.+
T Consensus 276 ~~~~i~~~~t~sf~V~IeN~g~~~d~y~L---e~~g~pe~w~~---~Fteg~~~vt~vkL~~gE~kdvtleV~ps~na~p 349 (513)
T COG1470 276 IYLEISPSTTASFTVSIENRGKQDDEYAL---ELSGLPEGWTA---EFTEGELRVTSVKLKPGEEKDVTLEVYPSLNATP 349 (513)
T ss_pred ceeEEccCCceEEEEEEccCCCCCceeEE---EeccCCCCcce---EEeeCceEEEEEEecCCCceEEEEEEecCCCCCC
Confidence 44677889999999999999987665543 233 4777655 55554443 56899999999999999999999
Q ss_pred cceeEEEEEEEeecC-Ccee----EEEEecceEEEEe
Q psy4382 85 RPFGLSVNLQYRDEH-NNFF----YEGIYNETVNIIT 116 (258)
Q Consensus 85 ~p~~L~l~l~Y~~~~-~~~~----~~~~~n~~v~~~t 116 (258)
..|.+.|+..=..+- -.+. +.+.||+.|++.+
T Consensus 350 G~Ynv~I~A~s~s~v~~e~~lki~~~g~~~~~v~l~~ 386 (513)
T COG1470 350 GTYNVTITASSSSGVTRELPLKIKNTGSYNELVKLDN 386 (513)
T ss_pred CceeEEEEEeccccceeeeeEEEEeccccceeEEccC
Confidence 999999888443211 1112 2567888888653
No 34
>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=51.85 E-value=1.2e+02 Score=29.79 Aligned_cols=69 Identities=16% Similarity=0.313 Sum_probs=55.3
Q ss_pred eeecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecc----------------eeeeceeecCCceeEEEE
Q psy4382 11 MDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFS----------------TIIYNRIVKPGHEATLGY 74 (258)
Q Consensus 11 ~~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfT----------------a~~~~~~V~pg~~at~~Y 74 (258)
.+..+|+++++-|.++++...++.+..+.=.|..... +..+++=. ...-+..+.||+...|.+
T Consensus 21 ~~~~~~~~~~~ql~i~S~~~~pi~~s~l~V~fs~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~l~p~~~kv~~~ 99 (554)
T PF07919_consen 21 SEGKVGEPVQFQLSIRSNAPSPIRFSSLKVNFSGSLY-PIVISHSDADASSADSSTSSGSPLSGSADLTLSPGQTKVFSF 99 (554)
T ss_pred CCccCCCeEEEEEEEEcCCCCCEEeeEEEEEeeCCCC-CceEeccccccccccCcccccccccCccceEEeecceEEEEE
Confidence 3678999999999999999999999999999998754 34444433 112246899999999999
Q ss_pred EEeeCc
Q psy4382 75 SFVPAE 80 (258)
Q Consensus 75 ~F~p~~ 80 (258)
.|.+.+
T Consensus 100 ~~~~~~ 105 (554)
T PF07919_consen 100 KFVPRE 105 (554)
T ss_pred EEeccc
Confidence 998887
No 35
>PF06280 DUF1034: Fn3-like domain (DUF1034); InterPro: IPR010435 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain of unknown function is present in bacterial and plant peptidases belonging to MEROPS peptidase family S8 (subfamily S8A subtilisin, clan SB). It is C-terminal to and adjacent to the S8 peptidase domain and can be found in conjunction with the PA (Protease associated) domain (IPR003137 from INTERPRO) and additionally in Gram-positive bacteria with the surface protein anchor domain (IPR001899 from INTERPRO).; GO: 0004252 serine-type endopeptidase activity, 0005618 cell wall, 0016020 membrane; PDB: 3EIF_A 1XF1_B.
Probab=51.17 E-value=1.2e+02 Score=23.78 Aligned_cols=67 Identities=16% Similarity=0.246 Sum_probs=36.6
Q ss_pred CceEEEEEEEEeCCCCcEEEEEEee-eeeccc----ccceEEEe------cceeeeceeecCCceeEEEEEEeeCccc
Q psy4382 16 GSVVEFLVGFTNKGKQDFTLDTLDA-SLRYPM----DFNFYIQN------FSTIIYNRIVKPGHEATLGYSFVPAEAV 82 (258)
Q Consensus 16 G~~~~~lv~~~N~g~~~~tV~~i~g-Sl~~P~----d~~~~iqN------fTa~~~~~~V~pg~~at~~Y~F~p~~~~ 82 (258)
|...++-+.++|.++++.+...-.. .+..-. .......+ .+...-...|+||+++++..+|.+...+
T Consensus 7 ~~~~~~~itl~N~~~~~~ty~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~vTV~ag~s~~v~vti~~p~~~ 84 (112)
T PF06280_consen 7 GNKFSFTITLHNYGDKPVTYTLSHVPVLTDKTDTEEGYSILVPPVPSISTVSFSPDTVTVPAGQSKTVTVTITPPSGL 84 (112)
T ss_dssp -SEEEEEEEEEE-SSS-EEEEEEEE-EEEEEE--ETTEEEEEEEE----EEE---EEEEE-TTEEEEEEEEEE--GGG
T ss_pred CCceEEEEEEEECCCCCEEEEEeeEEEEeeEeeccCCcccccccccceeeEEeCCCeEEECCCCEEEEEEEEEehhcC
Confidence 4458999999999997775443333 443322 11222222 2222234789999999999999885433
No 36
>PF14016 DUF4232: Protein of unknown function (DUF4232)
Probab=46.25 E-value=1.3e+02 Score=24.32 Aligned_cols=68 Identities=18% Similarity=0.110 Sum_probs=42.5
Q ss_pred cCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccce-----EEEecceeeeceeecCCceeEEEEEEeeCcccCC
Q psy4382 14 PAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNF-----YIQNFSTIIYNRIVKPGHEATLGYSFVPAEAVAG 84 (258)
Q Consensus 14 ~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~-----~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~~~~ 84 (258)
-.|+. .+.|.|+|.+..+.+|.+--+ +..-..... ..+.-. ..--..|.||+++++.=.+......++
T Consensus 16 ~~g~~-~~~l~~tN~s~~~C~l~G~P~-v~~~~~~g~~~~~~~~~~~~-~~~~vtL~PG~sA~a~l~~~~~~~~~~ 88 (131)
T PF14016_consen 16 GAGQR-HATLTFTNTSDTPCTLYGYPG-VALVDADGAPLGVPAVREGP-PPRPVTLAPGGSAYAGLRWSNVGSGGG 88 (131)
T ss_pred CCCcc-EEEEEEEECCCCcEEeccCCc-EEEECCCCCcCCccccccCC-CCCcEEECCCCEEEEEEEEecCCCCCC
Confidence 44555 999999999999998876533 221111111 111111 111278999999999999977665544
No 37
>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=42.92 E-value=47 Score=32.89 Aligned_cols=63 Identities=21% Similarity=0.273 Sum_probs=36.5
Q ss_pred cCCceEEEEEEEEeCCCCcEEEEE-Eeeeeec--ccc------cceEEEecceeee--ceeecCCceeEEEEEE
Q psy4382 14 PAGSVVEFLVGFTNKGKQDFTLDT-LDASLRY--PMD------FNFYIQNFSTIIY--NRIVKPGHEATLGYSF 76 (258)
Q Consensus 14 ~~G~~~~~lv~~~N~g~~~~tV~~-i~gSl~~--P~d------~~~~iqNfTa~~~--~~~V~pg~~at~~Y~F 76 (258)
+.|...++-+.++|+|++++.+.- ..|.+|. |.- +...+-.-...+. +..+.|||+.++.-+-
T Consensus 260 vpgR~l~~~l~VtN~g~~pv~LgeF~tA~vrFln~~v~~~~~~~P~~l~A~~gL~vs~~~pI~PGETrtl~V~a 333 (381)
T PF04744_consen 260 VPGRTLTMTLTVTNNGDSPVRLGEFNTANVRFLNPDVPTDDPDYPDELLAERGLSVSDNSPIAPGETRTLTVEA 333 (381)
T ss_dssp SSSSEEEEEEEEEEESSS-BEEEEEESSS-EEE-TTT-SS-S---TTTEETT-EEES--S-B-TT-EEEEEEEE
T ss_pred cCCcEEEEEEEEEcCCCCceEeeeEEeccEEEeCcccccCCCCCchhhhccCcceeCCCCCcCCCceEEEEEEe
Confidence 568899999999999999998754 4444443 321 1111112222333 3689999999998776
No 38
>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=42.49 E-value=47 Score=32.96 Aligned_cols=61 Identities=16% Similarity=0.294 Sum_probs=41.4
Q ss_pred cCCceEEEEEEEEeCCCCcEEEE-EEeeeee--ccc-------cc-ceEEEecceeee--ceeecCCceeEEEEEE
Q psy4382 14 PAGSVVEFLVGFTNKGKQDFTLD-TLDASLR--YPM-------DF-NFYIQNFSTIIY--NRIVKPGHEATLGYSF 76 (258)
Q Consensus 14 ~~G~~~~~lv~~~N~g~~~~tV~-~i~gSl~--~P~-------d~-~~~iqNfTa~~~--~~~V~pg~~at~~Y~F 76 (258)
+.|+..++-+.+||+|++++.+- .-+|.+| +|. ++ .+++-+ .... +..+.|||+.++.-.-
T Consensus 279 VPGR~l~~~~~VTN~g~~~vrlgEF~TA~vRFlN~~~v~~~~~~yP~~lla~--GL~v~d~~pI~PGETr~v~v~a 352 (399)
T TIGR03079 279 VPGRALRVTMEITNNGDQVISIGEFTTAGIRFMNANGVRVLDPDYPRELLAE--GLEVDDQSAIAPGETVEVKMEA 352 (399)
T ss_pred cCCcEEEEEEEEEcCCCCceEEEeEeecceEeeCcccccccCCCChHHHhhc--cceeCCCCCcCCCcceEEEEEE
Confidence 46899999999999999999773 3444444 331 11 234554 3333 3679999999988554
No 39
>PF11044 TMEMspv1-c74-12: Plectrovirus spv1-c74 ORF 12 transmembrane protein; InterPro: IPR022743 This is a group of proteins expressed by Plectroviruses. The Plectroviruses are single-stranded DNA viruses belonging to the Inoviridae. This entry represents putative transmembrane proteins of unknown function.
Probab=41.39 E-value=18 Score=25.70 Aligned_cols=22 Identities=14% Similarity=-0.011 Sum_probs=13.7
Q ss_pred eehhHHHHHHHHHHHHHHhhhh
Q psy4382 170 TFFLYVFLGACVVLLLVIGQHF 191 (258)
Q Consensus 170 ~iFLYlfL~a~~gll~y~~y~~ 191 (258)
+||--++++|+|+-++...|+-
T Consensus 7 ~iFsvvIil~If~~iGl~IyQk 28 (49)
T PF11044_consen 7 TIFSVVIILGIFAWIGLSIYQK 28 (49)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 5777777877765444444543
No 40
>PF12742 Gryzun-like: Gryzun, putative Golgi trafficking
Probab=40.26 E-value=35 Score=25.21 Aligned_cols=21 Identities=29% Similarity=0.585 Sum_probs=18.0
Q ss_pred eceeecCCceeEEEEEEeeCc
Q psy4382 60 YNRIVKPGHEATLGYSFVPAE 80 (258)
Q Consensus 60 ~~~~V~pg~~at~~Y~F~p~~ 80 (258)
.+..+-||++.+++|+|+|=.
T Consensus 26 ~~~~~~~~~~~~i~~~Fipl~ 46 (57)
T PF12742_consen 26 MNFHMWPGQKFEIPYNFIPLT 46 (57)
T ss_pred eEEEEccCceEEEEEEEEEee
Confidence 457899999999999998864
No 41
>COG5246 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=39.02 E-value=35 Score=30.96 Aligned_cols=62 Identities=18% Similarity=0.261 Sum_probs=38.9
Q ss_pred EEEeeCcccCCcceeEEEEEEEeecC--CceeEEE--EecceEEE--EeecccccccccccCCCCccc
Q psy4382 74 YSFVPAEAVAGRPFGLSVNLQYRDEH--NNFFYEG--IYNETVNI--ITLGYSFVPAEAVAGRPFGLS 135 (258)
Q Consensus 74 Y~F~p~~~~~~~p~~L~l~l~Y~~~~--~~~~~~~--~~n~~v~~--~t~~~~~~p~e~~~g~p~g~~ 135 (258)
|+...-..-.+..+||.+.++|.|.. .-|++++ ++.+.|.. ..+.|++++.|++----|-+.
T Consensus 123 ykv~~~~epk~G~~Gl~iqvnY~Dd~a~~~P~yRivs~lEq~ve~~d~~f~yLV~a~ePyEnIafk~~ 190 (222)
T COG5246 123 YKVRSLVEPKGGRRGLGIQVNYEDDLAEEMPQYRIVSSLEQNVEEYDESFRYLVFACEPYENIAFKFE 190 (222)
T ss_pred eeEEEeecCCCCceeeEEEEeccchhhccCcceehhhhhhhcchhhcccceEEEEEeccccceeeecC
Confidence 44433332346889999999999665 5677765 56555553 236677777776655444444
No 42
>COG2847 Copper(I)-binding protein [Inorganic ion transport and metabolism]
Probab=36.86 E-value=1.1e+02 Score=26.50 Aligned_cols=61 Identities=15% Similarity=0.251 Sum_probs=41.4
Q ss_pred eeecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEe-----cceeeeceeecCCceeEE
Q psy4382 11 MDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQN-----FSTIIYNRIVKPGHEATL 72 (258)
Q Consensus 11 ~~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqN-----fTa~~~~~~V~pg~~at~ 72 (258)
...|.....-+-+++.|++++++++.+++.-...-.+-...+-+ .-.+. +..||||....|
T Consensus 35 a~~pg~~~~a~~~ti~N~~~~~~~Lv~v~s~~a~~~ElHe~i~~~gvmkMr~v~-~i~Ipa~~~v~l 100 (151)
T COG2847 35 ATPPGAKMGAAFMTITNNGDKDDRLVGVSSPIAARAELHETIHDGGVMKMRKVP-GIVIPAGGTVEL 100 (151)
T ss_pred ecCCCCcceeEEEEEeCCCCCCceEEEEecCccceeEEEEEEecCCeEEEEEcC-cEEECCCceEEe
Confidence 34566666777889999999999999988765443322222222 33344 688999987766
No 43
>PF14851 FAM176: FAM176 family
Probab=36.40 E-value=51 Score=28.68 Aligned_cols=25 Identities=36% Similarity=0.574 Sum_probs=19.1
Q ss_pred CceeehhHHHHHHHHHHHHHHhhhh
Q psy4382 167 DGETFFLYVFLGACVVLLLVIGQHF 191 (258)
Q Consensus 167 D~q~iFLYlfL~a~~gll~y~~y~~ 191 (258)
.||.+-||+++.-|+||++-+..-.
T Consensus 18 ~PE~~aLYFv~gVC~GLlLtLcllV 42 (153)
T PF14851_consen 18 NPERFALYFVSGVCAGLLLTLCLLV 42 (153)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5788899999988888876655543
No 44
>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=35.60 E-value=3.6e+02 Score=26.52 Aligned_cols=80 Identities=11% Similarity=0.113 Sum_probs=53.5
Q ss_pred ecCCceEEEEEEEEeCCCCcEEEEEEeeeee-------cccccceEEEec--------ceeeec---eeecCCceeEEEE
Q psy4382 13 LPAGSVVEFLVGFTNKGKQDFTLDTLDASLR-------YPMDFNFYIQNF--------STIIYN---RIVKPGHEATLGY 74 (258)
Q Consensus 13 l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~-------~P~d~~~~iqNf--------Ta~~~~---~~V~pg~~at~~Y 74 (258)
..-||.+.+-+.+.|+++....+....-.++ ...+ .-+.+. .....+ -.+.+|++.+...
T Consensus 186 ~l~gE~~~i~i~I~n~e~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~lg~l~~~~s~~~~l 263 (554)
T PF07919_consen 186 ALTGEFYPIPITISNNEDEEASGVLEVRLLHPSQLGVSSEET--EDLSQVNWDSDKDDEPLFLGIPLGELAPGSSITVTL 263 (554)
T ss_pred eEcCCEEEEEEEEEcCCCccceeEEEEEEecccccccccccC--ccceecccccccccchhccCcccccCCCCCcEEEEE
Confidence 3679999999999999988877665555551 1111 111111 111112 2468999998888
Q ss_pred EEeeCcccCCcceeEEEEEEEee
Q psy4382 75 SFVPAEAVAGRPFGLSVNLQYRD 97 (258)
Q Consensus 75 ~F~p~~~~~~~p~~L~l~l~Y~~ 97 (258)
.+. ...+.++.|.+.+.|..
T Consensus 264 ~i~---~~~~~~~~L~i~~~Y~l 283 (554)
T PF07919_consen 264 YIR---TSRPGEYELSISVSYHL 283 (554)
T ss_pred EEE---eCCceeEEEEEEEEEEE
Confidence 887 34678899999999975
No 45
>PRK05461 apaG CO2+/MG2+ efflux protein ApaG; Reviewed
Probab=35.38 E-value=1.5e+02 Score=24.76 Aligned_cols=54 Identities=11% Similarity=0.158 Sum_probs=34.6
Q ss_pred EEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEEE
Q psy4382 20 EFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYS 75 (258)
Q Consensus 20 ~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~ 75 (258)
.-.|.+.|++++.+++..-.=-+.+-...-..|..-=.+---=.+.||+ +|.|+
T Consensus 32 ~Y~ItI~N~~~~~vQL~~R~W~I~d~~g~~~~V~G~GVVG~qP~L~PGe--~F~Y~ 85 (127)
T PRK05461 32 AYTITIENLGRVPVQLLSRHWLITDANGRVQEVRGEGVVGEQPVLAPGE--SFEYT 85 (127)
T ss_pred EEEEEEEECCCCCEEEEeeeEEEEECCCCEEEEECCceecCCceECCCC--CeEEe
Confidence 4467889999999888876666666544334444332332224689998 56665
No 46
>PF13598 DUF4139: Domain of unknown function (DUF4139)
Probab=33.60 E-value=2.1e+02 Score=26.17 Aligned_cols=58 Identities=17% Similarity=0.275 Sum_probs=37.4
Q ss_pred eEEEEEEEEeCCCCcEEEEEEeeeeecccccc-eE------------EEecceeeeceeecCCceeEEEEEEee
Q psy4382 18 VVEFLVGFTNKGKQDFTLDTLDASLRYPMDFN-FY------------IQNFSTIIYNRIVKPGHEATLGYSFVP 78 (258)
Q Consensus 18 ~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~-~~------------iqNfTa~~~~~~V~pg~~at~~Y~F~p 78 (258)
..+..+.++|+.+.+++|...+- -|..-+ .+ ..+--.......|+||++.+|.|.|.-
T Consensus 243 ~~~~~itv~N~~~~~v~v~v~d~---iPvs~~~~I~V~~~~~~~~~~~~~~g~~~W~~~l~~g~~~~l~~~y~v 313 (317)
T PF13598_consen 243 TYEYTITVRNNKDEPVTVTVEDQ---IPVSEDEDIKVELLEPPEPNEDEKDGILEWKVTLPPGESRTLEFSYEV 313 (317)
T ss_pred EEEEEEEEECCCCCCEEEEEEeC---CCCCCCceEEEEEcCCCCCcccCCCCEEEEEEEECCCCEEEEEEEEEE
Confidence 45678899999999998777653 232111 11 112222334578999999999999853
No 47
>PF15179 Myc_target_1: Myc target protein 1
Probab=32.30 E-value=36 Score=30.77 Aligned_cols=43 Identities=23% Similarity=0.131 Sum_probs=25.2
Q ss_pred eeeeeEEEEecCCCcCceeehhHHHH---HHHHHHHHHHhhhhhhh
Q psy4382 152 IYNETVNIIEIDEGLDGETFFLYVFL---GACVVLLLVIGQHFLYS 194 (258)
Q Consensus 152 vfN~TVtVvE~~~sfD~q~iFLYlfL---~a~~gll~y~~y~~~~~ 194 (258)
+.|+|-...|..++||.+-+.|-+.+ +|++.|.++|+.-+|.+
T Consensus 2 A~N~T~~~~~~~~~f~~~~lIlaF~vSm~iGLviG~li~~LltwlS 47 (197)
T PF15179_consen 2 ANNTTSLLLEWLENFDWEDLILAFCVSMAIGLVIGALIWALLTWLS 47 (197)
T ss_pred CCCcccccccchhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56888888899999987655444433 33333333334334443
No 48
>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=31.03 E-value=2.5e+02 Score=21.71 Aligned_cols=77 Identities=16% Similarity=0.190 Sum_probs=50.1
Q ss_pred CCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeee-ceeecCCceeEEEEEEeeCccc---CCcceeEE
Q psy4382 15 AGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIY-NRIVKPGHEATLGYSFVPAEAV---AGRPFGLS 90 (258)
Q Consensus 15 ~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~-~~~V~pg~~at~~Y~F~p~~~~---~~~p~~L~ 90 (258)
++....+.+.|+|+...+++=..+. +--|..+. +..... +..++|+.+.+-...+.- ..+ .+.+..+.
T Consensus 22 ~~~~~~i~~~f~N~s~~~it~f~~q--~avpk~~~-----l~l~~~s~~~i~p~~~i~Q~~~v~~-~~~~~~~~~~l~~~ 93 (115)
T PF02883_consen 22 NPNQGRIKLTFGNKSSQPITNFSFQ--AAVPKSFK-----LQLQPPSSSTIPPGQQITQVIKVEN-SPFSEPTPKPLKPR 93 (115)
T ss_dssp ETTEEEEEEEEEE-SSS-BEEEEEE--EEEBTTSE-----EEEEESS-SSB-TTTEEEEEEEEEE-SS-BSTTSSTTEEE
T ss_pred CCCEEEEEEEEEECCCCCcceEEEE--EEeccccE-----EEEeCCCCCeeCCCCeEEEEEEEEE-eecccCCCCCcCeE
Confidence 6888999999999988777543333 33343322 222223 578899999988888876 222 35778899
Q ss_pred EEEEEeecC
Q psy4382 91 VNLQYRDEH 99 (258)
Q Consensus 91 l~l~Y~~~~ 99 (258)
+.+.|..+.
T Consensus 94 ~~vsy~~~g 102 (115)
T PF02883_consen 94 LRVSYNVGG 102 (115)
T ss_dssp EEEEEEETT
T ss_pred EEEEEEECC
Confidence 999998887
No 49
>COG4743 Predicted membrane protein [Function unknown]
Probab=30.32 E-value=2.5e+02 Score=26.90 Aligned_cols=37 Identities=22% Similarity=0.441 Sum_probs=27.3
Q ss_pred ceeecCCceEEEEEEEEeCCCCcEE----EEEEeeeeeccc
Q psy4382 10 NMDLPAGSVVEFLVGFTNKGKQDFT----LDTLDASLRYPM 46 (258)
Q Consensus 10 ~~~l~~G~~~~~lv~~~N~g~~~~t----V~~i~gSl~~P~ 46 (258)
..++..|+..+++||+.|++-.++| +-.+.-+++.+.
T Consensus 217 Ptn~t~ge~g~VivGivNhEhRnvtY~meirl~n~tl~~~t 257 (316)
T COG4743 217 PTNLTVGERGEVIVGIVNHEHRNVTYRMEIRLVNLTLNFTT 257 (316)
T ss_pred CcceecCCceEEEEEeecccccceeEEEEEEEecceecccc
Confidence 4568899999999999999976654 334455666653
No 50
>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=29.97 E-value=1.9e+02 Score=32.24 Aligned_cols=80 Identities=23% Similarity=0.272 Sum_probs=0.0
Q ss_pred CccceeecCCceEEEEEEEEeCCCCcEEEEEEeeeee----------------------cccccceEEEecceeeeceee
Q psy4382 7 VYINMDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLR----------------------YPMDFNFYIQNFSTIIYNRIV 64 (258)
Q Consensus 7 ~~~~~~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~----------------------~P~d~~~~iqNfTa~~~~~~V 64 (258)
......+-.||..++.|+++|.+ ...|+.+.=+|. ...-.-...+++.-..-. .+
T Consensus 789 ~~~~~mlleGE~~~~~ItL~N~S--~~pvd~l~~sf~DS~~~~~~~~l~~k~l~~~e~yelE~~l~~~~~~~i~~~~-~I 865 (1185)
T PF08626_consen 789 TQGALMLLEGEKQTFTITLRNTS--SVPVDFLSFSFQDSTIEPLQKALSNKDLSPDELYELEWQLFKLPAFRILNKP-PI 865 (1185)
T ss_pred CCcceEEECCcEEEEEEEEEECC--ccccceEEEEEEeccHHHHhhhhhcccCChhhhhhhhhhhhcCcceeecccC-cc
Q ss_pred cCCceeEEEEEEeeCcccCCcce-----eEEEEEEE
Q psy4382 65 KPGHEATLGYSFVPAEAVAGRPF-----GLSVNLQY 95 (258)
Q Consensus 65 ~pg~~at~~Y~F~p~~~~~~~p~-----~L~l~l~Y 95 (258)
+||++++|++. ..|++. ...+.+.|
T Consensus 866 ~Pg~~~~~~~~------~~~~~~~~~~~~~~i~l~y 895 (1185)
T PF08626_consen 866 PPGESATFTVE------VDGKPGPIQLTYADIQLEY 895 (1185)
T ss_pred CCCCEEEEEEE------ecCcccccceeeeeEEEEe
No 51
>PF10622 Ehbp: Energy-converting hydrogenase B subunit P (EhbP); InterPro: IPR019597 Ehb (energy-converting hydrogenase B) is an methanogenic archaeal enzyme that functions in one of the metabolic pathways involved in methanol reduction to methane. This entry contains subunit P of Ehb.
Probab=28.78 E-value=13 Score=28.99 Aligned_cols=10 Identities=30% Similarity=0.680 Sum_probs=8.8
Q ss_pred CCCCCccChh
Q psy4382 219 DIDYDWIPKE 228 (258)
Q Consensus 219 ~yD~eWIP~~ 228 (258)
.||+|||.+|
T Consensus 39 v~d~~WIE~H 48 (78)
T PF10622_consen 39 VYDEEWIEEH 48 (78)
T ss_pred ccCHHHHHHH
Confidence 5999999887
No 52
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=28.64 E-value=35 Score=28.83 Aligned_cols=57 Identities=12% Similarity=0.096 Sum_probs=39.1
Q ss_pred ecccccccccccCCCCccc----------ccceecccCCceeeeeeeeeeEEEEecCCCcCceeehhHHH
Q psy4382 117 LGYSFVPAEAVAGRPFGLS----------VNLQYRDEHNNFFYEGIYNETVNIIEIDEGLDGETFFLYVF 176 (258)
Q Consensus 117 ~~~~~~p~e~~~g~p~g~~----------i~~~~~d~~g~~y~~~vfN~TVtVvE~~~sfD~q~iFLYlf 176 (258)
|.|..|.+|+.+...=++- |.-+.+|..=..|-+.=|=+.|.- +|+. ++.+++||+.
T Consensus 41 LRC~vCqnqsiadSna~iA~dmR~~Vr~~i~~G~sd~eI~~~~v~RYG~~Vl~-~Pp~--~~~t~~LW~~ 107 (126)
T PRK10144 41 LRCPQCQNQNLLESNAPVAVSMRHQVYSMVAEGKSEVEIIGWMTERYGDFVRY-NPPL--TGQTLVLWAL 107 (126)
T ss_pred CCCCCCCCCChhhcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEe-cCCC--CcchHHHHHH
Confidence 8899999999999877665 444444443334555556555644 4554 8999999984
No 53
>PF04379 DUF525: Protein of unknown function (DUF525); InterPro: IPR007474 This domain is found in the bacterial protein ApaG and at the C termini of some F-box proteins (IPR001810 from INTERPRO). F-box proteins contain a carboxy-terminal domain that interacts with protein substrates []. The ApaG domain is ~125 amino acids in length, and is named after the bacterial ApaG protein, of which it forms the core. The Salmonella typhimurium ApaG domain protein, CorD, is involved in Co(2+) resistance and Mg(2+) efflux. Tertiary structures from different ApaG proteins show a fold of several beta-sheets. The ApaG domain may be involved in protein-protein interactions which could be implicated in substrate-specificity [, , ].; PDB: 2F1E_A 1XVS_A 1TZA_A 1XQ4_D.
Probab=28.58 E-value=2.5e+02 Score=22.01 Aligned_cols=55 Identities=9% Similarity=0.140 Sum_probs=28.7
Q ss_pred EEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEEEE
Q psy4382 20 EFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSF 76 (258)
Q Consensus 20 ~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F 76 (258)
.--|.++|.++.++.|..-.=-+.+....-..|..-=.+--.=.|.||+ +|.|+=
T Consensus 15 ~Y~I~I~N~~~~~vqL~sR~W~I~d~~g~~~~V~G~GVVG~~P~L~pGe--~f~Y~S 69 (90)
T PF04379_consen 15 AYRIRIENHSDESVQLLSRHWIITDADGHVEEVEGEGVVGQQPVLAPGE--SFEYTS 69 (90)
T ss_dssp EEEEEEEE-SSS-EEEEEEEEEEEETTS-EEEEEEESBTTB--EE-TTE--EEEEEE
T ss_pred EEEEEEEECCCCCEEEEccEEEEEeCCCCEEEEECCceEccCceECCCC--cEEEcC
Confidence 4467889999998877765555555444323333211111124689999 777753
No 54
>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=28.05 E-value=2.7e+02 Score=21.04 Aligned_cols=75 Identities=21% Similarity=0.260 Sum_probs=47.6
Q ss_pred CceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEEEEeeCcccCCcceeEEEEEEE
Q psy4382 16 GSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAEAVAGRPFGLSVNLQY 95 (258)
Q Consensus 16 G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~~~~~p~~L~l~l~Y 95 (258)
+....+.+.|.|+...+++=..+.. .-|..+.--++..+ +..++||++.+-...+... .+.+..+.+.+.|
T Consensus 17 ~~~~~i~~~~~N~s~~~it~f~~~~--avpk~~~l~l~~~s----~~~l~p~~~i~q~~~i~~~---~~~~~~~~~~vsy 87 (104)
T smart00809 17 PGLIRITLTFTNKSPSPITNFSFQA--AVPKSLKLQLQPPS----SPTLPPGGQITQVLKVENP---GKFPLRLRLRLSY 87 (104)
T ss_pred CCeEEEEEEEEeCCCCeeeeEEEEE--EcccceEEEEcCCC----CCccCCCCCEEEEEEEECC---CCCCEEEEEEEEE
Confidence 4568899999999988776555544 34654322222222 3578999876555555433 2456778888888
Q ss_pred eecC
Q psy4382 96 RDEH 99 (258)
Q Consensus 96 ~~~~ 99 (258)
..+.
T Consensus 88 ~~~g 91 (104)
T smart00809 88 LLGG 91 (104)
T ss_pred EECC
Confidence 8765
No 55
>PF05283 MGC-24: Multi-glycosylated core protein 24 (MGC-24); InterPro: IPR007947 CD164 is a mucin-like receptor, or sialomucin, with specificity in receptor/ ligand interactions that depends on the structural characteristics of the mucin-like receptor. Its functions include mediating, or regulating, haematopoietic progenitor cell adhesion and the negative regulation of their growth and/or-differentiation. It exists in the native state as a disulphide- linked homodimer of two 80-85kDa subunits. It is usually expressed by CD34+ and CD341o/- haematopoietic stem cells and associated microenvironmental cells. It contains, in its extracellular region, two mucin domains (I and II) linked by a non-mucin domain, which has been predicted to contain intra- disulphide bridges. This receptor may play a key role in haematopoiesis by facilitating the adhesion of human CD34+ cells to bone marrow stroma and by negatively regulating CD34+ CD341o/- haematopoietic progenitor cell proliferation. These effects involve the CD164 class I and/or II epitopes recognised by the monoclonal antibodies (mAbs) 105A5 and 103B2/9E10. These epitopes are carbohydrate-dependent and are located on the N-terminal mucin domain I [, ]. It has been found that murine MGC-24v and rat endolyn share significant sequence similarities with human CD164. However, CD164 lacks the consensus glycosaminoglycan (GAG)-attachment site found in MGC-24; it is possible that GAG-association is responsible for the high molecular weight of the epithelial-derived MGC-24 glycoprotein []. Genomic structure studies have placed CD164 within the mucin-subgroup that comprises multiple exons, and demonstrate the diverse chromosomal distribution of this family of molecules. Molecules with such multiple exons may have sophisticated regulatory mechanisms that involve not only post-translational modifications of the oligosaccharide side chains, but also differential exon usage. Although differences in the intron and exon sizes are seen between the mouse and human genes, the predicted proteins are similar in size and structure, maintaining functionally important motifs that regulate cell proliferation or subcellular distribution []. CD164 is a gene whose expression depends on differential usage of poly- adenylation sites within the 3'-UTR. The conserved distribution of the 3.2- and 1.2-kb CD164 transcripts between mouse and human suggests that (i) a mechanism may exist to regulate tissue-specific polyadenylation, and (ii) differences in polyadenylation are important for the expression and function of CD164 in different tissues. Two other aspects of the structure of CD164 are of particular interest. First, it shares one of several conserved features of a cytokine-binding pocket - in this respect, it is notable that evidence exists for a class of cell-surface sialomucin modulators that directly interact with growth factor receptors to regulate their response to physiological ligands. Second, its cytoplasmic tail contains a C-terminal YHTL motif found in many endocytic membrane proteins or receptors. These Tyr-based motifs bind to adaptor proteins, which mediate the sorting of membrane proteins into transport vesicles from the plasma membrane to the endosomes, and between intracellular compartments.
Probab=27.75 E-value=57 Score=29.23 Aligned_cols=30 Identities=17% Similarity=0.268 Sum_probs=22.1
Q ss_pred CCC-cCceeehhHHHHHHHHHHHHHHhhhhh
Q psy4382 163 DEG-LDGETFFLYVFLGACVVLLLVIGQHFL 192 (258)
Q Consensus 163 ~~s-fD~q~iFLYlfL~a~~gll~y~~y~~~ 192 (258)
..+ ||.-.++-=++|.-.+-.++||+|+|+
T Consensus 154 ~~s~FD~~SFiGGIVL~LGv~aI~ff~~KF~ 184 (186)
T PF05283_consen 154 KKSTFDAASFIGGIVLTLGVLAIIFFLYKFC 184 (186)
T ss_pred CCCCCchhhhhhHHHHHHHHHHHHHHHhhhc
Confidence 345 999998887777544555689999885
No 56
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=27.09 E-value=64 Score=22.17 Aligned_cols=11 Identities=0% Similarity=0.087 Sum_probs=5.2
Q ss_pred HHHHHHHHHhh
Q psy4382 179 ACVVLLLVIGQ 189 (258)
Q Consensus 179 a~~gll~y~~y 189 (258)
+++.|+.+++|
T Consensus 20 ~~F~gi~~w~~ 30 (49)
T PF05545_consen 20 VFFIGIVIWAY 30 (49)
T ss_pred HHHHHHHHHHH
Confidence 34444445444
No 57
>PF06679 DUF1180: Protein of unknown function (DUF1180); InterPro: IPR009565 This entry consists of several hypothetical eukaryotic proteins thought to be membrane proteins. Their function is unknown.
Probab=26.15 E-value=1.2e+02 Score=26.53 Aligned_cols=21 Identities=24% Similarity=0.403 Sum_probs=15.0
Q ss_pred hHHHHHHHHHHHHHHhhhhhh
Q psy4382 173 LYVFLGACVVLLLVIGQHFLY 193 (258)
Q Consensus 173 LYlfL~a~~gll~y~~y~~~~ 193 (258)
+|++.+.+..+++||+...+.
T Consensus 98 ~~Vl~g~s~l~i~yfvir~~R 118 (163)
T PF06679_consen 98 LYVLVGLSALAILYFVIRTFR 118 (163)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 366666666677888888765
No 58
>PRK11875 psbT photosystem II reaction center protein T; Reviewed
Probab=25.71 E-value=84 Score=20.62 Aligned_cols=18 Identities=17% Similarity=0.414 Sum_probs=12.6
Q ss_pred hhHHHHHHHHHHHHHHhh
Q psy4382 172 FLYVFLGACVVLLLVIGQ 189 (258)
Q Consensus 172 FLYlfL~a~~gll~y~~y 189 (258)
+.|+||+++..++++|+-
T Consensus 4 l~Ytfll~~tlgiiFFAI 21 (31)
T PRK11875 4 FAYILILTLALVTLFFAI 21 (31)
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 578888877666666654
No 59
>PF02221 E1_DerP2_DerF2: ML domain; InterPro: IPR003172 The MD-2-related lipid-recognition (ML) domain is implicated in lipid recognition, particularly in the recognition of pathogen related products. It has an immunoglobulin-like beta-sandwich fold similar to that of E-set Ig domains. This domain is present in the following proteins: Epididymal secretory protein E1 (also known as Niemann-Pick C2 protein), which is known to bind cholesterol. Niemann-Pick disease type C2 is a fatal hereditary disease characterised by accumulation of low-density lipoprotein-derived cholesterol in lysosomes []. House-dust mite allergen proteins such as Der f 2 from Dermatophagoides farinae and Der p 2 from Dermatophagoides pteronyssinus []. ; PDB: 2AG9_B 1G13_B 2AG2_B 2AG4_A 1TJJ_C 1PU5_C 1PUB_A 2AF9_A 3T6Q_D 3M7O_B ....
Probab=25.02 E-value=3.4e+02 Score=21.23 Aligned_cols=83 Identities=16% Similarity=0.206 Sum_probs=48.6
Q ss_pred eeecCCceEEEEEEE-EeCCC-CcEE--EEEEeee-eecccc----cceEEEecceeeeceeecCCceeEEEEEEeeCcc
Q psy4382 11 MDLPAGSVVEFLVGF-TNKGK-QDFT--LDTLDAS-LRYPMD----FNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAEA 81 (258)
Q Consensus 11 ~~l~~G~~~~~lv~~-~N~g~-~~~t--V~~i~gS-l~~P~d----~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~ 81 (258)
..+..|+..++-+.| +.+.. +..+ |...-+. ++-|.- ....=++++.....=.+.+|+..++.+++.-...
T Consensus 26 C~~~~g~~~~i~~~f~~~~~~~~~~~~~v~~~~~g~~~ip~~g~~~~~d~C~~~~~~~~~CPi~~G~~~~~~~~~~i~~~ 105 (134)
T PF02221_consen 26 CPLKRGQPVTITIDFNTSKKDSDGLKVKVEAKVGGWIPIPFPGLCEYYDLCDNLFGNGLSCPIKAGEYYTYTYTIPIPKI 105 (134)
T ss_dssp EEEETTSEEEEEEEEEECSSBBSSEEEEEEEEETTEEEEEEESSSCEEEEEGTSCCSSTTSTBTTTEEEEEEEEEEESTT
T ss_pred CcccCCCEEEEEEEEEEccccccCCEEEEEEEECCcEEEccccccCccchhhhcccccccCccCCCcEEEEEEEEEcccc
Confidence 367889999999999 66654 3343 3333332 332321 1111222221112346999999999999976676
Q ss_pred cCCcceeEEEEE
Q psy4382 82 VAGRPFGLSVNL 93 (258)
Q Consensus 82 ~~~~p~~L~l~l 93 (258)
+....+.+.+.+
T Consensus 106 ~p~~~~~i~~~l 117 (134)
T PF02221_consen 106 YPPGKYTIQWKL 117 (134)
T ss_dssp SSSEEEEEEEEE
T ss_pred eeeEEEEEEEEE
Confidence 776766555555
No 60
>PHA03105 EEV glycoprotein; Provisional
Probab=24.38 E-value=91 Score=27.78 Aligned_cols=22 Identities=32% Similarity=0.422 Sum_probs=13.7
Q ss_pred CceeehhHHHH-HHHHHHHHHHh
Q psy4382 167 DGETFFLYVFL-GACVVLLLVIG 188 (258)
Q Consensus 167 D~q~iFLYlfL-~a~~gll~y~~ 188 (258)
+++.|+.|+++ +.++.|++|+.
T Consensus 1 m~~~iv~Y~vv~~SfiiLi~Yll 23 (188)
T PHA03105 1 MGIVIVVYVVVPLSFIVLILYIF 23 (188)
T ss_pred CceEEEEeeehHHHHHHHHHHHH
Confidence 35678888844 45555666653
No 61
>PF14524 Wzt_C: Wzt C-terminal domain; PDB: 2R5O_B.
Probab=24.14 E-value=3.4e+02 Score=20.95 Aligned_cols=81 Identities=11% Similarity=0.114 Sum_probs=47.6
Q ss_pred CccceeecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeec--eeecCCceeEEEEEEeeCcccCC
Q psy4382 7 VYINMDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYN--RIVKPGHEATLGYSFVPAEAVAG 84 (258)
Q Consensus 7 ~~~~~~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~--~~V~pg~~at~~Y~F~p~~~~~~ 84 (258)
+.....+..|++.++.+.+..+.+-+- ..++=.+++.... .+.. .++...+ .....++..++.+.| |.. |.+
T Consensus 25 g~~~~~~~~ge~~~i~i~~~~~~~i~~--~~~~~~i~~~~g~-~v~~-~~t~~~~~~~~~~~~g~~~~~~~i-~~~-L~~ 98 (142)
T PF14524_consen 25 GEPTSSFESGEPIRIRIDYEVNEDIDD--PVFGFAIRDSDGQ-RVFG-TNTYDSGFPIPLSEGGTYEVTFTI-PKP-LNP 98 (142)
T ss_dssp EES-SSEETTSEEEEEEEEEESS-EEE--EEEEEEEEETT---EEEE-EEHHHHT--EEE-TT-EEEEEEEE-E---B-S
T ss_pred CCEeeEEeCCCEEEEEEEEEECCCCCc--cEEEEEEEcCCCC-EEEE-ECccccCccccccCCCEEEEEEEE-cCc-cCC
Confidence 344556899999999999999654222 3344455655442 2232 3333333 344448888999998 444 888
Q ss_pred cceeEEEEE
Q psy4382 85 RPFGLSVNL 93 (258)
Q Consensus 85 ~p~~L~l~l 93 (258)
..|-+.+.+
T Consensus 99 G~Y~i~v~l 107 (142)
T PF14524_consen 99 GEYSISVGL 107 (142)
T ss_dssp EEEEEEEEE
T ss_pred CeEEEEEEE
Confidence 889888888
No 62
>PF14962 AIF-MLS: Mitochondria Localisation Sequence; PDB: 1M6I_A.
Probab=23.87 E-value=26 Score=31.32 Aligned_cols=30 Identities=17% Similarity=0.146 Sum_probs=0.0
Q ss_pred CceeehhHHHHHHHHHHHHHHhhhhhhhcc
Q psy4382 167 DGETFFLYVFLGACVVLLLVIGQHFLYSVG 196 (258)
Q Consensus 167 D~q~iFLYlfL~a~~gll~y~~y~~~~~~~ 196 (258)
++.-++.|||+.+.+.+.+|.+|+.+.+-+
T Consensus 42 sGsN~~Y~l~vG~t~~gag~YaYkTv~~dq 71 (180)
T PF14962_consen 42 SGSNMVYYLVVGVTVSGAGYYAYKTVKSDQ 71 (180)
T ss_dssp ------------------------------
T ss_pred CCceEEEEEEECeEEEeeEEEEEEeecchh
Confidence 567788888888888888999999887433
No 63
>CHL00031 psbT photosystem II protein T
Probab=23.23 E-value=94 Score=20.66 Aligned_cols=18 Identities=17% Similarity=0.392 Sum_probs=12.7
Q ss_pred hhHHHHHHHHHHHHHHhh
Q psy4382 172 FLYVFLGACVVLLLVIGQ 189 (258)
Q Consensus 172 FLYlfL~a~~gll~y~~y 189 (258)
+.|+||+++..++++|+-
T Consensus 4 lvYtfll~~tlgilFFAI 21 (33)
T CHL00031 4 LVYTFLLVSTLGIIFFAI 21 (33)
T ss_pred hHHHHHHHHHHHHHHHhh
Confidence 578888877666666654
No 64
>PF00287 Na_K-ATPase: Sodium / potassium ATPase beta chain; InterPro: IPR000402 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the beta subunit found in the P-type cation exchange ATPases located in the plasma membranes of animal cells. These P-ATPases include both H+/K+-ATPases (3.6.3.10 from EC) and Na+/K+-ATPases (3.6.3.9 from EC), which belong to the IIC subfamily of ATPases [, ]. These ATPases catalyse the hydrolysis of ATP coupled with the exchange of cations, pumping one cation out of the cell (H+ or Na+) in exchange for K+. These ATPases contain an alpha subunit (IPR005775 from INTERPRO) that is the catalytic component, and a glycosylated beta subunit that regulates the number of sodium pumps transported to the plasma membrane through the assembly of alpha/beta heterodimers. The beta subunit has three highly conserved disulphide bonds within the extracellular domain that stabilise the alpha subunit, the alpha/beta interaction, and the catalytic activity of the alpha subunit []. Different beta isoforms exist, permitting greater regulatory control. An example of a H+/K+-ATPase is the gastric pump responsible for acid secretion in the stomach, transporting protons from the cytoplasm of parietal cells to create a large pH gradient in exchange for the internalisation of potassium ions, using ATP hydrolysis to drive the pump []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0005391 sodium:potassium-exchanging ATPase activity, 0006754 ATP biosynthetic process, 0006813 potassium ion transport, 0006814 sodium ion transport, 0016020 membrane; PDB: 2XZB_B 3A3Y_B 3N2F_D 3B8E_D 3KDP_D 3N23_D.
Probab=23.07 E-value=65 Score=30.39 Aligned_cols=23 Identities=22% Similarity=0.342 Sum_probs=17.8
Q ss_pred ehhHHHHHHHHHHHHHHhhhhhh
Q psy4382 171 FFLYVFLGACVVLLLVIGQHFLY 193 (258)
Q Consensus 171 iFLYlfL~a~~gll~y~~y~~~~ 193 (258)
+++|++|+|+|++.++..|+++.
T Consensus 45 lifY~~La~lfa~~m~v~l~tld 67 (289)
T PF00287_consen 45 LIFYAFLAALFAICMWVFLQTLD 67 (289)
T ss_dssp HTTHHHHHHHHHHHHHHHHHTSS
T ss_pred HHHHHHHHHHHHHHHHHHHHHCC
Confidence 45677889999888888777664
No 65
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=23.02 E-value=59 Score=25.82 Aligned_cols=23 Identities=17% Similarity=0.225 Sum_probs=12.3
Q ss_pred ehhHHHHHHHHHHHHHHhhhhhh
Q psy4382 171 FFLYVFLGACVVLLLVIGQHFLY 193 (258)
Q Consensus 171 iFLYlfL~a~~gll~y~~y~~~~ 193 (258)
|-++++++.+..+++++||-.|.
T Consensus 2 i~l~iv~~~~~v~~~i~~y~~~k 24 (87)
T PF10883_consen 2 INLQIVGGVGAVVALILAYLWWK 24 (87)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHH
Confidence 45666555444455566665443
No 66
>cd00912 ML The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2 and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids.
Probab=22.89 E-value=3.9e+02 Score=21.25 Aligned_cols=84 Identities=7% Similarity=-0.055 Sum_probs=51.2
Q ss_pred eecCCceEEEEEEEEeCCCC---cEEEEEEeeeeecccc--cceEEEecceeeeceeecCCceeEEEEEEeeCc-ccCCc
Q psy4382 12 DLPAGSVVEFLVGFTNKGKQ---DFTLDTLDASLRYPMD--FNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAE-AVAGR 85 (258)
Q Consensus 12 ~l~~G~~~~~lv~~~N~g~~---~~tV~~i~gSl~~P~d--~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~-~~~~~ 85 (258)
.+..|..+++-+.|+-+++. ...|....+-+.-|.. ....=+|+......=.+.+|++.++.+++.-.+ .+.+.
T Consensus 25 ~~~~g~~~~i~~~f~~~~~~~~~~~~v~~~~~gi~~p~~~~~~d~C~~~~~~~~~CPl~~G~~~~~~~~~~v~~~~~P~~ 104 (127)
T cd00912 25 PDHRGGNYNLSVTGTLREDIKSLYVDLALMSQGIKVLNPDNSYDFCEAGLPKPSFCPLRKGQQYSYAKTVNVPEFTIPTI 104 (127)
T ss_pred cccCCCeEEEEEEEEECccccEEEEEEEEEECCEEeccCCCCCCcccccCcccccCCcCCCCEEEEEEEEecCcccCCCe
Confidence 57789999999999988763 3344444444444431 111112221112335789999999999996644 56666
Q ss_pred ceeEEEEEEE
Q psy4382 86 PFGLSVNLQY 95 (258)
Q Consensus 86 p~~L~l~l~Y 95 (258)
.+.+...|..
T Consensus 105 ~~~v~~~l~~ 114 (127)
T cd00912 105 EYQVVLEDVT 114 (127)
T ss_pred eEEEEEEEEc
Confidence 6666665533
No 67
>PF10342 GPI-anchored: Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored membrane family; InterPro: IPR018466 This entry represents glycoproteins involved in cell wall (1-->6)-beta-glucan assembly. In yeast a null mutation leads to severe growth defects, aberrant multi-budded morphology, and mating defects [, ]. The entry includes DRMIP and Hesp-379, which are involved in both fruiting body formation and in host attack respectively. Hesp-379 is a haustorially expressed secreted protein; the haustorium being the small sucker that penetrates host tissue [].
Probab=22.87 E-value=2.7e+02 Score=20.32 Aligned_cols=41 Identities=7% Similarity=-0.108 Sum_probs=29.4
Q ss_pred CccceeecCCceEEEEEEEEeCCCCcEEEEEEeeeeecccc
Q psy4382 7 VYINMDLPAGSVVEFLVGFTNKGKQDFTLDTLDASLRYPMD 47 (258)
Q Consensus 7 ~~~~~~l~~G~~~~~lv~~~N~g~~~~tV~~i~gSl~~P~d 47 (258)
+..+-.|.+|+.+++-=.-.+.....++|..+.|.-..+..
T Consensus 3 P~~~~~~~~g~~~~I~W~~~~~~~~~~~I~L~~g~~~~~~~ 43 (93)
T PF10342_consen 3 PTAGTVWTAGQPITITWTSDGTDPGNVTIYLCNGNNTNLNF 43 (93)
T ss_pred CCCCCEEECCCcEEEEEeCCCCCCcEEEEEEEcCCCCCcce
Confidence 34556788998876665555556788999999998754444
No 68
>COG4454 Uncharacterized copper-binding protein [Inorganic ion transport and metabolism]
Probab=22.45 E-value=90 Score=27.43 Aligned_cols=31 Identities=35% Similarity=0.468 Sum_probs=27.2
Q ss_pred cccCCccceeecCCceEEEEEEEEeCCCCcE
Q psy4382 3 KEHGVYINMDLPAGSVVEFLVGFTNKGKQDF 33 (258)
Q Consensus 3 ~~~~~~~~~~l~~G~~~~~lv~~~N~g~~~~ 33 (258)
.||......+|-.|+..++++.|+|.|+-.|
T Consensus 108 me~d~~~~v~L~PG~s~elvv~ft~~g~ye~ 138 (158)
T COG4454 108 MEHDDPNTVTLAPGKSGELVVVFTGAGKYEF 138 (158)
T ss_pred cccCCcceeEeCCCCcEEEEEEecCCccEEE
Confidence 4788888899999999999999999997655
No 69
>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=21.26 E-value=2.9e+02 Score=19.86 Aligned_cols=24 Identities=25% Similarity=0.346 Sum_probs=20.5
Q ss_pred eeecCCceEEEEEEEEeCCCCcEE
Q psy4382 11 MDLPAGSVVEFLVGFTNKGKQDFT 34 (258)
Q Consensus 11 ~~l~~G~~~~~lv~~~N~g~~~~t 34 (258)
.....|+.++.-|.++|.|..+..
T Consensus 35 ~~~~~Gd~v~ytitvtN~G~~~a~ 58 (76)
T PF01345_consen 35 STANPGDTVTYTITVTNTGPAPAT 58 (76)
T ss_pred CcccCCCEEEEEEEEEECCCCeeE
Confidence 346789999999999999987764
No 70
>PF06522 B12D: NADH-ubiquinone reductase complex 1 MLRQ subunit; InterPro: IPR010530 The MLRQ subunit of mitochondrial NADH-ubiquinone reductase complex I is nuclear [] and is found in plants [], insects, fungi and higher metazoans []. It appears to act within the membrane and, in mammals, is highly expressed in muscle and neural tissue, indicative of a role in ATP generation [].
Probab=21.25 E-value=1.1e+02 Score=22.93 Aligned_cols=27 Identities=22% Similarity=0.198 Sum_probs=20.7
Q ss_pred cCceeehhHHHHHHHHHHHHHHhhhhh
Q psy4382 166 LDGETFFLYVFLGACVVLLLVIGQHFL 192 (258)
Q Consensus 166 fD~q~iFLYlfL~a~~gll~y~~y~~~ 192 (258)
.+|+++=|++++.+.+++.+|+.+..+
T Consensus 2 ~~pel~PL~~~vg~a~~~a~~~~~r~l 28 (73)
T PF06522_consen 2 KHPELYPLFVIVGVAVGGATFYLYRLL 28 (73)
T ss_pred CCccccchHHHHHHHHHHHHHHHHHHH
Confidence 378889899988877777777777654
No 71
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=21.16 E-value=1.4e+02 Score=26.74 Aligned_cols=24 Identities=29% Similarity=0.380 Sum_probs=17.9
Q ss_pred ehhHHHHHHHHHHHHHHhhhhhhh
Q psy4382 171 FFLYVFLGACVVLLLVIGQHFLYS 194 (258)
Q Consensus 171 iFLYlfL~a~~gll~y~~y~~~~~ 194 (258)
.|.|+++++++|+++++.-.++..
T Consensus 2 ~~~~l~il~l~GvlLli~s~~f~~ 25 (186)
T TIGR02830 2 KLTYLLVLLLIGLLLLIVSSFFSS 25 (186)
T ss_pred chHHHHHHHHHHHHHHHhhccccC
Confidence 367888888888888777766654
No 72
>PF09451 ATG27: Autophagy-related protein 27; InterPro: IPR018939 Autophagy is a degradative transport pathway that delivers cytosolic proteins to the lysosome (vacuole) [] and is induced by starvation []. Cytosolic proteins appear inside the vacuole enclosed in autophagic vesicles. Autophagy significantly differs from other transport pathways by using double membrane layered transport intermediates, called autophagosomes [, ]. The breakdown of vesicular transport intermediates is a unique feature of autophagy []. Autophagy can also function in the elimination of invading bacteria and antigens []. There are more than 25 AuTophaGy-related (ATG) genes that are essential for autophagy, although it is still not known how the autophagosome is made. Atg9 is a potential membrane carrier to deliver lipids that are used to form the vesicle. Atg27 is another transmembrane protein, and is a cycling protein []. It acts as an effector of VPS34 phosphatidylinositol 3-phosphate kinase signalling and regulates the cytoplasm to vacuole transport (Cvt) vesicle formation. It is also required for autophagy-dependent cycling of ATG9.
Probab=20.63 E-value=92 Score=28.66 Aligned_cols=26 Identities=23% Similarity=0.310 Sum_probs=20.0
Q ss_pred ceeehhHHHHHHHHHHHHHHhhhhhh
Q psy4382 168 GETFFLYVFLGACVVLLLVIGQHFLY 193 (258)
Q Consensus 168 ~q~iFLYlfL~a~~gll~y~~y~~~~ 193 (258)
.-.+|.++|++.++++++|++...|.
T Consensus 199 ~~g~f~wl~i~~~l~~~~Y~i~g~~~ 224 (268)
T PF09451_consen 199 GWGFFTWLFIILFLFLAAYLIFGSWY 224 (268)
T ss_pred cccHHHHHHHHHHHHHHHHhhhhhhe
Confidence 45678888888888888888876654
No 73
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=20.48 E-value=58 Score=27.50 Aligned_cols=57 Identities=12% Similarity=0.105 Sum_probs=38.4
Q ss_pred ecccccccccccCCCCccc----------ccceecccCCceeeeeeeeeeEEEEecCCCcCceeehhHHH
Q psy4382 117 LGYSFVPAEAVAGRPFGLS----------VNLQYRDEHNNFFYEGIYNETVNIIEIDEGLDGETFFLYVF 176 (258)
Q Consensus 117 ~~~~~~p~e~~~g~p~g~~----------i~~~~~d~~g~~y~~~vfN~TVtVvE~~~sfD~q~iFLYlf 176 (258)
|-|-.|.+|+.+.+.=++- |.-+.+|..=..|-+.=|=+.|.- +|+- ++.+++||+.
T Consensus 41 LRC~vCqnqsiadS~a~iA~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~~Vly-~Pp~--~~~t~~LW~~ 107 (126)
T TIGR03147 41 LRCPQCQNQNLVESNSPIAYDLRHEVYSMVNEGKSNQQIIDFMTARFGDFVLY-NPPF--KWQTLLLWLL 107 (126)
T ss_pred CCCCCCCCCChhhcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEe-cCCC--CcchHHHHHH
Confidence 8899999999999887665 334444433334555555555543 4554 8999999984
No 74
>PF02468 PsbN: Photosystem II reaction centre N protein (psbN); InterPro: IPR003398 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbN found in PSII. PsbN may have a role in PSII stability, however its actual function unknown. PsbN does not appear to be essential for photoautotrophic growth or normal PSII function.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane
Probab=20.35 E-value=1.3e+02 Score=21.04 Aligned_cols=24 Identities=8% Similarity=-0.222 Sum_probs=13.2
Q ss_pred eehhHHHHHHHHHHHHHHhhhhhh
Q psy4382 170 TFFLYVFLGACVVLLLVIGQHFLY 193 (258)
Q Consensus 170 ~iFLYlfL~a~~gll~y~~y~~~~ 193 (258)
+++...+...+++..+|-.|..++
T Consensus 5 ~~~~i~i~~~lv~~Tgy~iYtaFG 28 (43)
T PF02468_consen 5 TVLAIFISCLLVSITGYAIYTAFG 28 (43)
T ss_pred eeHHHHHHHHHHHHHhhhhhheeC
Confidence 333434444445566677776666
No 75
>KOG3620|consensus
Probab=20.23 E-value=1.1e+02 Score=35.04 Aligned_cols=55 Identities=13% Similarity=0.140 Sum_probs=43.6
Q ss_pred EEEEeCCCCcEEEEEEeeeeecccccceEEEecceeeeceeecCCceeEEEEEEeeCcc
Q psy4382 23 VGFTNKGKQDFTLDTLDASLRYPMDFNFYIQNFSTIIYNRIVKPGHEATLGYSFVPAEA 81 (258)
Q Consensus 23 v~~~N~g~~~~tV~~i~gSl~~P~d~~~~iqNfTa~~~~~~V~pg~~at~~Y~F~p~~~ 81 (258)
..+.|.|.-+|+|.++.=+=..=++|++-|-|- ++-.+.|.+..-+.-.|.|+..
T Consensus 871 FkVeNsG~l~itVe~~~InGypCEgyGFkVldC----~~F~L~pNesrdi~IafTPDFt 925 (1626)
T KOG3620|consen 871 FKVENSGVLPITVEGFLINGYPCEGYGFKVLDC----AGFDLGPNESRDIEIAFTPDFT 925 (1626)
T ss_pred eEeeecceeeEEEEEEEEcccccCCCceeEEee----cccccCCCcccceEEEecCcch
Confidence 567899999999998875544446778877663 5678899999999999999863
No 76
>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=20.15 E-value=2.6e+02 Score=19.44 Aligned_cols=26 Identities=19% Similarity=0.222 Sum_probs=21.1
Q ss_pred eeecCCceEEEEEEEEeCCCCcEEEE
Q psy4382 11 MDLPAGSVVEFLVGFTNKGKQDFTLD 36 (258)
Q Consensus 11 ~~l~~G~~~~~lv~~~N~g~~~~tV~ 36 (258)
....-|+.++.-+.++|.|..+.+=.
T Consensus 6 ~~~~~Gd~v~Yti~v~N~g~~~a~~v 31 (53)
T TIGR01451 6 TVATIGDTITYTITVTNNGNVPATNV 31 (53)
T ss_pred cccCCCCEEEEEEEEEECCCCceEeE
Confidence 34678999999999999998776533
No 77
>PF10215 Ost4: Oligosaccaryltransferase ; InterPro: IPR018943 Ost4 is a very short, approximately 30 residues, enzyme found from fungi to vertebrates. It is a member of the ER oligosaccaryltansferase complex, 2.4.1.119 from EC, that catalyses the asparagine-linked glycosylation of proteins. It appears to be an integral membrane protein that mediates the en bloc transfer of a pre-assembled high-mannose oligosaccharide onto asparagine residues of nascent polypeptides as they enter the lumen of the rough endoplasmic reticulum. ; PDB: 1RKL_A 2LAT_A.
Probab=20.15 E-value=1.2e+02 Score=20.23 Aligned_cols=20 Identities=15% Similarity=0.215 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHhhhhhhhc
Q psy4382 176 FLGACVVLLLVIGQHFLYSV 195 (258)
Q Consensus 176 fL~a~~gll~y~~y~~~~~~ 195 (258)
..+|++..++.+.||++..-
T Consensus 12 n~lG~~~~~LIVlYH~v~~n 31 (35)
T PF10215_consen 12 NFLGVAAMVLIVLYHFVEVN 31 (35)
T ss_dssp HHHHHHHHHHHHHHHHHCCH
T ss_pred HHHHHHHHHHHHHHHHhhcc
Confidence 44566777788899998743
Done!