Query psy9572
Match_columns 163
No_of_seqs 112 out of 736
Neff 7.9
Searched_HMMs 46136
Date Fri Aug 16 23:04:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9572.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9572hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1366|consensus 99.9 6E-27 1.3E-31 218.3 13.8 154 4-163 785-956 (1436)
2 PF10569 Thiol-ester_cl: Alpha 99.8 1.3E-20 2.8E-25 102.6 1.6 31 133-163 1-31 (31)
3 COG2373 Large extracellular al 99.6 3E-15 6.5E-20 142.1 12.3 147 3-161 1035-1186(1621)
4 PF11614 FixG_C: IG-like fold 92.9 1.8 3.9E-05 30.1 9.2 55 4-58 39-101 (118)
5 PF10633 NPCBM_assoc: NPCBM-as 91.9 1.3 2.9E-05 28.4 7.0 51 66-119 24-76 (78)
6 COG1470 Predicted membrane pro 89.8 12 0.00025 32.8 12.4 56 5-60 293-361 (513)
7 PF10633 NPCBM_assoc: NPCBM-as 88.8 2.2 4.7E-05 27.4 5.9 55 4-58 13-76 (78)
8 PF07919 Gryzun: Gryzun, putat 87.9 1.1 2.3E-05 39.3 5.2 48 4-51 493-545 (554)
9 PF07705 CARDB: CARDB; InterP 87.6 4.9 0.00011 26.2 7.3 48 12-59 36-85 (101)
10 PF06030 DUF916: Bacterial pro 85.6 2.2 4.8E-05 30.2 4.9 45 3-47 34-105 (121)
11 PF05326 SVA: Seminal vesicle 83.6 8.3 0.00018 27.6 7.0 51 4-54 56-111 (124)
12 PF05506 DUF756: Domain of unk 80.3 8.5 0.00018 25.3 5.9 18 26-43 48-65 (89)
13 PF00927 Transglut_C: Transglu 73.8 8.2 0.00018 26.1 4.5 53 4-56 23-87 (107)
14 PRK13211 N-acetylglucosamine-b 69.2 51 0.0011 29.0 9.3 34 26-60 357-390 (478)
15 KOG2649|consensus 69.2 22 0.00048 31.2 6.9 34 40-78 414-447 (500)
16 cd08695 C2_Dock-B C2 domains f 68.0 17 0.00037 27.9 5.5 62 50-112 24-85 (189)
17 PF13600 DUF4140: N-terminal d 63.8 35 0.00077 22.9 6.0 41 70-114 2-42 (104)
18 TIGR02745 ccoG_rdxA_fixG cytoc 63.7 56 0.0012 28.3 8.4 56 4-59 354-417 (434)
19 PF05753 TRAP_beta: Translocon 61.6 38 0.00082 25.7 6.3 27 29-55 81-107 (181)
20 PF03170 BcsB: Bacterial cellu 59.0 33 0.00072 30.7 6.5 80 35-119 29-109 (605)
21 PF14310 Fn3-like: Fibronectin 52.7 28 0.0006 21.8 3.7 25 25-49 23-47 (71)
22 PF07718 Coatamer_beta_C: Coat 49.6 38 0.00082 24.7 4.3 47 5-51 78-131 (140)
23 PF14742 GDE_N_bis: N-terminal 45.4 1E+02 0.0022 23.3 6.4 21 4-24 99-119 (194)
24 cd03864 M14_CPN Peptidase M14 44.5 1.2E+02 0.0025 26.0 7.2 22 1-23 268-290 (392)
25 cd08694 C2_Dock-A C2 domains f 43.9 1E+02 0.0022 23.8 6.1 62 50-112 24-85 (196)
26 PF06280 DUF1034: Fn3-like dom 43.4 34 0.00074 23.3 3.3 42 4-45 16-80 (112)
27 PF00731 AIRC: AIR carboxylase 42.3 21 0.00046 26.3 2.1 31 119-149 82-112 (150)
28 PF06030 DUF916: Bacterial pro 41.5 1.2E+02 0.0027 21.2 8.1 87 28-118 20-118 (121)
29 PF07703 A2M_N_2: Alpha-2-macr 40.5 1.2E+02 0.0026 20.9 10.5 15 104-119 103-117 (136)
30 PF14874 PapD-like: Flagellar- 38.9 1.1E+02 0.0024 20.0 8.1 22 30-51 58-80 (102)
31 PF10572 UPF0556: Uncharacteri 33.5 2E+02 0.0044 21.4 7.0 20 64-83 22-41 (158)
32 PF12080 GldM_C: GldM C-termin 33.2 1.6E+02 0.0035 22.2 5.8 39 40-79 46-87 (181)
33 PF15418 DUF4625: Domain of un 33.1 1.8E+02 0.004 20.8 9.5 80 29-119 30-116 (132)
34 PF08308 PEGA: PEGA domain; I 31.1 1.3E+02 0.0028 18.4 6.0 31 40-73 26-56 (71)
35 PF08626 TRAPPC9-Trs120: Trans 30.4 70 0.0015 31.3 4.1 42 3-46 968-1009(1185)
36 PF02120 Flg_hook: Flagellar h 29.3 95 0.0021 19.7 3.5 34 35-72 11-44 (85)
37 PRK15098 beta-D-glucoside gluc 28.2 1.4E+02 0.0031 27.7 5.6 24 26-49 708-731 (765)
38 PF09394 Inhibitor_I42: Chagas 27.8 1.7E+02 0.0037 18.7 6.0 28 34-61 50-77 (92)
39 COG4871 Uncharacterized protei 25.2 44 0.00095 25.2 1.4 16 142-157 140-155 (193)
40 COG3534 AbfA Alpha-L-arabinofu 25.0 28 0.00061 30.4 0.4 16 130-145 54-73 (501)
41 PF06205 GT36_AF: Glycosyltran 24.1 1.3E+02 0.0029 19.8 3.5 20 26-45 65-84 (90)
42 KOG4386|consensus 23.3 1.3E+02 0.0028 27.2 4.1 48 4-51 716-768 (809)
43 PF13157 DUF3992: Protein of u 23.1 2.2E+02 0.0048 19.1 4.4 8 29-36 56-63 (92)
44 PF06943 zf-LSD1: LSD1 zinc fi 22.6 28 0.00061 17.7 -0.0 9 136-144 6-14 (25)
45 COG1470 Predicted membrane pro 22.6 5.5E+02 0.012 22.8 11.3 35 83-119 325-359 (513)
46 PF11797 DUF3324: Protein of u 21.3 3.1E+02 0.0068 19.5 7.2 46 27-72 82-129 (140)
47 PF11622 DUF3251: Protein of u 21.3 3.6E+02 0.0079 20.2 8.8 90 29-123 45-144 (165)
48 PF12584 TRAPPC10: Trafficking 20.8 2.5E+02 0.0055 20.1 4.7 24 28-51 80-103 (147)
49 COG2967 ApaG Uncharacterized p 20.5 3.3E+02 0.0071 19.4 5.7 66 8-78 4-69 (126)
No 1
>KOG1366|consensus
Probab=99.94 E-value=6e-27 Score=218.33 Aligned_cols=154 Identities=42% Similarity=0.706 Sum_probs=141.1
Q ss_pred CCCCCCCcEEEEEEEeeccceE-----------------EEE-EEEcCCCeEEEEEEEEecccceEEEEEEEeecCCCCe
Q psy9572 4 HKNVLRYNIREKVYLYEFEVFR-----------------RKK-LTIKANSGSTTTFVITPKELGYIGIKVTATSNLAGDS 65 (163)
Q Consensus 4 ~~Ny~~~~~~v~V~l~~~~~~~-----------------~~~-v~v~~~~~~~v~f~v~~~~~G~~~i~v~a~~~~~~d~ 65 (163)
++||+.+++.|.|.+..+++++ .+. ...++.+.+.+.|+++|...|.+.++++|.....+|+
T Consensus 785 v~NYl~k~~~v~V~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~s~~~~~~~v~p~~~g~~~~~~~~~t~~~~da 864 (1436)
T KOG1366|consen 785 VFNYLTKELDVSVILLSSEDFCYDATSKANEQVGVSQRSVQVSRVTPAQSGKLVYFPVRPGVIGLILVTISALTLLGGDA 864 (1436)
T ss_pred EecccCcceEEEEEEccCCCeeeecccccCcccccccceEEEEEEcccccceEEEEEeccccccccceEEEEeecCCCcc
Confidence 6899999999999999977752 122 3355888889999999999999999999999999999
Q ss_pred EEEEEEEeeCCeeEEEEEEEEEecCCCCceEEEEecCCCCCCcCCcceEEEEEEeccCCCcccchhhhHhhhhhCCCCch
Q psy9572 66 MEGKLLVKPEGETQYKNKAIFVDLRKNKTFSVNVTLDMPKNIVPGSEHVEVSAVACKIGDLLGPSIPNLANLIKMPFGCG 145 (163)
Q Consensus 66 v~~~l~V~~~g~~~~~~~~~~l~~~~~~~~~~~~~~~lp~~~vpgS~~~~v~v~~~~~~~~~~~~~~~l~~Li~~PyGC~ 145 (163)
+.|+|.|+|+|+.+.++.+..||++ ...+..+++.+|++.++||+++++++. ||.+|+.+++++.|+++|||||
T Consensus 865 v~k~l~V~~eG~~~~~~~~~~i~l~--~~~~~~~~~~~p~~~V~~S~~~~~~~v----gD~lGps~~~l~~Ll~lP~GcG 938 (1436)
T KOG1366|consen 865 VHKTLLVEPEGITQERNFSVLIDLS--VSASKELSLGVPNDVVPGSERARISVV----GDVLGPSMNNLSNLLRLPYGCG 938 (1436)
T ss_pred EEEEEEEeccCccceeeeeEEeccC--CCcCcceeecCCCCcCccccceeeEEE----ecccccChhhhHHhccCCCCcc
Confidence 9999999999999999999999986 347788999999999999999999999 9999999999999999999999
Q ss_pred hhhhhhhhHHHHHHhhcC
Q psy9572 146 EQNMLNFVPNIVVLEYLK 163 (163)
Q Consensus 146 EQt~s~~~P~l~~~~YL~ 163 (163)
||||+.|+|++|+++||+
T Consensus 939 EQnMi~faPni~v~~YL~ 956 (1436)
T KOG1366|consen 939 EQNMINFAPNIYVLKYLP 956 (1436)
T ss_pred cceeecccchhhHHHHHh
Confidence 999999999999999995
No 2
>PF10569 Thiol-ester_cl: Alpha-macro-globulin thiol-ester bond-forming region; InterPro: IPR019565 This entry contains serum complement C3 and C4 precursors and alpha-macrogrobulins. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ]. This short highly conserved region of proteinase-binding alpha-macro-globulins contains the cysteine and a glutamine of a thiol-ester bond that is cleaved at the moment of proteinase binding, and mediates the covalent binding of the alpha-macro-globulin to the proteinase. The GCGEQ motif is highly conserved. ; PDB: 2B39_B 2PN5_A 4ACQ_C 1HZF_A 2WIN_H 2I07_B 2ICF_B 2XWJ_D 3G6J_B 2NOJ_C ....
Probab=99.80 E-value=1.3e-20 Score=102.58 Aligned_cols=31 Identities=55% Similarity=1.112 Sum_probs=27.6
Q ss_pred hHhhhhhCCCCchhhhhhhhhHHHHHHhhcC
Q psy9572 133 NLANLIKMPFGCGEQNMLNFVPNIVVLEYLK 163 (163)
Q Consensus 133 ~l~~Li~~PyGC~EQt~s~~~P~l~~~~YL~ 163 (163)
++++|+++||||+|||||+++|++++++||+
T Consensus 1 ~l~~Li~~P~GCgEQtm~~~~P~v~~~~YL~ 31 (31)
T PF10569_consen 1 NLDSLIRYPYGCGEQTMSSFAPNVYALRYLD 31 (31)
T ss_dssp TGGGGSSS--SSTTHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHhcCCCcHHHHHHHHhHHHHHHHHhC
Confidence 5889999999999999999999999999995
No 3
>COG2373 Large extracellular alpha-helical protein [General function prediction only]
Probab=99.62 E-value=3e-15 Score=142.14 Aligned_cols=147 Identities=19% Similarity=0.248 Sum_probs=119.2
Q ss_pred CCCCCCCCcEEEEEEEee----ccceEEEEEEEcCCCeEEEEEEEEecc-cceEEEEEEEeecCCCCeEEEEEEEeeCCe
Q psy9572 3 DHKNVLRYNIREKVYLYE----FEVFRRKKLTIKANSGSTTTFVITPKE-LGYIGIKVTATSNLAGDSMEGKLLVKPEGE 77 (163)
Q Consensus 3 ~~~Ny~~~~~~v~V~l~~----~~~~~~~~v~v~~~~~~~v~f~v~~~~-~G~~~i~v~a~~~~~~d~v~~~l~V~~~g~ 77 (163)
|++|.+++...+ ++.+. ...-..+.+++.+|++..+.|++++.. .|.+.++++..+. .+|.+++++.|+|.++
T Consensus 1035 ~v~N~~~~~g~~-~~~~~~l~~~~~~~~~~~~l~~g~~~~l~~~l~a~~g~g~~~~~~~~~~~-~~~~~~~~~~vr~~~~ 1112 (1621)
T COG2373 1035 DVFNLTGKAGDV-LTVEGTLKFNGKEAPQTLTLAEGSATTLFFPLRALDGSGKIDATLSVSGQ-VGDKLERHLNVRPAVP 1112 (1621)
T ss_pred EEeccCCCCcce-eeccceecccccccceEEEecCCCceEEEEEeeccCCCceeeEEEEecCc-ccceeeeeeccccCcc
Confidence 789999998663 33332 222257899999999999999999986 5555555555443 5789999999999999
Q ss_pred eEEEEEEEEEecCCCCceEEEEecCCCCCCcCCcceEEEEEEeccCCCcccchhhhHhhhhhCCCCchhhhhhhhhHHHH
Q psy9572 78 TQYKNKAIFVDLRKNKTFSVNVTLDMPKNIVPGSEHVEVSAVACKIGDLLGPSIPNLANLIKMPFGCGEQNMLNFVPNIV 157 (163)
Q Consensus 78 ~~~~~~~~~l~~~~~~~~~~~~~~~lp~~~vpgS~~~~v~v~~~~~~~~~~~~~~~l~~Li~~PyGC~EQt~s~~~P~l~ 157 (163)
+++.+....+.++ +.++.+++.++.|++..+.++++ +.+..+.-..++.|.+|||||.||+.|+++|.+|
T Consensus 1113 ~~~~~~~~~l~~~------~~~~~~~l~~l~~~~~~~~l~ls----~~~~~~~~~~~~~L~~YPygc~EQt~S~~~pll~ 1182 (1621)
T COG2373 1113 PQTQVKTVVLAPG------FTISGDLLAGLSPQAVNAQLQLS----GTPAADIAALLDVLDDYPYGCAEQTASRLLPLLY 1182 (1621)
T ss_pred ceeeeEEEecccc------cccCchhhhhcCccccceEEEec----cCccccHHHHHHHHHhCCccchhhhhhhHHHHHh
Confidence 9999998888773 56677888899999999999999 6666666678999999999999999999999999
Q ss_pred HHhh
Q psy9572 158 VLEY 161 (163)
Q Consensus 158 ~~~Y 161 (163)
+..-
T Consensus 1183 ~~~~ 1186 (1621)
T COG2373 1183 AQKA 1186 (1621)
T ss_pred hhhh
Confidence 8653
No 4
>PF11614 FixG_C: IG-like fold at C-terminal of FixG, putative oxidoreductase; PDB: 2R39_A.
Probab=92.90 E-value=1.8 Score=30.05 Aligned_cols=55 Identities=13% Similarity=0.067 Sum_probs=36.2
Q ss_pred CCCCCCCcEEEEEEEeeccceE----EEEEEEcCCCeEEEEEEEEecc----cceEEEEEEEe
Q psy9572 4 HKNVLRYNIREKVYLYEFEVFR----RKKLTIKANSGSTTTFVITPKE----LGYIGIKVTAT 58 (163)
Q Consensus 4 ~~Ny~~~~~~v~V~l~~~~~~~----~~~v~v~~~~~~~v~f~v~~~~----~G~~~i~v~a~ 58 (163)
+.|-+.+++.+++++...+.+. ...+.|+||+...+.|.|.+.+ .|...|++++.
T Consensus 39 l~Nkt~~~~~~~i~~~g~~~~~l~~~~~~i~v~~g~~~~~~v~v~~p~~~~~~~~~~i~f~v~ 101 (118)
T PF11614_consen 39 LTNKTNQPRTYTISVEGLPGAELQGPENTITVPPGETREVPVFVTAPPDALKSGSTPITFTVT 101 (118)
T ss_dssp EEE-SSS-EEEEEEEES-SS-EE-ES--EEEE-TT-EEEEEEEEEE-GGG-SSSEEEEEEEEE
T ss_pred EEECCCCCEEEEEEEecCCCeEEECCCcceEECCCCEEEEEEEEEECHHHccCCCeeEEEEEE
Confidence 4688899999999998744543 3679999999999999888853 35567777776
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=91.92 E-value=1.3 Score=28.39 Aligned_cols=51 Identities=25% Similarity=0.326 Sum_probs=25.0
Q ss_pred EEEEEEEeeCCeeEE--EEEEEEEecCCCCceEEEEecCCCCCCcCCcceEEEEEE
Q psy9572 66 MEGKLLVKPEGETQY--KNKAIFVDLRKNKTFSVNVTLDMPKNIVPGSEHVEVSAV 119 (163)
Q Consensus 66 v~~~l~V~~~g~~~~--~~~~~~l~~~~~~~~~~~~~~~lp~~~vpgS~~~~v~v~ 119 (163)
+...+.+ |+|-... -.....|.++ +..+..|.+..|++..+|+-.+.+.+.
T Consensus 24 v~~~l~~-P~GW~~~~~~~~~~~l~pG--~s~~~~~~V~vp~~a~~G~y~v~~~a~ 76 (78)
T PF10633_consen 24 VSLSLSL-PEGWTVSASPASVPSLPPG--ESVTVTFTVTVPADAAPGTYTVTVTAR 76 (78)
T ss_dssp -EEEEE---TTSE---EEEEE--B-TT--SEEEEEEEEEE-TT--SEEEEEEEEEE
T ss_pred EEEEEeC-CCCccccCCccccccCCCC--CEEEEEEEEECCCCCCCceEEEEEEEE
Confidence 4444444 6666522 1122245554 246788888999999999877766553
No 6
>COG1470 Predicted membrane protein [Function unknown]
Probab=89.83 E-value=12 Score=32.82 Aligned_cols=56 Identities=20% Similarity=0.195 Sum_probs=40.0
Q ss_pred CCCCCCcEEEEEEEe-eccc---------eEEEEEEEcCCCeEEEEEEEEec---ccceEEEEEEEeec
Q psy9572 5 KNVLRYNIREKVYLY-EFEV---------FRRKKLTIKANSGSTTTFVITPK---ELGYIGIKVTATSN 60 (163)
Q Consensus 5 ~Ny~~~~~~v~V~l~-~~~~---------~~~~~v~v~~~~~~~v~f~v~~~---~~G~~~i~v~a~~~ 60 (163)
.|...++.+..+.+. ..+. +.--++.|.||.++.+...|.|. .+|.=+++++|.+.
T Consensus 293 eN~g~~~d~y~Le~~g~pe~w~~~Fteg~~~vt~vkL~~gE~kdvtleV~ps~na~pG~Ynv~I~A~s~ 361 (513)
T COG1470 293 ENRGKQDDEYALELSGLPEGWTAEFTEGELRVTSVKLKPGEEKDVTLEVYPSLNATPGTYNVTITASSS 361 (513)
T ss_pred ccCCCCCceeEEEeccCCCCcceEEeeCceEEEEEEecCCCceEEEEEEecCCCCCCCceeEEEEEecc
Confidence 355556666665555 2233 23457999999999999999995 58988888888763
No 7
>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=88.85 E-value=2.2 Score=27.42 Aligned_cols=55 Identities=20% Similarity=0.110 Sum_probs=29.9
Q ss_pred CCCCCCCc-EEEEEEEeeccce----E-EEEEEEcCCCeEEEEEEEEec---ccceEEEEEEEe
Q psy9572 4 HKNVLRYN-IREKVYLYEFEVF----R-RKKLTIKANSGSTTTFVITPK---ELGYIGIKVTAT 58 (163)
Q Consensus 4 ~~Ny~~~~-~~v~V~l~~~~~~----~-~~~v~v~~~~~~~v~f~v~~~---~~G~~~i~v~a~ 58 (163)
+.|..+.. ..+++.+..-+.. . .+.-.|++|++..+.|.|.+. ..|.-.|+++|+
T Consensus 13 v~N~g~~~~~~v~~~l~~P~GW~~~~~~~~~~~l~pG~s~~~~~~V~vp~~a~~G~y~v~~~a~ 76 (78)
T PF10633_consen 13 VTNTGTAPLTNVSLSLSLPEGWTVSASPASVPSLPPGESVTVTFTVTVPADAAPGTYTVTVTAR 76 (78)
T ss_dssp EE--SSS-BSS-EEEEE--TTSE---EEEEE--B-TTSEEEEEEEEEE-TT--SEEEEEEEEEE
T ss_pred EEECCCCceeeEEEEEeCCCCccccCCccccccCCCCCEEEEEEEEECCCCCCCceEEEEEEEE
Confidence 45665544 2355555543221 2 223379999999999999985 368888888775
No 8
>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=87.90 E-value=1.1 Score=39.32 Aligned_cols=48 Identities=13% Similarity=0.128 Sum_probs=42.6
Q ss_pred CCCCCCCcEEEEEEEeeccce-----EEEEEEEcCCCeEEEEEEEEecccceE
Q psy9572 4 HKNVLRYNIREKVYLYEFEVF-----RRKKLTIKANSGSTTTFVITPKELGYI 51 (163)
Q Consensus 4 ~~Ny~~~~~~v~V~l~~~~~~-----~~~~v~v~~~~~~~v~f~v~~~~~G~~ 51 (163)
++|.+.+-+++.+.|+.+++| ....+.|.|++++.+.|.+.|...|..
T Consensus 493 I~N~T~~~~~~~~~me~s~~F~fsG~k~~~~~llP~s~~~~~y~l~pl~~G~~ 545 (554)
T PF07919_consen 493 IENPTNHFQTFELSMEPSDDFMFSGPKQTTFSLLPFSRHTVRYNLLPLVAGWW 545 (554)
T ss_pred EECCCCccEEEEEEEccCCCEEEECCCcCceEECCCCcEEEEEEEEEccCCcE
Confidence 579999999999999998887 245789999999999999999998875
No 9
>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=87.62 E-value=4.9 Score=26.25 Aligned_cols=48 Identities=23% Similarity=0.227 Sum_probs=31.2
Q ss_pred EEEEEEEeeccce-EEEEE-EEcCCCeEEEEEEEEecccceEEEEEEEee
Q psy9572 12 IREKVYLYEFEVF-RRKKL-TIKANSGSTTTFVITPKELGYIGIKVTATS 59 (163)
Q Consensus 12 ~~v~V~l~~~~~~-~~~~v-~v~~~~~~~v~f~v~~~~~G~~~i~v~a~~ 59 (163)
-.+.|++..++.. ....+ .|++|+...+.|.+.+...|...|++.+-.
T Consensus 36 ~~~~v~~~~~~~~~~~~~i~~L~~g~~~~v~~~~~~~~~G~~~i~~~iD~ 85 (101)
T PF07705_consen 36 ENVTVRLYLDGNSVSTVTIPSLAPGESETVTFTWTPPSPGSYTIRVVIDP 85 (101)
T ss_dssp EEEEEEEEETTEEEEEEEESEB-TTEEEEEEEEEE-SS-CEEEEEEEEST
T ss_pred CCEEEEEEECCceeccEEECCcCCCcEEEEEEEEEeCCCCeEEEEEEEee
Confidence 3355555544443 45566 789999999999999988888887776643
No 10
>PF06030 DUF916: Bacterial protein of unknown function (DUF916); InterPro: IPR010317 This family consists of putative cell surface proteins, from Firmicutes, of unknown function.
Probab=85.59 E-value=2.2 Score=30.23 Aligned_cols=45 Identities=27% Similarity=0.200 Sum_probs=33.9
Q ss_pred CCCCCCCCcEEEEEEEee-----ccce----------------------EEEEEEEcCCCeEEEEEEEEecc
Q psy9572 3 DHKNVLRYNIREKVYLYE-----FEVF----------------------RRKKLTIKANSGSTTTFVITPKE 47 (163)
Q Consensus 3 ~~~Ny~~~~~~v~V~l~~-----~~~~----------------------~~~~v~v~~~~~~~v~f~v~~~~ 47 (163)
.++|.+++.++++|.+.. ++.+ ..+.|+|+|++++.|.|.|...+
T Consensus 34 ~i~N~s~~~~tv~v~~~~A~Tn~nG~I~Y~~~~~~~d~sl~~~~~~~v~~~~~Vtl~~~~sk~V~~~i~~P~ 105 (121)
T PF06030_consen 34 RITNNSDKEITVKVSANTATTNDNGVIDYSQNNPKKDKSLKYPFSDLVKIPKEVTLPPNESKTVTFTIKMPK 105 (121)
T ss_pred EEEeCCCCCEEEEEEEeeeEecCCEEEEECCCCcccCcccCcchHHhccCCcEEEECCCCEEEEEEEEEcCC
Confidence 368999999999888764 1111 12349999999999999998754
No 11
>PF05326 SVA: Seminal vesicle autoantigen (SVA); InterPro: IPR007990 This family consists of seminal vesicle autoantigen and prolactin-inducible (PIP) proteins. Seminal vesicle autoantigen (SVA) is specifically present in the seminal plasma of mice. This 19 kDa secretory glycoprotein suppresses the motility of spermatozoa by interacting with phospholipid. PIP has several known functions. In saliva, this protein plays a role in host defence by binding to microorganisms such as Streptococcus. PIP is an aspartyl proteinase and it acts as a factor capable of suppressing T-cell apoptosis through its interaction with CD4 [].; GO: 0005576 extracellular region; PDB: 3ES6_B.
Probab=83.64 E-value=8.3 Score=27.55 Aligned_cols=51 Identities=16% Similarity=0.029 Sum_probs=32.1
Q ss_pred CCCCCCCcEEEEEEEeeccce-----EEEEEEEcCCCeEEEEEEEEecccceEEEE
Q psy9572 4 HKNVLRYNIREKVYLYEFEVF-----RRKKLTIKANSGSTTTFVITPKELGYIGIK 54 (163)
Q Consensus 4 ~~Ny~~~~~~v~V~l~~~~~~-----~~~~v~v~~~~~~~v~f~v~~~~~G~~~i~ 54 (163)
|+|++.+|+.|++.+..+..+ ..-+-+++.+..+...|.+...+.+.+...
T Consensus 56 V~t~~~eCmvVk~yl~sn~~i~~~fny~YTaCLC~d~~r~FyWDi~~~~t~~i~~~ 111 (124)
T PF05326_consen 56 VTTELRECMVVKIYLESNPPIDGSFNYKYTACLCDDYPRTFYWDIQVNRTVTIAAV 111 (124)
T ss_dssp EEE--SS-EEEEEEEEESS---SGGG-EEEEEE-SSS-EEEEEEE--SS-EEEEEE
T ss_pred EEcchheeEEEEEEeccCCCccccccceEEEEeCCCCCccEEEEEEECceEEEEEE
Confidence 578889999999999886554 356789999999999999999885544333
No 12
>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=80.29 E-value=8.5 Score=25.34 Aligned_cols=18 Identities=17% Similarity=0.171 Sum_probs=10.4
Q ss_pred EEEEEEcCCCeEEEEEEE
Q psy9572 26 RKKLTIKANSGSTTTFVI 43 (163)
Q Consensus 26 ~~~v~v~~~~~~~v~f~v 43 (163)
.++++|++|+...+.|.+
T Consensus 48 ~~~~~v~ag~~~~~~w~l 65 (89)
T PF05506_consen 48 PWTYTVAAGQTVSLTWPL 65 (89)
T ss_pred CEEEEECCCCEEEEEEee
Confidence 345566666666666655
No 13
>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=73.84 E-value=8.2 Score=26.14 Aligned_cols=53 Identities=17% Similarity=0.164 Sum_probs=33.4
Q ss_pred CCCCCCCc-EEEEEEEee-----ccce------EEEEEEEcCCCeEEEEEEEEecccceEEEEEE
Q psy9572 4 HKNVLRYN-IREKVYLYE-----FEVF------RRKKLTIKANSGSTTTFVITPKELGYIGIKVT 56 (163)
Q Consensus 4 ~~Ny~~~~-~~v~V~l~~-----~~~~------~~~~v~v~~~~~~~v~f~v~~~~~G~~~i~v~ 56 (163)
++|-++.. -+|++.+.. ++.. ....++|+|++...+.+.+.+.+.|...+-+.
T Consensus 23 ~~N~~~~~l~~v~~~l~~~~v~ytG~~~~~~~~~~~~~~l~p~~~~~~~~~i~p~~yG~~~~l~~ 87 (107)
T PF00927_consen 23 FTNPSSEPLRNVSLNLCAFTVEYTGLTRDQFKKEKFEVTLKPGETKSVEVTITPSQYGPKQLLVD 87 (107)
T ss_dssp EEE-SSS-EECEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE-HHSHEEECCEEE
T ss_pred EEeCCcCccccceeEEEEEEEEECCcccccEeEEEcceeeCCCCEEEEEEEEEceeEecchhcch
Confidence 35777777 556666633 3332 23468999999999999999999887444433
No 14
>PRK13211 N-acetylglucosamine-binding protein A; Reviewed
Probab=69.20 E-value=51 Score=28.98 Aligned_cols=34 Identities=18% Similarity=0.209 Sum_probs=24.6
Q ss_pred EEEEEEcCCCeEEEEEEEEecccceEEEEEEEeec
Q psy9572 26 RKKLTIKANSGSTTTFVITPKELGYIGIKVTATSN 60 (163)
Q Consensus 26 ~~~v~v~~~~~~~v~f~v~~~~~G~~~i~v~a~~~ 60 (163)
.+..+|..++ ..+.+.+...+.|...|.++++..
T Consensus 357 ~~~~~v~d~s-~~vtL~Ls~~~AG~y~Lvv~~t~~ 390 (478)
T PRK13211 357 SKSQTVNDGS-QSVSLDLSKLKAGHHMLVVKAKPK 390 (478)
T ss_pred eeeEEecCCc-eeEEEecccCCCceEEEEEEEEeC
Confidence 4456666655 777777777788888888888765
No 15
>KOG2649|consensus
Probab=69.18 E-value=22 Score=31.17 Aligned_cols=34 Identities=21% Similarity=0.311 Sum_probs=22.2
Q ss_pred EEEEEecccceEEEEEEEeecCCCCeEEEEEEEeeCCee
Q psy9572 40 TFVITPKELGYIGIKVTATSNLAGDSMEGKLLVKPEGET 78 (163)
Q Consensus 40 ~f~v~~~~~G~~~i~v~a~~~~~~d~v~~~l~V~~~g~~ 78 (163)
+|.+.+ .|+-.|+++|.+- +.+.|...|.+.+..
T Consensus 414 YWRLL~--PG~y~vta~A~Gy---~~~tk~v~V~~~~a~ 447 (500)
T KOG2649|consen 414 YWRLLP--PGKYIITASAEGY---DPVTKTVTVPPDRAA 447 (500)
T ss_pred eEEeeC--CcceEEEEecCCC---cceeeEEEeCCCCcc
Confidence 344443 5777788877764 677777777764443
No 16
>cd08695 C2_Dock-B C2 domains found in Dedicator Of CytoKinesis (Dock) class B proteins. Dock-B is one of 4 classes of Dock family proteins. The members here include: Dock3/MOCA (modifier of cell adhesion) and Dock4. Most of these members have been shown to be GEFs specific for Rac, although Dock4 has also been shown to interact indirectly with the Ras family GTPase Rap1, probably through Rap regulatory proteins. In addition to the C2 domain (AKA Dock homology region (DHR)-1, CED-5, Dock180, MBC-zizimin homology (CZH) 1) and the DHR-2 (AKA CZH2, or Docker), which all Dock180-related proteins have, Dock-B members contain a SH3 domain upstream of the C2 domain and a proline-rich region downstream. DHR-2 has the catalytic activity for Rac and/or Cdc42, but is structurally unrelated to the DH domain. The C2/DHR-1 domains of Dock180 and Dock4 have been shown to bind phosphatidylinositol-3, 4, 5-triphosphate (PtdIns(3,4,5)P3). The C2 domain was first identified in PKC. C2 domains fold int
Probab=67.98 E-value=17 Score=27.87 Aligned_cols=62 Identities=10% Similarity=0.205 Sum_probs=41.9
Q ss_pred eEEEEEEEeecCCCCeEEEEEEEeeCCeeEEEEEEEEEecCCCCceEEEEecCCCCCCcCCcc
Q psy9572 50 YIGIKVTATSNLAGDSMEGKLLVKPEGETQYKNKAIFVDLRKNKTFSVNVTLDMPKNIVPGSE 112 (163)
Q Consensus 50 ~~~i~v~a~~~~~~d~v~~~l~V~~~g~~~~~~~~~~l~~~~~~~~~~~~~~~lp~~~vpgS~ 112 (163)
++.|++..... .++.++..|...+...+.++..+.++--.+.-...++|++.+|.+..+++-
T Consensus 24 NIeV~v~v~~~-~G~~~~~cI~~~~g~~~~se~~S~V~yH~~~P~W~EtiKi~lP~~~~~~~H 85 (189)
T cd08695 24 NIEVTMVVLDA-DGQVLKDCISLGSGEPPCSEYRSFVLYHNNSPRWNETIKLPIPIDKFRGSH 85 (189)
T ss_pred eEEEEEEEEcC-CCCCccCCEEcCCCCCccceEEEEEEEcCCCCCCceeEEEecChhhCCCee
Confidence 45666666544 344577788887777777777777665333334778899999988777644
No 17
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=63.83 E-value=35 Score=22.90 Aligned_cols=41 Identities=17% Similarity=0.254 Sum_probs=28.2
Q ss_pred EEEeeCCeeEEEEEEEEEecCCCCceEEEEecCCCCCCcCCcceE
Q psy9572 70 LLVKPEGETQYKNKAIFVDLRKNKTFSVNVTLDMPKNIVPGSEHV 114 (163)
Q Consensus 70 l~V~~~g~~~~~~~~~~l~~~~~~~~~~~~~~~lp~~~vpgS~~~ 114 (163)
+.|.+.|..+++...+.|..+ .+.-+-..+|..+.++|.++
T Consensus 2 VTVy~~gA~Vtr~~~v~l~~G----~~~i~~~~Lp~~~d~~Sl~V 42 (104)
T PF13600_consen 2 VTVYPDGAQVTREASVSLPAG----ENEIIFEGLPPSLDPDSLRV 42 (104)
T ss_pred EEEECCceEEEEEEEEEeCCC----ceEEEEeCCCcccCCCcEEE
Confidence 457889999988888777553 23222336888888887654
No 18
>TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein FixG. Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum.
Probab=63.74 E-value=56 Score=28.31 Aligned_cols=56 Identities=11% Similarity=0.086 Sum_probs=38.5
Q ss_pred CCCCCCCcEEEEEEEeeccceE---E-EEEEEcCCCeEEEEEEEEec----ccceEEEEEEEee
Q psy9572 4 HKNVLRYNIREKVYLYEFEVFR---R-KKLTIKANSGSTTTFVITPK----ELGYIGIKVTATS 59 (163)
Q Consensus 4 ~~Ny~~~~~~v~V~l~~~~~~~---~-~~v~v~~~~~~~v~f~v~~~----~~G~~~i~v~a~~ 59 (163)
+.|-+.++.+++++++..++.. . ..+.|+||+...+.+.+... +.|..+|++++.+
T Consensus 354 i~Nk~~~~~~~~l~v~g~~~~~~~~~~~~i~v~~g~~~~~~v~v~~~~~~~~~~~~~i~~~v~~ 417 (434)
T TIGR02745 354 ILNKTEQPHEYYLSVLGLPGIKIEGPGAPIHVKAGEKVKLPVFLRTPPDALKSGITSIEIRAYA 417 (434)
T ss_pred EEECCCCCEEEEEEEecCCCcEEEcCCceEEECCCCEEEEEEEEEechhhccCCceeEEEEEEE
Confidence 4577778888888877644421 1 36899999999888877774 3566666666654
No 19
>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=61.62 E-value=38 Score=25.70 Aligned_cols=27 Identities=22% Similarity=0.492 Sum_probs=21.5
Q ss_pred EEEcCCCeEEEEEEEEecccceEEEEE
Q psy9572 29 LTIKANSGSTTTFVITPKELGYIGIKV 55 (163)
Q Consensus 29 v~v~~~~~~~v~f~v~~~~~G~~~i~v 55 (163)
=.|+||+..+..|.++|.+.|..+++-
T Consensus 81 ~~i~pg~~vsh~~vv~p~~~G~f~~~~ 107 (181)
T PF05753_consen 81 ERIPPGENVSHSYVVRPKKSGYFNFTP 107 (181)
T ss_pred EEECCCCeEEEEEEEeeeeeEEEEccC
Confidence 468899988889999998888766553
No 20
>PF03170 BcsB: Bacterial cellulose synthase subunit; InterPro: IPR018513 An operon encoding 4 proteins required for bacterial cellulose biosynthesis (bcs) in Acetobacter xylinus (Gluconacetobacter xylinus) has been isolated via genetic complementation with strains lacking cellulose synthase activity []. Nucleotide sequence analysis showed the cellulose synthase operon to consist of 4 genes, designated bcsA, bcsB, bcsC and bcsD, all of which are required for maximal bacterial cellulose synthesis in A. xylinum. The calculated molecular mass of the protein encoded by bcsB is 85.3kDa []. BcsB encodes the catalytic subunit of cellulose synthase. The protein polymerises uridine 5'-diphosphate glucose to cellulose: UDP-glucose + (1,4-beta-D-glucosyl)(N) = UDP + (1,4-beta-D-glucosyl)(N+1). The enzyme is specifically activated by the nucleotide cyclic diguanylic acid. Sequence analysis suggests that BcsB contains several transmembrane (TM) domains, and shares a high degree of similarity with Escherichia coli YhjN.; GO: 0006011 UDP-glucose metabolic process, 0016020 membrane
Probab=58.99 E-value=33 Score=30.65 Aligned_cols=80 Identities=15% Similarity=0.177 Sum_probs=50.7
Q ss_pred CeEEEEEEEEecc-cceEEEEEEEeecCCCCeEEEEEEEeeCCeeEEEEEEEEEecCCCCceEEEEecCCCCCCcCCcce
Q psy9572 35 SGSTTTFVITPKE-LGYIGIKVTATSNLAGDSMEGKLLVKPEGETQYKNKAIFVDLRKNKTFSVNVTLDMPKNIVPGSEH 113 (163)
Q Consensus 35 ~~~~v~f~v~~~~-~G~~~i~v~a~~~~~~d~v~~~l~V~~~g~~~~~~~~~~l~~~~~~~~~~~~~~~lp~~~vpgS~~ 113 (163)
....+.|.+.... .-.+.+++.-..+..-..-.-.|.|.-.|.++. +..+...+. +...+++.+|..+..|...
T Consensus 29 ~~~~~~f~v~~~~~v~~a~L~L~~~~S~~l~~~~S~L~V~lNg~~v~---s~~l~~~~~--~~~~~~i~Ip~~l~~g~N~ 103 (605)
T PF03170_consen 29 ASRTIYFPVPADWVVTKATLNLSYTYSPSLLPERSQLTVSLNGQPVG---SIPLDAESA--QPQTVTIPIPPALIKGFNR 103 (605)
T ss_pred CceEEEEEcCCCccccceEEEEEEEECcccCCCcceEEEEECCEEeE---EEecCcCCC--CceEEEEecChhhcCCceE
Confidence 3567788888753 334555555444322222234577888887763 223444322 3567788899889999999
Q ss_pred EEEEEE
Q psy9572 114 VEVSAV 119 (163)
Q Consensus 114 ~~v~v~ 119 (163)
++|++.
T Consensus 104 l~~~~~ 109 (605)
T PF03170_consen 104 LTFEFI 109 (605)
T ss_pred EEEEEE
Confidence 999988
No 21
>PF14310 Fn3-like: Fibronectin type III-like domain; PDB: 3ABZ_D 3AC0_D 2X40_A 2X41_A 2X42_A.
Probab=52.75 E-value=28 Score=21.77 Aligned_cols=25 Identities=16% Similarity=0.490 Sum_probs=19.0
Q ss_pred EEEEEEEcCCCeEEEEEEEEecccc
Q psy9572 25 RRKKLTIKANSGSTTTFVITPKELG 49 (163)
Q Consensus 25 ~~~~v~v~~~~~~~v~f~v~~~~~G 49 (163)
..+++.|+||+++++.|.+.+...+
T Consensus 23 gF~rv~l~pGes~~v~~~l~~~~l~ 47 (71)
T PF14310_consen 23 GFERVSLAPGESKTVSFTLPPEDLA 47 (71)
T ss_dssp EEEEEEE-TT-EEEEEEEEEHHHHE
T ss_pred ceEEEEECCCCEEEEEEEECHHHEe
Confidence 4678889999999999999986543
No 22
>PF07718 Coatamer_beta_C: Coatomer beta C-terminal region; InterPro: IPR011710 Proteins synthesised 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. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C-terminal domain of the beta subunit from coatomer proteins (Beta-coat proteins). The C-terminal domain probably adapts the function of the N-terminal IPR002553 from INTERPRO domain. Coatomer protein complex I (COPI)-coated vesicles are involved in transport between the endoplasmic reticulum and the Golgi but also participate in transport from early to late endosomes within the endocytic pathway []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat
Probab=49.60 E-value=38 Score=24.75 Aligned_cols=47 Identities=17% Similarity=0.110 Sum_probs=33.5
Q ss_pred CCCCCCc-EEEEEEEeeccceE----EEEEEEcCCCeEEEEEEEEe--cccceE
Q psy9572 5 KNVLRYN-IREKVYLYEFEVFR----RKKLTIKANSGSTTTFVITP--KELGYI 51 (163)
Q Consensus 5 ~Ny~~~~-~~v~V~l~~~~~~~----~~~v~v~~~~~~~v~f~v~~--~~~G~~ 51 (163)
-|-++.. ++++|.|...+++. .+.+++.|++...+...++. .+.|.+
T Consensus 78 vNqT~~tLqNl~vElat~gdLklve~p~~~tL~P~~~~~i~~~iKVsStetGvI 131 (140)
T PF07718_consen 78 VNQTNETLQNLTVELATLGDLKLVERPQPITLAPHGFARIKATIKVSSTETGVI 131 (140)
T ss_pred EeCChhhhhcEEEEEEecCCcEEccCCCceeeCCCcEEEEEEEEEEEeccCCEE
Confidence 3666666 56888888888763 45789999999888766655 455643
No 23
>PF14742 GDE_N_bis: N-terminal domain of (some) glycogen debranching enzymes
Probab=45.36 E-value=1e+02 Score=23.33 Aligned_cols=21 Identities=14% Similarity=-0.124 Sum_probs=16.0
Q ss_pred CCCCCCCcEEEEEEEeeccce
Q psy9572 4 HKNVLRYNIREKVYLYEFEVF 24 (163)
Q Consensus 4 ~~Ny~~~~~~v~V~l~~~~~~ 24 (163)
++||...+..+++.+.-..+|
T Consensus 99 l~N~~~~pv~~~l~l~~~aDF 119 (194)
T PF14742_consen 99 LTNYSPEPVELTLSLEFDADF 119 (194)
T ss_pred EEeCCCCCEEEEEEEEEECCc
Confidence 578888888887777776665
No 24
>cd03864 M14_CPN Peptidase M14 Carboxypeptidase N (CPN, also known as kininase I, creatine kinase conversion factor, plasma carboxypeptidase B, arginine carboxypeptidase, and protaminase; EC 3.4.17.3) is an extracellular glycoprotein synthesized in the liver and released into the blood, where it is present in high concentrations. CPN belongs to the N/E subfamily of the M14 family of metallocarboxypeptidases (MCPs).The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPN plays an important role in protecting the body from excessive buildup of potentially deleterious peptides that normally act as local autocrine or paracrine hormones. It specifically removes C-terminal basic residues. As CPN can cleave lysine more avidly than arginine residues it is also called lysine carboxypeptidase. CPN substrates inclu
Probab=44.54 E-value=1.2e+02 Score=25.97 Aligned_cols=22 Identities=23% Similarity=0.060 Sum_probs=16.7
Q ss_pred CCCCCCCCCC-cEEEEEEEeeccc
Q psy9572 1 MNDHKNVLRY-NIREKVYLYEFEV 23 (163)
Q Consensus 1 ~~~~~Ny~~~-~~~v~V~l~~~~~ 23 (163)
|.| +||+.+ |.++++.|.+.+-
T Consensus 268 mqD-~~Y~~~nc~e~t~el~c~k~ 290 (392)
T cd03864 268 MQD-FNYLHTNCFEITLELSCDKF 290 (392)
T ss_pred chh-hhhhccCeeEEEEeccccCC
Confidence 678 888877 6888888887443
No 25
>cd08694 C2_Dock-A C2 domains found in Dedicator Of CytoKinesis (Dock) class A proteins. Dock-A is one of 4 classes of Dock family proteins. The members here include: Dock180/Dock1, Dock2, and Dock5. Most of these members have been shown to be GEFs specific for Rac. Dock5 has not been well characterized to date, but most likely also is a GEF specific for Rac. In addition to the C2 domain (AKA Dock homology region (DHR)-1, CED-5, Dock180, MBC-zizimin homology (CZH) 1) and the DHR-2 (AKA CZH2, or Docker), which all Dock180-related proteins have, Dock-A members contain a proline-rich region and a SH3 domain upstream of the C2 domain. DHR-2 has the catalytic activity for Rac and/or Cdc42, but is structurally unrelated to the DH domain. The C2/DHR-1 domains of Dock180 and Dock4 have been shown to bind phosphatidylinositol-3, 4, 5-triphosphate (PtdIns(3,4,5)P3). The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangemen
Probab=43.90 E-value=1e+02 Score=23.84 Aligned_cols=62 Identities=11% Similarity=0.172 Sum_probs=32.8
Q ss_pred eEEEEEEEeecCCCCeEEEEEEEeeCCeeEEEEEEEEEecCCCCceEEEEecCCCCCCcCCcc
Q psy9572 50 YIGIKVTATSNLAGDSMEGKLLVKPEGETQYKNKAIFVDLRKNKTFSVNVTLDMPKNIVPGSE 112 (163)
Q Consensus 50 ~~~i~v~a~~~~~~d~v~~~l~V~~~g~~~~~~~~~~l~~~~~~~~~~~~~~~lp~~~vpgS~ 112 (163)
++.|++..... .++.++..|-.-......++..+.++--.+.....++|++.+|.+..+++-
T Consensus 24 NIeVtv~vr~~-~G~~i~~~i~~gsg~~~~se~~S~V~Yh~~~P~W~EtIKl~lP~~~~~~~H 85 (196)
T cd08694 24 NVEVTVSVCNE-DGKIIPGVISLGAGEEPIDEYKSVIYYQVDKPKWFETFKVAIPIEDFKSSH 85 (196)
T ss_pred eEEEEEEEECC-CCCCCceeEEcCCCCCcceeEEEEEEeecCCCCCceeEEEecChhhCCCeE
Confidence 45555555443 344455444332223344444555443232334677888888887776643
No 26
>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=43.42 E-value=34 Score=23.30 Aligned_cols=42 Identities=21% Similarity=0.157 Sum_probs=23.1
Q ss_pred CCCCCCCcEEEEEEEe-e-------ccce---------------EEEEEEEcCCCeEEEEEEEEe
Q psy9572 4 HKNVLRYNIREKVYLY-E-------FEVF---------------RRKKLTIKANSGSTTTFVITP 45 (163)
Q Consensus 4 ~~Ny~~~~~~v~V~l~-~-------~~~~---------------~~~~v~v~~~~~~~v~f~v~~ 45 (163)
++|+.++.+..++.-. . .+.+ ....++|+||+++.+.+.+.+
T Consensus 16 l~N~~~~~~ty~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~vTV~ag~s~~v~vti~~ 80 (112)
T PF06280_consen 16 LHNYGDKPVTYTLSHVPVLTDKTDTEEGYSILVPPVPSISTVSFSPDTVTVPAGQSKTVTVTITP 80 (112)
T ss_dssp EEE-SSS-EEEEEEEE-EEEEEE--ETTEEEEEEEE----EEE---EEEEE-TTEEEEEEEEEE-
T ss_pred EEECCCCCEEEEEeeEEEEeeEeeccCCcccccccccceeeEEeCCCeEEECCCCEEEEEEEEEe
Confidence 5788888877666544 1 0111 134677888888877777777
No 27
>PF00731 AIRC: AIR carboxylase; InterPro: IPR000031 Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain []. The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme [].; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process; PDB: 3TRH_O 2YWX_A 2NSL_A 1D7A_A 2NSJ_A 1QCZ_A 2ATE_A 2NSH_A 3RG8_C 3RGG_D ....
Probab=42.25 E-value=21 Score=26.30 Aligned_cols=31 Identities=13% Similarity=0.273 Sum_probs=16.1
Q ss_pred EeccCCCcccchhhhHhhhhhCCCCchhhhh
Q psy9572 119 VACKIGDLLGPSIPNLANLIKMPFGCGEQNM 149 (163)
Q Consensus 119 ~~~~~~~~~~~~~~~l~~Li~~PyGC~EQt~ 149 (163)
.|.|+..--..-++.+-++++||.||.=-|+
T Consensus 82 IgvP~~~~~~~g~d~l~S~vqMp~g~pvatv 112 (150)
T PF00731_consen 82 IGVPVSSGYLGGLDSLLSIVQMPSGVPVATV 112 (150)
T ss_dssp EEEEE-STTTTTHHHHHHHHT--TTS--EE-
T ss_pred EEeecCcccccCcccHHHHHhccCCCCceEE
Confidence 3444444334445788899999999974443
No 28
>PF06030 DUF916: Bacterial protein of unknown function (DUF916); InterPro: IPR010317 This family consists of putative cell surface proteins, from Firmicutes, of unknown function.
Probab=41.47 E-value=1.2e+02 Score=21.22 Aligned_cols=87 Identities=21% Similarity=0.192 Sum_probs=47.5
Q ss_pred EEEEcCCCeEEEEEEEEecccceEEEEEEEeecCCCC-----------eEEEEEEEe-eCCeeEEEEEEEEEecCCCCce
Q psy9572 28 KLTIKANSGSTTTFVITPKELGYIGIKVTATSNLAGD-----------SMEGKLLVK-PEGETQYKNKAIFVDLRKNKTF 95 (163)
Q Consensus 28 ~v~v~~~~~~~v~f~v~~~~~G~~~i~v~a~~~~~~d-----------~v~~~l~V~-~~g~~~~~~~~~~l~~~~~~~~ 95 (163)
.+.+.||+...+.+.|.-...-.+.+++.+....-++ ...+.+... .+.+.. ...+.|.++ ...
T Consensus 20 dL~~~P~q~~~l~v~i~N~s~~~~tv~v~~~~A~Tn~nG~I~Y~~~~~~~d~sl~~~~~~~v~~--~~~Vtl~~~--~sk 95 (121)
T PF06030_consen 20 DLKVKPGQKQTLEVRITNNSDKEITVKVSANTATTNDNGVIDYSQNNPKKDKSLKYPFSDLVKI--PKEVTLPPN--ESK 95 (121)
T ss_pred EEEeCCCCEEEEEEEEEeCCCCCEEEEEEEeeeEecCCEEEEECCCCcccCcccCcchHHhccC--CcEEEECCC--CEE
Confidence 4778999999998888876555666666654321000 011122210 111111 111556554 346
Q ss_pred EEEEecCCCCCCcCCcceEEEEE
Q psy9572 96 SVNVTLDMPKNIVPGSEHVEVSA 118 (163)
Q Consensus 96 ~~~~~~~lp~~~vpgS~~~~v~v 118 (163)
...+.+.+|++..+|-...-|.+
T Consensus 96 ~V~~~i~~P~~~f~G~ilGGi~~ 118 (121)
T PF06030_consen 96 TVTFTIKMPKKAFDGIILGGIYF 118 (121)
T ss_pred EEEEEEEcCCCCcCCEEEeeEEE
Confidence 67788889988777755544443
No 29
>PF07703 A2M_N_2: Alpha-2-macroglobulin family N-terminal region; InterPro: IPR011625 This is a domain of the alpha-2-macroglobulin family. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; PDB: 2QKI_D 3L3O_D 3NMS_A 2ICF_A 2A73_A 2ICE_D 2HR0_A 2A74_A 2XWJ_G 3OHX_A ....
Probab=40.51 E-value=1.2e+02 Score=20.86 Aligned_cols=15 Identities=33% Similarity=0.601 Sum_probs=9.5
Q ss_pred CCCCcCCcceEEEEEE
Q psy9572 104 PKNIVPGSEHVEVSAV 119 (163)
Q Consensus 104 p~~~vpgS~~~~v~v~ 119 (163)
++.+.||+. +++.+.
T Consensus 103 ~~~~~Pg~~-~~~~i~ 117 (136)
T PF07703_consen 103 PDEYKPGEE-VTLRIK 117 (136)
T ss_dssp SSSBTTTSE-EEEEEE
T ss_pred cceeCCCCE-EEEEEE
Confidence 567888844 555555
No 30
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=38.87 E-value=1.1e+02 Score=20.00 Aligned_cols=22 Identities=14% Similarity=0.176 Sum_probs=10.7
Q ss_pred EEcCCCeEEEEEEEE-ecccceE
Q psy9572 30 TIKANSGSTTTFVIT-PKELGYI 51 (163)
Q Consensus 30 ~v~~~~~~~v~f~v~-~~~~G~~ 51 (163)
.|+||....+...+. +...|..
T Consensus 58 ~l~PG~~~~~~V~~~~~~~~g~~ 80 (102)
T PF14874_consen 58 FLAPGESVELEVTFSPTKPLGDY 80 (102)
T ss_pred EECCCCEEEEEEEEEeCCCCceE
Confidence 455555555555555 2334433
No 31
>PF10572 UPF0556: Uncharacterised protein family UPF0556; InterPro: IPR018887 This family of proteins has no known function.
Probab=33.51 E-value=2e+02 Score=21.40 Aligned_cols=20 Identities=20% Similarity=0.280 Sum_probs=11.6
Q ss_pred CeEEEEEEEeeCCeeEEEEE
Q psy9572 64 DSMEGKLLVKPEGETQYKNK 83 (163)
Q Consensus 64 d~v~~~l~V~~~g~~~~~~~ 83 (163)
+...+.+.|+|.|...+...
T Consensus 22 e~~t~eFdvkP~G~~~t~~~ 41 (158)
T PF10572_consen 22 EPTTKEFDVKPGGVVHTFSE 41 (158)
T ss_pred cccceeEEecCCCEEEEeEE
Confidence 44556666777776554443
No 32
>PF12080 GldM_C: GldM C-terminal domain; InterPro: IPR022719 This domain is found in bacteria at the C terminus of the GldM protein. This domain is typically between 169 to 182 amino acids in length and has two completely conserved residues (Y and N) that may be functionally important. GldM, is named for the member from Bacteriodetes Flavobacterium johnsoniae, which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes [].
Probab=33.18 E-value=1.6e+02 Score=22.16 Aligned_cols=39 Identities=23% Similarity=0.305 Sum_probs=27.4
Q ss_pred EEEEEecccceEEEEEEEeecCCCCeEE---EEEEEeeCCeeE
Q psy9572 40 TFVITPKELGYIGIKVTATSNLAGDSME---GKLLVKPEGETQ 79 (163)
Q Consensus 40 ~f~v~~~~~G~~~i~v~a~~~~~~d~v~---~~l~V~~~g~~~ 79 (163)
.|.++|..-+++.|+|+|+... ++.+. +.++|++---|.
T Consensus 46 ~y~~~P~~g~~v~I~Vs~~~~~-g~~~~l~s~~FRVk~lP~P~ 87 (181)
T PF12080_consen 46 KYIARPTSGKEVTITVSATNPD-GKGVSLGSFTFRVKPLPDPT 87 (181)
T ss_pred cEEEEeCCCCeEEEEEEEEecC-CCceeecceEEEeeeCCCCc
Confidence 7999998777899999988763 33333 777786544444
No 33
>PF15418 DUF4625: Domain of unknown function (DUF4625)
Probab=33.11 E-value=1.8e+02 Score=20.77 Aligned_cols=80 Identities=14% Similarity=0.218 Sum_probs=45.9
Q ss_pred EEEcCCCeEEEEEEEEec-ccceEEEEE------EEeecCCCCeEEEEEEEeeCCeeEEEEEEEEEecCCCCceEEEEec
Q psy9572 29 LTIKANSGSTTTFVITPK-ELGYIGIKV------TATSNLAGDSMEGKLLVKPEGETQYKNKAIFVDLRKNKTFSVNVTL 101 (163)
Q Consensus 29 v~v~~~~~~~v~f~v~~~-~~G~~~i~v------~a~~~~~~d~v~~~l~V~~~g~~~~~~~~~~l~~~~~~~~~~~~~~ 101 (163)
..+.+|+.-.+.+.|.+. ++|.+.|.+ -..+....+. ++.|. + .+..-+ +.+.....+...+
T Consensus 30 ~~~~~G~~ihfe~~i~d~~~i~si~VeIH~nfd~H~h~~~~~~~-~~~~~-----~----~~~~~~-~~g~~~~~~h~~i 98 (132)
T PF15418_consen 30 KVATRGDDIHFEADISDNSAIKSIKVEIHNNFDHHTHSTEAGEC-EKPWV-----F----EQDYDI-YGGKKNYDFHEHI 98 (132)
T ss_pred eEEecCCcEEEEEEEEcccceeEEEEEEecCcCccccccccccc-ccCcE-----E----EEEEcc-cCCcccEeEEEee
Confidence 445667776777777774 577777777 3232211121 11111 1 111111 1222235566688
Q ss_pred CCCCCCcCCcceEEEEEE
Q psy9572 102 DMPKNIVPGSEHVEVSAV 119 (163)
Q Consensus 102 ~lp~~~vpgS~~~~v~v~ 119 (163)
++|+++.+|--...|+|+
T Consensus 99 ~IPa~a~~G~YH~~i~Vt 116 (132)
T PF15418_consen 99 DIPADAPAGDYHFMITVT 116 (132)
T ss_pred eCCCCCCCcceEEEEEEE
Confidence 999999999999999997
No 34
>PF08308 PEGA: PEGA domain; InterPro: IPR013229 This domain is found in both archaea and bacteria and has similarity to S-layer (surface layer) proteins. It is named after the characteristic PEGA sequence motif found in this domain. The secondary structure of this domain is predicted to be beta-strands.
Probab=31.10 E-value=1.3e+02 Score=18.37 Aligned_cols=31 Identities=13% Similarity=0.154 Sum_probs=18.9
Q ss_pred EEEEEecccceEEEEEEEeecCCCCeEEEEEEEe
Q psy9572 40 TFVITPKELGYIGIKVTATSNLAGDSMEGKLLVK 73 (163)
Q Consensus 40 ~f~v~~~~~G~~~i~v~a~~~~~~d~v~~~l~V~ 73 (163)
++.+.....|...|++++.+. ...++.+.|.
T Consensus 26 p~~~~~l~~G~~~v~v~~~Gy---~~~~~~v~v~ 56 (71)
T PF08308_consen 26 PLTLKDLPPGEHTVTVEKPGY---EPYTKTVTVK 56 (71)
T ss_pred cceeeecCCccEEEEEEECCC---eeEEEEEEEC
Confidence 444555567777777777764 4455555555
No 35
>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=30.38 E-value=70 Score=31.30 Aligned_cols=42 Identities=19% Similarity=0.158 Sum_probs=34.6
Q ss_pred CCCCCCCCcEEEEEEEeeccceEEEEEEEcCCCeEEEEEEEEec
Q psy9572 3 DHKNVLRYNIREKVYLYEFEVFRRKKLTIKANSGSTTTFVITPK 46 (163)
Q Consensus 3 ~~~Ny~~~~~~v~V~l~~~~~~~~~~v~v~~~~~~~v~f~v~~~ 46 (163)
|+.|-.++.+.+++++ .+.+..+...|++|...++.+++.-.
T Consensus 968 DlrNsw~~~~~v~l~~--~~~~~~~~~~I~pg~t~Ri~vPi~Ri 1009 (1185)
T PF08626_consen 968 DLRNSWPNPLSVNLHY--DEDFSSSEITIEPGHTSRIIVPIKRI 1009 (1185)
T ss_pred EEEecCCCceEEEEEe--ccCccccceEECCCCeEEEEEEeccc
Confidence 8899999998888887 55555666899999999998888864
No 36
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=29.34 E-value=95 Score=19.65 Aligned_cols=34 Identities=15% Similarity=0.321 Sum_probs=18.8
Q ss_pred CeEEEEEEEEecccceEEEEEEEeecCCCCeEEEEEEE
Q psy9572 35 SGSTTTFVITPKELGYIGIKVTATSNLAGDSMEGKLLV 72 (163)
Q Consensus 35 ~~~~v~f~v~~~~~G~~~i~v~a~~~~~~d~v~~~l~V 72 (163)
....+.|.+.|...|.+.++++..+ +.+.-.|.+
T Consensus 11 ~~~~~~l~L~p~~LG~v~v~l~~~~----~~l~v~~~~ 44 (85)
T PF02120_consen 11 GSWELSLQLDPPELGSVEVKLRLQG----GNLSVQFTA 44 (85)
T ss_dssp T--EEEE--SSGGG--EEEEEEEET----TEEEEEEE-
T ss_pred CceEEEEEEcccccCcEEEEEEEeC----CEEEEEEEE
Confidence 4566788888889999888887765 345444443
No 37
>PRK15098 beta-D-glucoside glucohydrolase; Provisional
Probab=28.18 E-value=1.4e+02 Score=27.72 Aligned_cols=24 Identities=25% Similarity=0.336 Sum_probs=19.1
Q ss_pred EEEEEEcCCCeEEEEEEEEecccc
Q psy9572 26 RKKLTIKANSGSTTTFVITPKELG 49 (163)
Q Consensus 26 ~~~v~v~~~~~~~v~f~v~~~~~G 49 (163)
.+++.|+||++++|.|.+.....+
T Consensus 708 F~Kv~L~pGes~~V~~~l~~~~L~ 731 (765)
T PRK15098 708 FEKIMLKPGETQTVSFPIDIEALK 731 (765)
T ss_pred ceeEeECCCCeEEEEEeecHHHhc
Confidence 457889999999999999876543
No 38
>PF09394 Inhibitor_I42: Chagasin family peptidase inhibitor I42; InterPro: IPR018990 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. Chagasin reversible inhibitor of papain-like cysteine proteases []. Chagasin has a beta-barrel structure, which is a unique variant of the immunoglobulin fold with homology to human CD8alpha [, ].; PDB: 2NQD_A 2NNR_A 2H7W_B 3E1Z_A 3CBK_B 3CBJ_B 2OUL_B 2FO8_A 2WGN_B 2C34_A ....
Probab=27.80 E-value=1.7e+02 Score=18.73 Aligned_cols=28 Identities=21% Similarity=0.196 Sum_probs=21.6
Q ss_pred CCeEEEEEEEEecccceEEEEEEEeecC
Q psy9572 34 NSGSTTTFVITPKELGYIGIKVTATSNL 61 (163)
Q Consensus 34 ~~~~~v~f~v~~~~~G~~~i~v~a~~~~ 61 (163)
|+...-.|.+++.+.|...|++.-....
T Consensus 50 G~~g~~~f~f~a~~~G~~~i~~~y~r~w 77 (92)
T PF09394_consen 50 GAPGTRTFTFKALKPGTTTIKFEYRRPW 77 (92)
T ss_dssp TSSEEEEEEEEESSSEEEEEEEEEEBTT
T ss_pred CCCcEEEEEEEEecCeeEEEEEEEECcC
Confidence 5556667999999999999988766543
No 39
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.17 E-value=44 Score=25.18 Aligned_cols=16 Identities=31% Similarity=0.627 Sum_probs=12.0
Q ss_pred CCchhhhhhhhhHHHH
Q psy9572 142 FGCGEQNMLNFVPNIV 157 (163)
Q Consensus 142 yGC~EQt~s~~~P~l~ 157 (163)
.-|||||...|+--+.
T Consensus 140 g~CGEqtCmaFAiKLl 155 (193)
T COG4871 140 GKCGEQTCMAFAIKLL 155 (193)
T ss_pred ccchhHHHHHHHHHHH
Confidence 3599999888875543
No 40
>COG3534 AbfA Alpha-L-arabinofuranosidase [Carbohydrate transport and metabolism]
Probab=25.02 E-value=28 Score=30.40 Aligned_cols=16 Identities=25% Similarity=0.362 Sum_probs=11.9
Q ss_pred hhhhHhhh----hhCCCCch
Q psy9572 130 SIPNLANL----IKMPFGCG 145 (163)
Q Consensus 130 ~~~~l~~L----i~~PyGC~ 145 (163)
+++.|+.| +|||.|||
T Consensus 54 Vle~lk~Lk~P~lR~PGGnF 73 (501)
T COG3534 54 VLEALKDLKIPVLRWPGGNF 73 (501)
T ss_pred HHHHHHhcCCceeecCCccc
Confidence 34556555 89999997
No 41
>PF06205 GT36_AF: Glycosyltransferase 36 associated family ; InterPro: IPR010403 This domain is found in the NvdB protein (P20471 from SWISSPROT), which is involved in the production of beta-(1-->2)-glucan.; PDB: 1V7V_A 1V7W_A 1V7X_A 3ACT_B 2CQT_A 3QFY_B 3QFZ_A 2CQS_A 3QG0_B 3AFJ_A ....
Probab=24.11 E-value=1.3e+02 Score=19.78 Aligned_cols=20 Identities=10% Similarity=0.363 Sum_probs=14.8
Q ss_pred EEEEEEcCCCeEEEEEEEEe
Q psy9572 26 RKKLTIKANSGSTTTFVITP 45 (163)
Q Consensus 26 ~~~v~v~~~~~~~v~f~v~~ 45 (163)
+..++|+||+++.+.|.+-.
T Consensus 65 ~~~v~L~PGe~~~v~f~lG~ 84 (90)
T PF06205_consen 65 QVRVTLEPGEEKEVVFLLGA 84 (90)
T ss_dssp EEEEEE-TT-EEEEEEEEEE
T ss_pred EEEEEECCCCEEEEEEEEEE
Confidence 56799999999999987654
No 42
>KOG4386|consensus
Probab=23.31 E-value=1.3e+02 Score=27.18 Aligned_cols=48 Identities=15% Similarity=0.201 Sum_probs=35.2
Q ss_pred CCCCCCCcEEEEEEEeeccce-----EEEEEEEcCCCeEEEEEEEEecccceE
Q psy9572 4 HKNVLRYNIREKVYLYEFEVF-----RRKKLTIKANSGSTTTFVITPKELGYI 51 (163)
Q Consensus 4 ~~Ny~~~~~~v~V~l~~~~~~-----~~~~v~v~~~~~~~v~f~v~~~~~G~~ 51 (163)
++|.++--+.|...++.++.| ...++.+-||..+.+.+.+-|.-.|..
T Consensus 716 LqnktdlvqdveisvepsDaFMFSGlkqirlriLPGteqemlynfypLmAGyq 768 (809)
T KOG4386|consen 716 LQNKTDLVQDVEISVEPSDAFMFSGLKQIRLRILPGTEQEMLYNFYPLMAGYQ 768 (809)
T ss_pred eccccceeeeEEeecccchhheecccceEEEEEcCCCceEEEEEEehhhchhh
Confidence 467777777777788877776 344678888888888888887776643
No 43
>PF13157 DUF3992: Protein of unknown function (DUF3992)
Probab=23.15 E-value=2.2e+02 Score=19.15 Aligned_cols=8 Identities=13% Similarity=0.463 Sum_probs=3.1
Q ss_pred EEEcCCCe
Q psy9572 29 LTIKANSG 36 (163)
Q Consensus 29 v~v~~~~~ 36 (163)
++|.+|++
T Consensus 56 ftV~pG~S 63 (92)
T PF13157_consen 56 FTVQPGNS 63 (92)
T ss_pred EEECCCce
Confidence 33343333
No 44
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=22.65 E-value=28 Score=17.69 Aligned_cols=9 Identities=33% Similarity=0.637 Sum_probs=6.8
Q ss_pred hhhhCCCCc
Q psy9572 136 NLIKMPFGC 144 (163)
Q Consensus 136 ~Li~~PyGC 144 (163)
.|+.||+|-
T Consensus 6 ~~L~yp~GA 14 (25)
T PF06943_consen 6 TLLMYPRGA 14 (25)
T ss_pred ceEEcCCCC
Confidence 578899883
No 45
>COG1470 Predicted membrane protein [Function unknown]
Probab=22.55 E-value=5.5e+02 Score=22.81 Aligned_cols=35 Identities=17% Similarity=0.243 Sum_probs=25.9
Q ss_pred EEEEEecCCCCceEEEEecCCCCCCcCCcceEEEEEE
Q psy9572 83 KAIFVDLRKNKTFSVNVTLDMPKNIVPGSEHVEVSAV 119 (163)
Q Consensus 83 ~~~~l~~~~~~~~~~~~~~~lp~~~vpgS~~~~v~v~ 119 (163)
.++.|+++. .....+.+..|.++.||.-.+.|.++
T Consensus 325 t~vkL~~gE--~kdvtleV~ps~na~pG~Ynv~I~A~ 359 (513)
T COG1470 325 TSVKLKPGE--EKDVTLEVYPSLNATPGTYNVTITAS 359 (513)
T ss_pred EEEEecCCC--ceEEEEEEecCCCCCCCceeEEEEEe
Confidence 455677752 24555666678999999999998888
No 46
>PF11797 DUF3324: Protein of unknown function C-terminal (DUF3324); InterPro: IPR021759 This family consists of several hypothetical bacterial proteins of unknown function.
Probab=21.35 E-value=3.1e+02 Score=19.49 Aligned_cols=46 Identities=15% Similarity=0.169 Sum_probs=32.5
Q ss_pred EEEEEcCCCeEEEEEEEE--ecccceEEEEEEEeecCCCCeEEEEEEE
Q psy9572 27 KKLTIKANSGSTTTFVIT--PKELGYIGIKVTATSNLAGDSMEGKLLV 72 (163)
Q Consensus 27 ~~v~v~~~~~~~v~f~v~--~~~~G~~~i~v~a~~~~~~d~v~~~l~V 72 (163)
..+.+.|++.-..++.+. ..+.|+=.+++++.+....=..++.+.|
T Consensus 82 ~~~~mAPNS~f~~~i~~~~~~lk~G~Y~l~~~~~~~~~~W~f~k~F~I 129 (140)
T PF11797_consen 82 ENMQMAPNSNFNFPIPLGGKKLKPGKYTLKITAKSGKKTWTFTKDFTI 129 (140)
T ss_pred cCCEECCCCeEEeEecCCCcCccCCEEEEEEEEEcCCcEEEEEEEEEE
Confidence 347899999988888884 5689999999998876432233334333
No 47
>PF11622 DUF3251: Protein of unknown function (DUF3251); InterPro: IPR021658 This entry represents immunoglobulin-like domain found in a group of putative lipoprotein YajI. ; PDB: 2JWY_A.
Probab=21.25 E-value=3.6e+02 Score=20.23 Aligned_cols=90 Identities=11% Similarity=0.200 Sum_probs=39.4
Q ss_pred EEEcCCCeEEEEEEEEecccceEEEEEEEeecCCCCeEEEEEEEeeCCe------eEEEEEEEEEecCCCC---ceEEEE
Q psy9572 29 LTIKANSGSTTTFVITPKELGYIGIKVTATSNLAGDSMEGKLLVKPEGE------TQYKNKAIFVDLRKNK---TFSVNV 99 (163)
Q Consensus 29 v~v~~~~~~~v~f~v~~~~~G~~~i~v~a~~~~~~d~v~~~l~V~~~g~------~~~~~~~~~l~~~~~~---~~~~~~ 99 (163)
+.+-|+....+ .+. ...|...+.+.-... ..++....|.++...- .-...|. -+++...+ .....-
T Consensus 45 vyLlP~a~t~~--~L~-s~iG~L~~~l~~I~~-~AnGs~a~L~i~~~~~~pLpaf~~~veWG-~ld~~t~k~l~~~~qsq 119 (165)
T PF11622_consen 45 VYLLPAANTPA--RLN-SQIGTLRLSLSNIEP-EANGSRATLRIQNLSSAPLPAFSATVEWG-QLDPTTGKPLEVDSQSQ 119 (165)
T ss_dssp EEE-TTT---E--EEE--SS-EEEEEEEEEEE--SSSEEEEEEEEESSSS----EEEEEEEE-EE-S-SSS--EEEEEEE
T ss_pred eEECcCCCCce--Ecc-cceeEEEEEEecccc-cCCccEEEEEEeCCCCCcccCceeEEEEc-cccCCCCCccccchhce
Confidence 44555544333 333 567877777766554 3466666777654332 2222232 34444322 123344
Q ss_pred ecCCCCCCcCCcce-EEEEEEeccC
Q psy9572 100 TLDMPKNIVPGSEH-VEVSAVACKI 123 (163)
Q Consensus 100 ~~~lp~~~vpgS~~-~~v~v~~~~~ 123 (163)
.++.|..+.|+|.. +.++++|-.|
T Consensus 120 ~~~~~~~llp~s~~~i~L~L~GvtP 144 (165)
T PF11622_consen 120 LINAPASLLPGSWVDIELRLSGVTP 144 (165)
T ss_dssp EEEE----SSS-EEEEEEEE-S--G
T ss_pred eEccccccCCCcceeEEEEECCCCH
Confidence 56678888999986 6788884433
No 48
>PF12584 TRAPPC10: Trafficking protein particle complex subunit 10, TRAPPC10; InterPro: IPR022233 The trafficking protein particle complex TRAPP is a multi-protein complex needed in the early stages of the secretory pathway. To date, two kinds of TRAPP complexes have been studied, TRAPPI and TRAPP II. These complexes differ in subunit composition []. TRAPP I binds vesicles derived from the endoplasmic reticulum bringing them closer to the acceptor membrane. This entry represents a domain which forms part of the TRAPP complex for mediating vesicle docking and fusion in the Golgi apparatus. The fungal version is referred to as Trs130, and an alternative vertebrate alias is TMEM1 [, ].
Probab=20.79 E-value=2.5e+02 Score=20.11 Aligned_cols=24 Identities=17% Similarity=0.439 Sum_probs=17.5
Q ss_pred EEEEcCCCeEEEEEEEEecccceE
Q psy9572 28 KLTIKANSGSTTTFVITPKELGYI 51 (163)
Q Consensus 28 ~v~v~~~~~~~v~f~v~~~~~G~~ 51 (163)
.+.+..++...+.+.+.|.+.|..
T Consensus 80 ~f~~~~~~~~~~~l~LIPL~~G~L 103 (147)
T PF12584_consen 80 VFSLSDGSEHEIPLTLIPLRAGYL 103 (147)
T ss_pred eEEecCCCeEEEEEEEEeccccee
Confidence 466677777777778888777765
No 49
>COG2967 ApaG Uncharacterized protein affecting Mg2+/Co2+ transport [Inorganic ion transport and metabolism]
Probab=20.52 E-value=3.3e+02 Score=19.43 Aligned_cols=66 Identities=17% Similarity=0.122 Sum_probs=35.9
Q ss_pred CCCcEEEEEEEeeccceEEEEEEEcCCCeEEEEEEEEecccceEEEEEEEeecCCCCeEEEEEEEeeCCee
Q psy9572 8 LRYNIREKVYLYEFEVFRRKKLTIKANSGSTTTFVITPKELGYIGIKVTATSNLAGDSMEGKLLVKPEGET 78 (163)
Q Consensus 8 ~~~~~~v~V~l~~~~~~~~~~v~v~~~~~~~v~f~v~~~~~G~~~i~v~a~~~~~~d~v~~~l~V~~~g~~ 78 (163)
...+|+|+|.-.--+. -+-|..++....++|+-...|+.++++-++-+...|+--+.-.|+-+|+.
T Consensus 4 ~~~~I~V~V~~~ylee-----QS~P~~~RyvfaYtitI~N~g~~~vqLlsR~W~ITd~~g~v~eV~G~GVV 69 (126)
T COG2967 4 SSPDIEVQVQPRYLEE-----QSSPEEERYVFAYTVTIRNLGEVPVQLLSRYWLITDGNGRVTEVEGEGVV 69 (126)
T ss_pred ccCceEEEEeeEEccc-----cCCcccceEEEEEEEEEecCCCccceeeeeEEEEecCCCcEEEEEcCcee
Confidence 4566777666332111 01123334444666666677777777777766544544455556555553
Done!