Query psy2164
Match_columns 68
No_of_seqs 105 out of 191
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 17:57:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2164.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2164hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3547|consensus 99.9 6.1E-28 1.3E-32 182.1 6.2 64 5-68 176-240 (450)
2 PF01062 Bestrophin: Bestrophi 98.8 3.7E-09 8.1E-14 73.8 3.9 61 5-67 161-221 (293)
3 COG3781 Predicted membrane pro 88.4 0.92 2E-05 33.6 4.2 48 15-66 164-214 (306)
4 PF02284 COX5A: Cytochrome c o 73.3 3.8 8.3E-05 26.4 2.5 20 45-64 28-47 (108)
5 PF08828 DSX_dimer: Doublesex 72.3 1.7 3.8E-05 25.4 0.7 26 41-66 4-29 (62)
6 PF13624 SurA_N_3: SurA N-term 71.0 9.1 0.0002 24.0 3.9 31 19-49 88-118 (154)
7 PF11848 DUF3368: Domain of un 70.2 8.6 0.00019 20.6 3.1 24 18-44 6-29 (48)
8 KOG1562|consensus 61.5 15 0.00033 27.7 4.0 49 17-66 218-271 (337)
9 PF09491 RE_AlwI: AlwI restric 58.7 14 0.00031 27.8 3.5 44 9-52 56-111 (435)
10 PF14394 DUF4423: Domain of un 56.6 14 0.00031 24.7 2.9 23 32-54 130-152 (171)
11 cd01421 IMPCH Inosine monophos 54.4 30 0.00065 24.0 4.2 34 19-52 126-170 (187)
12 PF11464 Rbsn: Rabenosyn Rab b 52.6 15 0.00033 19.8 2.0 28 17-44 8-35 (42)
13 PF13310 Virulence_RhuM: Virul 52.6 32 0.00069 25.2 4.3 36 15-50 47-93 (260)
14 KOG4077|consensus 47.5 10 0.00022 25.6 1.0 20 45-64 67-86 (149)
15 PF04677 CwfJ_C_1: Protein sim 47.1 18 0.00039 23.0 2.1 17 38-54 65-81 (121)
16 KOG2477|consensus 46.6 15 0.00033 29.6 2.0 21 34-54 458-478 (628)
17 PF09202 Rio2_N: Rio2, N-termi 44.7 16 0.00035 21.9 1.5 19 46-64 12-30 (82)
18 cd00923 Cyt_c_Oxidase_Va Cytoc 43.0 14 0.00031 23.6 1.1 21 44-64 24-44 (103)
19 PF11892 DUF3412: Domain of un 42.8 22 0.00047 23.4 2.0 20 40-59 2-21 (123)
20 cd07311 terB_like_1 tellurium 42.6 60 0.0013 21.4 4.1 31 13-44 23-53 (150)
21 PF14767 RPA_interact_M: Repli 41.3 35 0.00076 20.6 2.7 24 37-60 6-33 (83)
22 PF06424 PRP1_N: PRP1 splicing 40.0 16 0.00034 24.1 1.0 27 38-64 101-127 (133)
23 TIGR02147 Fsuc_second hypothet 39.1 36 0.00079 24.5 2.9 22 32-53 228-249 (271)
24 PF12444 Sox_N: Sox developmen 39.1 13 0.00028 22.8 0.5 12 52-63 69-80 (84)
25 PF02787 CPSase_L_D3: Carbamoy 37.7 65 0.0014 20.5 3.6 39 18-58 62-104 (123)
26 PF09111 SLIDE: SLIDE; InterP 37.5 56 0.0012 20.8 3.3 33 20-58 60-92 (118)
27 KOG3326|consensus 36.2 37 0.0008 23.1 2.4 24 18-41 61-84 (154)
28 PF00681 Plectin: Plectin repe 35.4 32 0.0007 18.0 1.7 15 21-35 24-38 (45)
29 PF10845 DUF2576: Protein of u 35.3 36 0.00077 18.9 1.8 23 33-55 10-32 (48)
30 PF04437 RINT1_TIP1: RINT-1 / 34.5 1.2E+02 0.0026 23.1 5.2 50 14-63 68-125 (494)
31 PF08671 SinI: Anti-repressor 33.6 40 0.00086 16.8 1.7 13 18-30 6-18 (30)
32 TIGR02289 M3_not_pepF oligoend 33.6 52 0.0011 25.5 3.1 27 31-57 174-200 (549)
33 TIGR02697 WPE_wolbac Wolbachia 32.8 16 0.00034 19.2 0.1 9 6-14 22-30 (36)
34 PRK12275 hypothetical protein; 32.4 1.2E+02 0.0026 18.5 4.4 35 19-54 78-112 (116)
35 COG3462 Predicted membrane pro 31.5 80 0.0017 20.6 3.3 22 22-44 95-116 (117)
36 PF07017 PagP: Antimicrobial p 30.1 19 0.00041 24.3 0.2 13 54-66 104-116 (147)
37 PF10303 DUF2408: Protein of u 29.8 79 0.0017 20.5 3.1 26 29-54 100-125 (134)
38 PF07026 DUF1317: Protein of u 29.4 72 0.0016 18.5 2.5 23 30-52 32-54 (60)
39 PF01432 Peptidase_M3: Peptida 29.3 77 0.0017 23.6 3.3 35 23-57 16-52 (458)
40 PF13041 PPR_2: PPR repeat fam 28.2 91 0.002 15.7 4.1 25 17-41 22-46 (50)
41 PRK01631 hypothetical protein; 27.8 1.2E+02 0.0025 18.4 3.3 35 17-51 8-44 (76)
42 COG4981 Enoyl reductase domain 27.7 1E+02 0.0022 25.5 3.9 36 9-44 97-147 (717)
43 PF10474 DUF2451: Protein of u 27.0 1.3E+02 0.0029 21.0 4.1 43 12-54 67-112 (234)
44 PHA03419 E4 protein; Provision 26.9 77 0.0017 22.4 2.8 20 33-52 179-198 (200)
45 TIGR01147 V_ATP_synt_G vacuola 26.8 71 0.0015 20.4 2.4 32 17-50 18-51 (113)
46 PF05791 Bacillus_HBL: Bacillu 26.7 63 0.0014 21.7 2.3 19 34-52 124-142 (184)
47 PHA03418 hypothetical E4 prote 26.1 79 0.0017 22.8 2.8 20 33-52 209-228 (230)
48 COG3969 Predicted phosphoadeno 26.0 1.1E+02 0.0025 23.7 3.7 35 30-64 64-99 (407)
49 PF15187 Augurin: Oesophageal 25.2 44 0.00095 21.6 1.2 22 15-36 52-73 (114)
50 COG3943 Virulence protein [Gen 25.2 2E+02 0.0043 21.5 4.7 39 15-53 104-151 (329)
51 PF03487 IL13: Interleukin-13; 25.1 81 0.0017 17.1 2.1 24 26-49 19-42 (43)
52 PF05979 DUF896: Bacterial pro 25.1 75 0.0016 18.5 2.1 34 17-50 7-42 (65)
53 PF00458 WHEP-TRS: WHEP-TRS do 24.8 1.4E+02 0.003 16.7 4.5 41 19-61 10-50 (56)
54 PF06569 DUF1128: Protein of u 24.5 72 0.0016 19.0 2.0 21 27-48 51-71 (71)
55 PLN02350 phosphogluconate dehy 24.3 1.8E+02 0.0038 22.8 4.6 46 16-62 381-431 (493)
56 PF03290 Peptidase_C57: Vaccin 24.0 49 0.0011 25.8 1.5 56 5-65 56-119 (423)
57 PRK09282 pyruvate carboxylase 24.0 1.1E+02 0.0025 24.3 3.6 34 17-53 301-334 (592)
58 PLN03075 nicotianamine synthas 23.9 1.2E+02 0.0027 22.2 3.5 35 17-55 38-72 (296)
59 PF03979 Sigma70_r1_1: Sigma-7 23.4 75 0.0016 18.5 1.9 17 17-33 9-25 (82)
60 PF09779 Ima1_N: Ima1 N-termin 23.3 70 0.0015 20.5 1.9 22 32-53 98-119 (131)
61 TIGR01987 HI0074 nucleotidyltr 23.3 1.4E+02 0.0031 19.0 3.4 30 18-51 63-92 (123)
62 PF08044 DUF1707: Domain of un 23.1 1.4E+02 0.003 16.4 2.9 17 17-33 11-27 (53)
63 KOG0506|consensus 22.8 1.3E+02 0.0029 24.4 3.7 30 19-48 107-136 (622)
64 KOG2351|consensus 22.7 1.1E+02 0.0024 20.3 2.8 21 27-48 112-132 (134)
65 PF08780 NTase_sub_bind: Nucle 22.6 2.1E+02 0.0045 18.0 4.7 32 18-53 63-94 (124)
66 PF06547 DUF1117: Protein of u 22.3 30 0.00064 22.5 0.0 8 61-68 30-37 (117)
67 PRK01546 hypothetical protein; 22.2 1.6E+02 0.0036 17.8 3.3 34 17-50 10-45 (79)
68 PF11458 Mistic: Membrane-inte 22.1 78 0.0017 19.4 1.8 29 18-46 46-75 (84)
69 PF11900 DUF3420: Domain of un 21.4 95 0.0021 17.1 2.0 16 37-52 13-28 (49)
70 cd01055 Nonheme_Ferritin nonhe 21.2 1.9E+02 0.0041 18.0 3.6 38 19-56 101-142 (156)
71 PF10625 UspB: Universal stres 20.7 2.3E+02 0.0049 18.2 3.8 29 36-68 16-44 (107)
72 PF09454 Vps23_core: Vps23 cor 20.7 1.4E+02 0.0031 17.0 2.7 21 17-37 27-47 (65)
73 PF09312 SurA_N: SurA N-termin 20.7 1.9E+02 0.0041 17.7 3.5 26 20-45 56-81 (118)
74 COG3784 Uncharacterized protei 20.5 2E+02 0.0043 18.5 3.5 28 21-48 26-64 (109)
75 PF07751 Abi_2: Abi-like prote 20.2 2E+02 0.0042 18.1 3.6 20 32-51 164-183 (191)
No 1
>KOG3547|consensus
Probab=99.94 E-value=6.1e-28 Score=182.08 Aligned_cols=64 Identities=39% Similarity=0.752 Sum_probs=61.3
Q ss_pred CCCC-cceeeHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhhchhhcCcceecccccccC
Q psy2164 5 HPMT-KYWLPLTWATNIINRARREATITSDHMVQTILNEMSDIRWRLGSLIGYDNVNLPLVYTQK 68 (68)
Q Consensus 5 ~~~~-kyWvPi~Wa~~l~~~ar~eg~I~s~~~~~~l~~ei~~fR~~l~~L~~yDWVpIPLvYtQv 68 (68)
.+++ |||+||+||.+|+++|++||+|++|..++.+++||++||++|++|++|||||||||||||
T Consensus 176 ~~~~~kyw~Pi~Wa~sl~~~a~~~g~i~~d~~~~~~~~ei~~fR~~l~~L~~yDwVpIPL~YpQv 240 (450)
T KOG3547|consen 176 DSKYMKYWVPINWAFSLLRKARKEGRIESDYLYNSLLGEIKKFRTGLSLLCNYDWVPIPLVYPQV 240 (450)
T ss_pred cccccceeecHHHHHHHHHHHHHcCCccccHHHHHHHHHHHHHHHhhccccCCCceeccccccce
Confidence 3444 999999999999999999999999999999999999999999999999999999999997
No 2
>PF01062 Bestrophin: Bestrophin, RFP-TM, chloride channel; InterPro: IPR021134 Bestrophin is a 68kDa basolateral plasma membrane protein expressed in retinal pigment epithelial cells (RPE). It is encoded by the VMD2 gene, which is mutated in Best macular dystrophy, a disease characterised by a depressed light peak in the electrooculogram []. VMD2 encodes a 585-amino acid protein with an approximate mass of 68 kDa which has been designated bestrophin. Bestrophin shares homology with the Caenorhabditis elegans RFP gene family, named for the presence of a conserved arginine (R), phenylalanine (F), proline (P), amino acid sequence motif. Bestrophin is a plasma membrane protein, localised to the basolateral surface of RPE cells consistent with a role for bestrophin in the generation or regulation of the EOG light peak. Bestrophin and other RFP family members represent a new class of chloride channels, indicating a direct role for bestrophin in generating the light peak []. The VMD2 gene underlying Best disease was shown to represent the first human member of the RFP-TM protein family. More than 97% of the disease-causing mutations are located in the N-terminal RFP-TM domain implying important functional properties []. This entry also includes a number of hypothetical proteins belonging to protein family UPF0187.
Probab=98.82 E-value=3.7e-09 Score=73.79 Aligned_cols=61 Identities=26% Similarity=0.497 Sum_probs=57.0
Q ss_pred CCCCcceeeHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhhchhhcCcceeccccccc
Q psy2164 5 HPMTKYWLPLTWATNIINRARREATITSDHMVQTILNEMSDIRWRLGSLIGYDNVNLPLVYTQ 67 (68)
Q Consensus 5 ~~~~kyWvPi~Wa~~l~~~ar~eg~I~s~~~~~~l~~ei~~fR~~l~~L~~yDWVpIPLvYtQ 67 (68)
.++...+++..|+..+ ++++++|.+ ++..+..+.+++.+|+..++.+..++++|||++|+|
T Consensus 161 ~~~~p~~i~~~~~~~l-~~~~~~g~~-~~~~~~~l~~~l~~l~~~~g~~eri~~TPiP~~Y~~ 221 (293)
T PF01062_consen 161 ADNPPNWILIQWSQRL-REARREGLI-DSFQLAQLDNELNALRDAQGGCERIKNTPIPFAYTQ 221 (293)
T ss_pred hcCcHHHHHHHHHHHH-HHHHHcCCC-ChHHHHHHHHHHHHHHHHHhhhheeCCCcCCHHHHH
Confidence 4678899999999999 999999995 688899999999999999999999999999999998
No 3
>COG3781 Predicted membrane protein [Function unknown]
Probab=88.42 E-value=0.92 Score=33.64 Aligned_cols=48 Identities=19% Similarity=0.343 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHhCCCCCHHHH---HHHHHHHHHHHHhhchhhcCcceecccccc
Q psy2164 15 TWATNIINRARREATITSDHMV---QTILNEMSDIRWRLGSLIGYDNVNLPLVYT 66 (68)
Q Consensus 15 ~Wa~~l~~~ar~eg~I~s~~~~---~~l~~ei~~fR~~l~~L~~yDWVpIPLvYt 66 (68)
-|.-.-++..|++|.++ +..+ +..++.|.+--++|+.+-+ .|||++||
T Consensus 164 ~wmGe~l~~q~r~g~l~-~~~~~sl~~~L~~~s~vlggCERI~~---TPiPfAYt 214 (306)
T COG3781 164 LWMGEWLQQQRRNGQLD-AIQFTSLDRRLNSISAVLGGCERIAY---TPIPFAYT 214 (306)
T ss_pred HHHHHHHHHHHhcCCcc-HHHHHHHHHHHHHHHHHHHhHHHHhc---CCccHHHH
Confidence 38888899999999995 5554 4455566666677777664 89999997
No 4
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=73.30 E-value=3.8 Score=26.37 Aligned_cols=20 Identities=40% Similarity=0.705 Sum_probs=15.5
Q ss_pred HHHHhhchhhcCcceecccc
Q psy2164 45 DIRWRLGSLIGYDNVNLPLV 64 (68)
Q Consensus 45 ~fR~~l~~L~~yDWVpIPLv 64 (68)
+.|.+|..|+.||.||=|=+
T Consensus 28 e~rrglN~l~~~DlVP~P~i 47 (108)
T PF02284_consen 28 ELRRGLNNLFGYDLVPEPKI 47 (108)
T ss_dssp HHHHHHHHHTTSSB---HHH
T ss_pred HHHHHHHHHhccccCCChHH
Confidence 89999999999999998854
No 5
>PF08828 DSX_dimer: Doublesex dimerisation domain; InterPro: IPR014932 Doublesex (DSX) is a transcription factor that regulates somatic sexual differences in Drosophila. The structure has revealed a novel dimeric arrangement of ubiquitin-associated folds that has not previously been identified in a transcription factor []. ; PDB: 1ZV1_B 2JZ0_A 2JZ1_B.
Probab=72.32 E-value=1.7 Score=25.43 Aligned_cols=26 Identities=23% Similarity=0.312 Sum_probs=21.4
Q ss_pred HHHHHHHHhhchhhcCcceecccccc
Q psy2164 41 NEMSDIRWRLGSLIGYDNVNLPLVYT 66 (68)
Q Consensus 41 ~ei~~fR~~l~~L~~yDWVpIPLvYt 66 (68)
+++.++=++|-.-+.|-|=.+||+|.
T Consensus 4 e~Ll~~cqkLlEkf~YpWEmmpLmyV 29 (62)
T PF08828_consen 4 EELLERCQKLLEKFRYPWEMMPLMYV 29 (62)
T ss_dssp HHHHHHHHHHHHHTT--GGGHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 67888889999999999999999984
No 6
>PF13624 SurA_N_3: SurA N-terminal domain; PDB: 3NRK_A.
Probab=70.95 E-value=9.1 Score=23.97 Aligned_cols=31 Identities=13% Similarity=0.226 Sum_probs=20.7
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHHHHHHHHh
Q psy2164 19 NIINRARREATITSDHMVQTILNEMSDIRWR 49 (68)
Q Consensus 19 ~l~~~ar~eg~I~s~~~~~~l~~ei~~fR~~ 49 (68)
-+..+|++.|..-||..++..++++..|..+
T Consensus 88 ll~q~A~~~gi~vsd~ev~~~i~~~~~f~~~ 118 (154)
T PF13624_consen 88 LLLQEAKKLGISVSDAEVDDAIKQIPAFQEN 118 (154)
T ss_dssp HHHHHHHHTT----HHHHHHHHHH--HHHHH
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHHHHHHHHC
Confidence 3667889999988999999999998888554
No 7
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=70.21 E-value=8.6 Score=20.63 Aligned_cols=24 Identities=25% Similarity=0.432 Sum_probs=17.7
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHHH
Q psy2164 18 TNIINRARREATITSDHMVQTILNEMS 44 (68)
Q Consensus 18 ~~l~~~ar~eg~I~s~~~~~~l~~ei~ 44 (68)
+-++.+|.++|.|. ....+++++.
T Consensus 6 lGiL~~Ak~~GlI~---~~~~~l~~l~ 29 (48)
T PF11848_consen 6 LGILLLAKRRGLIS---EVKPLLDRLQ 29 (48)
T ss_pred HHHHHHHHHcCChh---hHHHHHHHHH
Confidence 45788999999996 5566666663
No 8
>KOG1562|consensus
Probab=61.53 E-value=15 Score=27.74 Aligned_cols=49 Identities=12% Similarity=0.182 Sum_probs=39.3
Q ss_pred HHHHHHHHHHhCCC-----CCHHHHHHHHHHHHHHHHhhchhhcCcceecccccc
Q psy2164 17 ATNIINRARREATI-----TSDHMVQTILNEMSDIRWRLGSLIGYDNVNLPLVYT 66 (68)
Q Consensus 17 a~~l~~~ar~eg~I-----~s~~~~~~l~~ei~~fR~~l~~L~~yDWVpIPLvYt 66 (68)
.+.++.+|++.|=+ ++-.....++.|+++|=.....+..|-|..+| -||
T Consensus 218 ~~~~v~~aLk~dgv~~~q~ec~wl~~~~i~e~r~~~~~~f~~t~ya~ttvP-Typ 271 (337)
T KOG1562|consen 218 YFGLVLDALKGDGVVCTQGECMWLHLDYIKEGRSFCYVIFDLTAYAITTVP-TYP 271 (337)
T ss_pred HHHHHHHhhCCCcEEEEecceehHHHHHHHHHHHhHHHhcCccceeeecCC-CCc
Confidence 36778888875431 35567789999999999999999999999999 554
No 9
>PF09491 RE_AlwI: AlwI restriction endonuclease; InterPro: IPR018573 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes AlwI (recognises GGATC), Bsp6I (recognises GC^NGC), BstNBI (recognises GASTC), PleI(recognises GAGTC) and MlyI (recognises GAGTC) restriction endonucleases. ; PDB: 2EWF_A 2P14_A.
Probab=58.70 E-value=14 Score=27.81 Aligned_cols=44 Identities=16% Similarity=0.382 Sum_probs=31.6
Q ss_pred cceeeHHHHHHHHHHHHHhCCC------------CCHHHHHHHHHHHHHHHHhhch
Q psy2164 9 KYWLPLTWATNIINRARREATI------------TSDHMVQTILNEMSDIRWRLGS 52 (68)
Q Consensus 9 kyWvPi~Wa~~l~~~ar~eg~I------------~s~~~~~~l~~ei~~fR~~l~~ 52 (68)
.+.-|+.+++.++.+-+.++.| .++..++.++++|.+||..-..
T Consensus 56 ~~~~Pfr~lL~ll~~l~~~~~ls~~E~~~~v~~~~~~~~~~~lv~~I~~fR~~~~~ 111 (435)
T PF09491_consen 56 FYIYPFRFLLKLLNELELDSYLSKEEFAYFVQTISDDNDIEELVNKILDFRKEREN 111 (435)
T ss_dssp -BB-HHHHHHHHHHHH---S-B-HHHHHHHTTT--BGGGHHHHHHHHHHHHHHHHH
T ss_pred eeeehHHHHHHHHHHHhcccccChhhheeEEEEccchhhHHHHHHHHHHHHHhhhh
Confidence 7889999999999999777664 3456778999999999987654
No 10
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=56.56 E-value=14 Score=24.69 Aligned_cols=23 Identities=17% Similarity=0.257 Sum_probs=20.1
Q ss_pred CHHHHHHHHHHHHHHHHhhchhh
Q psy2164 32 SDHMVQTILNEMSDIRWRLGSLI 54 (68)
Q Consensus 32 s~~~~~~l~~ei~~fR~~l~~L~ 54 (68)
|+..+..+.+||.+||.++..+-
T Consensus 130 s~~~~~ki~~~i~~fRk~i~~i~ 152 (171)
T PF14394_consen 130 SREDYEKIKKEIREFRKKIIAIA 152 (171)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHH
Confidence 67889999999999999987653
No 11
>cd01421 IMPCH Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates 5-aminoimidazole-4-carboxamide-ribonucleotide. The IMPCH domain then converts the formyl-5-aminoimidazole-4-carboxamide-ribonucleotide to inosine monophosphate. This is the final step in de novo purine production.
Probab=54.38 E-value=30 Score=24.01 Aligned_cols=34 Identities=21% Similarity=0.341 Sum_probs=26.5
Q ss_pred HHHHHHHHhCC----CCCHHHHHHHHHHHHH-------HHHhhch
Q psy2164 19 NIINRARREAT----ITSDHMVQTILNEMSD-------IRWRLGS 52 (68)
Q Consensus 19 ~l~~~ar~eg~----I~s~~~~~~l~~ei~~-------fR~~l~~ 52 (68)
+|++.|-|-.. +.++..|..+++||++ ||.+|+.
T Consensus 126 smlRaAAKN~~~V~vv~dp~dY~~v~~~l~~~g~~~~~~R~~lA~ 170 (187)
T cd01421 126 SLLRAAAKNYKDVTVLVDPADYQKVLEELKSNGSISEETRRRLAL 170 (187)
T ss_pred HHHHHHHhcCCCeEEEcCHHHHHHHHHHHHhcCCCCHHHHHHHHH
Confidence 56777766543 7789999999999986 8888753
No 12
>PF11464 Rbsn: Rabenosyn Rab binding domain; InterPro: IPR021565 Rabenosyn-5 (Rbsn) is a multivalent effector with interacts with the Rab family.Rsbn contains distinct Rab4 and Rab5 binding sites within residues 264-500 and 627-784 respectively []. Rab proteins are GTPases involved in the regulation of all stages of membrane trafficking []. ; PDB: 1Z0K_B 1YZM_A 1Z0J_B.
Probab=52.60 E-value=15 Score=19.85 Aligned_cols=28 Identities=14% Similarity=0.213 Sum_probs=18.6
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHH
Q psy2164 17 ATNIINRARREATITSDHMVQTILNEMS 44 (68)
Q Consensus 17 a~~l~~~ar~eg~I~s~~~~~~l~~ei~ 44 (68)
+-+.+..|++.|+++.-..+..=+.||.
T Consensus 8 I~~~I~qAk~~~r~dEV~~L~~NL~EL~ 35 (42)
T PF11464_consen 8 IESYIKQAKAARRFDEVATLEENLRELQ 35 (42)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCcHHHHHHHHHHHHHH
Confidence 3467889999999876555555555554
No 13
>PF13310 Virulence_RhuM: Virulence protein RhuM family
Probab=52.59 E-value=32 Score=25.19 Aligned_cols=36 Identities=22% Similarity=0.418 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhCCCCCH-----------HHHHHHHHHHHHHHHhh
Q psy2164 15 TWATNIINRARREATITSD-----------HMVQTILNEMSDIRWRL 50 (68)
Q Consensus 15 ~Wa~~l~~~ar~eg~I~s~-----------~~~~~l~~ei~~fR~~l 50 (68)
.||.+.|++-.-+|+..++ ..+..+++.|++.|.+=
T Consensus 47 ~WAt~~Lkey~~KGf~~d~erLk~~~~~~~dyf~ell~rIr~IRaSE 93 (260)
T PF13310_consen 47 QWATKVLKEYLIKGFVLDDERLKNGGVFGKDYFDELLERIRDIRASE 93 (260)
T ss_pred HHHHHhHHHHHHhhhhhhHHHHHccCcccHHHHHHHHHHHHhhHHHH
Confidence 5999999988877775544 55677888888888764
No 14
>KOG4077|consensus
Probab=47.54 E-value=10 Score=25.58 Aligned_cols=20 Identities=40% Similarity=0.587 Sum_probs=17.8
Q ss_pred HHHHhhchhhcCcceecccc
Q psy2164 45 DIRWRLGSLIGYDNVNLPLV 64 (68)
Q Consensus 45 ~fR~~l~~L~~yDWVpIPLv 64 (68)
+.|.+|..|+.||-||=|=+
T Consensus 67 EvrkglN~l~~yDlVP~pkv 86 (149)
T KOG4077|consen 67 EVRKGLNNLFDYDLVPSPKV 86 (149)
T ss_pred HHHHHHHhhhccccCCChHH
Confidence 67999999999999998854
No 15
>PF04677 CwfJ_C_1: Protein similar to CwfJ C-terminus 1; InterPro: IPR006768 This group of sequences contain a conserved C-terminal domain which is found in the Schizosaccharomyces pombe (Fission yeast) protein Cwf19 (Q09909 from SWISSPROT) and its homologues. Cwf19 is part of the Cdc5p complex involved in mRNA splicing []. This domain is found in association with IPR006767 from INTERPRO, which is generally C-terminal and adjacent to this domain.
Probab=47.08 E-value=18 Score=22.98 Aligned_cols=17 Identities=12% Similarity=0.335 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHhhchhh
Q psy2164 38 TILNEMSDIRWRLGSLI 54 (68)
Q Consensus 38 ~l~~ei~~fR~~l~~L~ 54 (68)
++++||++|+.+|..++
T Consensus 65 ~~~~Ei~~f~~~L~~mf 81 (121)
T PF04677_consen 65 EVWEEIRNFQKSLRKMF 81 (121)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 78999999999997764
No 16
>KOG2477|consensus
Probab=46.61 E-value=15 Score=29.65 Aligned_cols=21 Identities=14% Similarity=0.324 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHhhchhh
Q psy2164 34 HMVQTILNEMSDIRWRLGSLI 54 (68)
Q Consensus 34 ~~~~~l~~ei~~fR~~l~~L~ 54 (68)
..=..++|||++||.+|.+++
T Consensus 458 slDEdvWDEIrnfrKcL~~Mf 478 (628)
T KOG2477|consen 458 SLDEDVWDEIRNFRKCLALMF 478 (628)
T ss_pred ccchHHHHHHHHHHHHHHHHH
Confidence 334579999999999998876
No 17
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=44.65 E-value=16 Score=21.92 Aligned_cols=19 Identities=21% Similarity=0.120 Sum_probs=11.8
Q ss_pred HHHhhchhhcCcceecccc
Q psy2164 46 IRWRLGSLIGYDNVNLPLV 64 (68)
Q Consensus 46 fR~~l~~L~~yDWVpIPLv 64 (68)
.+.=-....+|.|||+++.
T Consensus 12 L~aiE~gmk~hE~VP~~~I 30 (82)
T PF09202_consen 12 LRAIEMGMKNHEWVPLELI 30 (82)
T ss_dssp HHHHHTTTTT-SSEEHHHH
T ss_pred HHHHHHcccCCccCCHHHH
Confidence 3344445788999998763
No 18
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=42.98 E-value=14 Score=23.58 Aligned_cols=21 Identities=43% Similarity=0.624 Sum_probs=18.0
Q ss_pred HHHHHhhchhhcCcceecccc
Q psy2164 44 SDIRWRLGSLIGYDNVNLPLV 64 (68)
Q Consensus 44 ~~fR~~l~~L~~yDWVpIPLv 64 (68)
-+.|++|..|+.||-||=|=+
T Consensus 24 we~rr~mN~l~~~DlVP~P~i 44 (103)
T cd00923 24 WELRRGLNNLFGYDLVPEPKV 44 (103)
T ss_pred HHHHHHHHHHhccccCCCcHH
Confidence 367999999999999998844
No 19
>PF11892 DUF3412: Domain of unknown function (DUF3412); InterPro: IPR021826 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain is found associated with PF03641 from PFAM. ; PDB: 3BQ9_A 2PMB_D 3GH1_D.
Probab=42.84 E-value=22 Score=23.39 Aligned_cols=20 Identities=15% Similarity=0.287 Sum_probs=15.5
Q ss_pred HHHHHHHHHhhchhhcCcce
Q psy2164 40 LNEMSDIRWRLGSLIGYDNV 59 (68)
Q Consensus 40 ~~ei~~fR~~l~~L~~yDWV 59 (68)
++++++||...+.=+.|.|-
T Consensus 2 m~~V~~~R~~~~Day~fNW~ 21 (123)
T PF11892_consen 2 MEEVKEYRRETGDAYYFNWS 21 (123)
T ss_dssp HHHHHHHHHHTT--SSS-TS
T ss_pred chHHHHHHHhcCCceeeeee
Confidence 68999999999999999994
No 20
>cd07311 terB_like_1 tellurium resistance terB-like protein, subgroup 1. This family includes several uncharacterized bacterial proteins. The prototype of this CD is tellurite resistance protein from Nostoc punctiforme that belongs to COG3793. Its precise biological function and its mechanism responsible for tellurium resistance still remains rather poorly understood.
Probab=42.58 E-value=60 Score=21.40 Aligned_cols=31 Identities=10% Similarity=0.152 Sum_probs=22.6
Q ss_pred eHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Q psy2164 13 PLTWATNIINRARREATITSDHMVQTILNEMS 44 (68)
Q Consensus 13 Pi~Wa~~l~~~ar~eg~I~s~~~~~~l~~ei~ 44 (68)
|..|..+|+.-|+..|.+. +.....+-+-+.
T Consensus 23 ~~~~~~~Ll~iAkADG~Vs-e~Ei~~~~~~m~ 53 (150)
T cd07311 23 KLAYLKALLVCAKGDGVIS-PEERDWAIGYAA 53 (150)
T ss_pred HHHHHHHHHHHHHcCCCCC-HHHHHHHHHHHH
Confidence 5789999999999999995 544544443333
No 21
>PF14767 RPA_interact_M: Replication protein A interacting middle
Probab=41.34 E-value=35 Score=20.59 Aligned_cols=24 Identities=25% Similarity=0.342 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHH---hhc-hhhcCccee
Q psy2164 37 QTILNEMSDIRW---RLG-SLIGYDNVN 60 (68)
Q Consensus 37 ~~l~~ei~~fR~---~l~-~L~~yDWVp 60 (68)
.-+=+|++++|+ +.. +|+.|||++
T Consensus 6 eVm~eE~~~L~~~~~~~~d~lw~~~~~~ 33 (83)
T PF14767_consen 6 EVMEEEWKALQSSSSGLPDSLWEYDGLP 33 (83)
T ss_pred HHHHHHHHHHHhcCCCchhhhhccccch
Confidence 345579999999 444 999999975
No 22
>PF06424 PRP1_N: PRP1 splicing factor, N-terminal; InterPro: IPR010491 This domain is specific to the N-terminal part of the prp1 splicing factor, which is involved in mRNA splicing (and possibly also poly(A)+ RNA nuclear export and cell cycle progression). This domain is specific to the N terminus of the RNA splicing factor encoded by prp1 []. It is involved in mRNA splicing and possibly also poly(A)and RNA nuclear export and cell cycle progression.; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005634 nucleus
Probab=40.00 E-value=16 Score=24.13 Aligned_cols=27 Identities=19% Similarity=0.337 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHhhchhhcCcceecccc
Q psy2164 38 TILNEMSDIRWRLGSLIGYDNVNLPLV 64 (68)
Q Consensus 38 ~l~~ei~~fR~~l~~L~~yDWVpIPLv 64 (68)
+|-+++.++..+|+.|.-=+|-.||=|
T Consensus 101 kI~~QFaDLKR~La~VS~eeW~~IPE~ 127 (133)
T PF06424_consen 101 KIQQQFADLKRSLATVSEEEWENIPEA 127 (133)
T ss_pred hHHHHHHHHHHHHccCCHHHHhcCCcc
Confidence 577889999999999999999999943
No 23
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=39.10 E-value=36 Score=24.53 Aligned_cols=22 Identities=14% Similarity=0.335 Sum_probs=19.6
Q ss_pred CHHHHHHHHHHHHHHHHhhchh
Q psy2164 32 SDHMVQTILNEMSDIRWRLGSL 53 (68)
Q Consensus 32 s~~~~~~l~~ei~~fR~~l~~L 53 (68)
|+..+..+.+||.+||.++..+
T Consensus 228 ~~~~~~~i~~~i~~fRk~i~~i 249 (271)
T TIGR02147 228 SEEAYKEIVKKIQEFRKEVLAI 249 (271)
T ss_pred CHHHHHHHHHHHHHHHHHHHHH
Confidence 6788999999999999998765
No 24
>PF12444 Sox_N: Sox developmental protein N terminal ; InterPro: IPR022151 This domain family is found in eukaryotes, and is typically between 69 and 88 amino acids in length. The family is found in association with PF00505 from PFAM. There are two conserved sequence motifs: YDW and PVR. This family contains Sox8, Sox9 and Sox10 proteins which have structural similarity. Sox proteins are involved in developmental processes.
Probab=39.09 E-value=13 Score=22.77 Aligned_cols=12 Identities=42% Similarity=0.711 Sum_probs=9.4
Q ss_pred hhhcCcceeccc
Q psy2164 52 SLIGYDNVNLPL 63 (68)
Q Consensus 52 ~L~~yDWVpIPL 63 (68)
.|..|||.=||+
T Consensus 69 VLkGYDWtLVPm 80 (84)
T PF12444_consen 69 VLKGYDWTLVPM 80 (84)
T ss_pred HhccCCceeeec
Confidence 578999977765
No 25
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=37.66 E-value=65 Score=20.49 Aligned_cols=39 Identities=21% Similarity=0.378 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHH----HHHHHHHHhhchhhcCcc
Q psy2164 18 TNIINRARREATITSDHMVQTIL----NEMSDIRWRLGSLIGYDN 58 (68)
Q Consensus 18 ~~l~~~ar~eg~I~s~~~~~~l~----~ei~~fR~~l~~L~~yDW 58 (68)
-.++.+|.+-|. ||.....++ +||++.|.+.+..-.|--
T Consensus 62 ~~~L~~aK~~GF--sD~~IA~l~~~~e~~vr~~R~~~~i~p~yk~ 104 (123)
T PF02787_consen 62 PELLRKAKRLGF--SDRQIARLWGVSEEEVRELRKEHGIVPVYKM 104 (123)
T ss_dssp HHHHHHHHHTT----HHHHHHHHTS-HHHHHHHHHHHT---EEEE
T ss_pred HHHHHHHHHcCC--CHHHHHhccCCCHHHHHHHHHHcCCceeeee
Confidence 358889999994 666666654 589999999887666543
No 26
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=37.47 E-value=56 Score=20.84 Aligned_cols=33 Identities=12% Similarity=0.197 Sum_probs=24.3
Q ss_pred HHHHHHHhCCCCCHHHHHHHHHHHHHHHHhhchhhcCcc
Q psy2164 20 IINRARREATITSDHMVQTILNEMSDIRWRLGSLIGYDN 58 (68)
Q Consensus 20 l~~~ar~eg~I~s~~~~~~l~~ei~~fR~~l~~L~~yDW 58 (68)
|+....+-|+ .++..+..+-+||+. +-++.|||
T Consensus 60 Ll~~~~~~G~-~~~~~~e~Ik~~Ir~-----~p~FrFDw 92 (118)
T PF09111_consen 60 LLCMLYKYGY-DAEGNWEKIKQEIRE-----SPLFRFDW 92 (118)
T ss_dssp HHHHHHHHTT-TSTTHHHHHHHHHHH------CGGCT-H
T ss_pred HHHHHHHhCC-CCCchHHHHHHHHHh-----CCCcccch
Confidence 5667778898 568889999888875 46777887
No 27
>KOG3326|consensus
Probab=36.23 E-value=37 Score=23.09 Aligned_cols=24 Identities=8% Similarity=0.371 Sum_probs=20.8
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHH
Q psy2164 18 TNIINRARREATITSDHMVQTILN 41 (68)
Q Consensus 18 ~~l~~~ar~eg~I~s~~~~~~l~~ 41 (68)
..|+++.||.|..+.|..+..+.+
T Consensus 61 aRLlYqSrKRGiLEnDLLLs~Fa~ 84 (154)
T KOG3326|consen 61 ARLLYQSRKRGILENDLLLSNFAA 84 (154)
T ss_pred HHHHHHHhhcchhHHHHHHHHHHH
Confidence 579999999999999988877654
No 28
>PF00681 Plectin: Plectin repeat; InterPro: IPR001101 Plectin may have a role in cross-linking intermediate filaments, in inter-linking intermediate filaments with microtubules and microfilaments and in anchoring intermediate filaments to the plasma and nuclear membranes. Plectin is recruited into hemidesmosomes, multiprotein complexes that facilitate adhesion of epithelia to the basement membrane, thereby providing linkage between the intracellular keratin filaments to the laminins of the extracellular matrix. Plectin binds to hemidesmosomes through association of its actin-binding domain with the first pair of fibronectin type III repeats and a small part of the connecting segment of the integrin-beta4 subunit, the latter (integrin-alpha6,beta4) acting as a receptor for the extracellular matrix component laminin-5. The plectin repeat is also seen in the cell adhesion junction plaque proteins, desmoplakin, envoplakin, and bullous pemphigoid antigen. The domains in plakins show considerable sequence homology. The N terminus consists of a plakin domain containing a number of subdomains with high alpha-helical content, while the central coiled-coil domain is composed of heptad repeats involved in the dimerisation of plakin, and the C terminus contains one or more homologous repeat sequences referred to plectin repeats []. This entry represents the plectin repeats found in the C terminus of plakin proteins.; GO: 0005856 cytoskeleton; PDB: 1LM7_A 1LM5_A.
Probab=35.44 E-value=32 Score=17.97 Aligned_cols=15 Identities=27% Similarity=0.344 Sum_probs=10.8
Q ss_pred HHHHHHhCCCCCHHH
Q psy2164 21 INRARREATITSDHM 35 (68)
Q Consensus 21 ~~~ar~eg~I~s~~~ 35 (68)
+.+|.++|+|+++.+
T Consensus 24 v~~A~~~glId~~~~ 38 (45)
T PF00681_consen 24 VEEAIQRGLIDSDTA 38 (45)
T ss_dssp HHHHHHTTSS-HHHH
T ss_pred HHHHHHCCCcCHHHH
Confidence 468999999975543
No 29
>PF10845 DUF2576: Protein of unknown function (DUF2576); InterPro: IPR022556 The function of this viral family of proteins is unknown. The entry contains Orf5 from Autographa californica nuclear polyhedrosis virus (AcMNPV).
Probab=35.31 E-value=36 Score=18.90 Aligned_cols=23 Identities=17% Similarity=0.234 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHhhchhhc
Q psy2164 33 DHMVQTILNEMSDIRWRLGSLIG 55 (68)
Q Consensus 33 ~~~~~~l~~ei~~fR~~l~~L~~ 55 (68)
|..-.++-.|+++.|.++..||.
T Consensus 10 dydreqlrrelnsLR~~vhelct 32 (48)
T PF10845_consen 10 DYDREQLRRELNSLRRSVHELCT 32 (48)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHH
Confidence 55667899999999999999873
No 30
>PF04437 RINT1_TIP1: RINT-1 / TIP-1 family; InterPro: IPR007528 This family includes RINT-1, a Rad50 interacting protein which participates in radiation induced checkpoint control [], that interacts with Rad50 only during late S and G2/M phases. RINT1 also functions in membrane trafficking from the endoplasmic reticulum(ER) to the Golgi complex in interphase cells [, , ]. In addition to this, the TIP-1 protein, which is involved in the retrograde transport from the Golgi to the ER []. They share a similar domain organisation with an N-terminal leucine heptad repeat rich coiled coil and an ~500-residue C-terminal RINT1/TIP20 domain, which might be a protein-protein interaction module necessary for the formation of functional complexes.; PDB: 3FHN_A.
Probab=34.53 E-value=1.2e+02 Score=23.07 Aligned_cols=50 Identities=16% Similarity=0.304 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHh------CCCCCHHHHHHHHHHHHHHHHhhchhhcCc--ceeccc
Q psy2164 14 LTWATNIINRARRE------ATITSDHMVQTILNEMSDIRWRLGSLIGYD--NVNLPL 63 (68)
Q Consensus 14 i~Wa~~l~~~ar~e------g~I~s~~~~~~l~~ei~~fR~~l~~L~~yD--WVpIPL 63 (68)
..|+..|+.-+|++ ....++..+..+++|+..|-+.+....+|+ |-|+++
T Consensus 68 ~~fi~~ll~~~~~Kl~~~l~~~~~~~~~l~HlI~e~~~FD~~L~~~~~y~~d~~~~~~ 125 (494)
T PF04437_consen 68 EEFIRGLLPPVREKLRSDLPELLDDPSLLSHLIDEILSFDKELRSLYGYPGDWQGSTL 125 (494)
T ss_dssp HHHHHHHHHHHHHHHHHHH--TTS-HHHHHHHHHHHHHHHHHHHHTS---S------C
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccChhHHHHHHHHHHHHHHHHHHHcCCCCccchhHH
Confidence 45666677666642 356788889999999999999999998886 444443
No 31
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=33.61 E-value=40 Score=16.84 Aligned_cols=13 Identities=15% Similarity=0.309 Sum_probs=9.7
Q ss_pred HHHHHHHHHhCCC
Q psy2164 18 TNIINRARREATI 30 (68)
Q Consensus 18 ~~l~~~ar~eg~I 30 (68)
..|+.+|++.|.=
T Consensus 6 ~~Li~eA~~~Gls 18 (30)
T PF08671_consen 6 VELIKEAKESGLS 18 (30)
T ss_dssp HHHHHHHHHTT--
T ss_pred HHHHHHHHHcCCC
Confidence 4789999999953
No 32
>TIGR02289 M3_not_pepF oligoendopeptidase, M3 family. This family consists of probable oligoendopeptidases in the M3 family, related to lactococcal PepF and group B streptococcal PepB (TIGR00181) but in a distinct clade with considerable sequence differences. The likely substrate is small peptides and not whole proteins, as with PepF, but members are not characterized and the activity profile may differ. Several bacteria have both a member of this family and a member of the PepF family.
Probab=33.56 E-value=52 Score=25.47 Aligned_cols=27 Identities=19% Similarity=0.433 Sum_probs=23.0
Q ss_pred CCHHHHHHHHHHHHHHHHhhchhhcCc
Q psy2164 31 TSDHMVQTILNEMSDIRWRLGSLIGYD 57 (68)
Q Consensus 31 ~s~~~~~~l~~ei~~fR~~l~~L~~yD 57 (68)
.....+..+++++..-|..++.+.+|+
T Consensus 174 ~~~~~~~~il~~lv~~R~~~Akl~Gy~ 200 (549)
T TIGR02289 174 VVEEELDRIYDELVQIRTQIALNLGFS 200 (549)
T ss_pred cCchhHHHHHHHHHHHHHHHHHHCCCC
Confidence 344567789999999999999999997
No 33
>TIGR02697 WPE_wolbac Wolbachia palindromic element (WPE) domain. This domain conceptually resembles TIGR01045, the Rickettsial palindromic element (RPE) domain. In both cases, a protein-coding palindromic element spreads through a genome, inserting usually in protein-coding regions. The additional protein coding sequence is thought to allow function of the host protein because of location in surface-exposed regions of the protein structure. Note that this model appears to work better in fragment mode.
Probab=32.77 E-value=16 Score=19.24 Aligned_cols=9 Identities=33% Similarity=0.970 Sum_probs=7.3
Q ss_pred CCCcceeeH
Q psy2164 6 PMTKYWLPL 14 (68)
Q Consensus 6 ~~~kyWvPi 14 (68)
-|+|.|+|+
T Consensus 22 l~nk~WIPV 30 (36)
T TIGR02697 22 LYNKNWIPV 30 (36)
T ss_pred HhccCceee
Confidence 378999996
No 34
>PRK12275 hypothetical protein; Reviewed
Probab=32.43 E-value=1.2e+02 Score=18.47 Aligned_cols=35 Identities=29% Similarity=0.322 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhhchhh
Q psy2164 19 NIINRARREATITSDHMVQTILNEMSDIRWRLGSLI 54 (68)
Q Consensus 19 ~l~~~ar~eg~I~s~~~~~~l~~ei~~fR~~l~~L~ 54 (68)
..+.-|++.|+|. ...+..+.+|+.+....++.+.
T Consensus 78 ~~L~la~~~~~i~-~~~~~~l~~~~~ei~kml~~~i 112 (116)
T PRK12275 78 TQLYIAKELGYIT-KEQYESILQEYDEIAKMLNGLI 112 (116)
T ss_pred HHHHHHHHcCCCC-HHHHHHHHHHHHHHHHHHHHHH
Confidence 4567788889885 4556777777777766665543
No 35
>COG3462 Predicted membrane protein [Function unknown]
Probab=31.54 E-value=80 Score=20.56 Aligned_cols=22 Identities=14% Similarity=0.258 Sum_probs=11.0
Q ss_pred HHHHHhCCCCCHHHHHHHHHHHH
Q psy2164 22 NRARREATITSDHMVQTILNEMS 44 (68)
Q Consensus 22 ~~ar~eg~I~s~~~~~~l~~ei~ 44 (68)
++-..+|-|+ +..++++.+||+
T Consensus 95 kER~AkGEIt-EEEY~r~~~~ir 116 (117)
T COG3462 95 KERYAKGEIT-EEEYRRIIRTIR 116 (117)
T ss_pred HHHHhcCCCC-HHHHHHHHHHhc
Confidence 3333455553 444666655554
No 36
>PF07017 PagP: Antimicrobial peptide resistance and lipid A acylation protein PagP; InterPro: IPR009746 This family consists of several bacterial antimicrobial peptide resistance and lipid A acylation (PagP) proteins. The bacterial outer membrane enzyme PagP transfers a palmitate chain from a phospholipid to lipid A. In a number of pathogenic Gram-negative bacteria, PagP confers resistance to certain cationic antimicrobial peptides produced during the host innate immune response.; PDB: 1MM5_A 1MM4_A 1THQ_A 3GP6_A.
Probab=30.13 E-value=19 Score=24.30 Aligned_cols=13 Identities=15% Similarity=0.434 Sum_probs=9.1
Q ss_pred hcCcceecccccc
Q psy2164 54 IGYDNVNLPLVYT 66 (68)
Q Consensus 54 ~~yDWVpIPLvYt 66 (68)
-.|++||+|++-|
T Consensus 104 ~d~~yiP~P~~LP 116 (147)
T PF07017_consen 104 DDYHYIPFPAILP 116 (147)
T ss_dssp GCCTT-EEEEEEE
T ss_pred ccccccccceeee
Confidence 3578999998765
No 37
>PF10303 DUF2408: Protein of unknown function (DUF2408); InterPro: IPR018810 This entry represents a family of proteins conserved in fungi whose function is unknown.
Probab=29.79 E-value=79 Score=20.50 Aligned_cols=26 Identities=31% Similarity=0.475 Sum_probs=21.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhchhh
Q psy2164 29 TITSDHMVQTILNEMSDIRWRLGSLI 54 (68)
Q Consensus 29 ~I~s~~~~~~l~~ei~~fR~~l~~L~ 54 (68)
-+.-+..+..+.+++.+.|++|..|.
T Consensus 100 ~~~~~~~l~~iY~~L~~ik~~LE~L~ 125 (134)
T PF10303_consen 100 EIEVDPSLQPIYDQLIDIKNTLENLL 125 (134)
T ss_pred cccccHHHHHHHHHHHHHHHHHHhhh
Confidence 34456889999999999999998874
No 38
>PF07026 DUF1317: Protein of unknown function (DUF1317); InterPro: IPR009750 This entry is represented by Bacteriophage lambda, Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=29.43 E-value=72 Score=18.51 Aligned_cols=23 Identities=22% Similarity=0.232 Sum_probs=19.4
Q ss_pred CCCHHHHHHHHHHHHHHHHhhch
Q psy2164 30 ITSDHMVQTILNEMSDIRWRLGS 52 (68)
Q Consensus 30 I~s~~~~~~l~~ei~~fR~~l~~ 52 (68)
|.++.-...+-+|+++++.++..
T Consensus 32 i~NPlkAqR~AE~~n~~~~~l~~ 54 (60)
T PF07026_consen 32 ITNPLKAQRLAEELNSKQVNLCD 54 (60)
T ss_pred EcCHHHHHHHHHHHHhhHhhhhh
Confidence 56778889999999999998864
No 39
>PF01432 Peptidase_M3: Peptidase family M3 This Prosite motif covers only the active site. This family belongs to family M3 of the peptidase classification.; InterPro: IPR001567 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M3 (clan MA(E)), subfamilies M3A and M3B. The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. The Thimet oligopeptidase family, is a large family of archaeal, bacterial and eukaryotic oligopeptidases that cleave medium sized peptides. The group contains: mitochondrial intermediate peptidase (3.4.24.59 from EC) Neurolysin, mitochondrial precursor, (3.4.24.16 from EC) Thimet oligopeptidase (3.4.24.15 from EC) Dipeptidyl carboxypeptidase (3.4.15.5 from EC) Oligopeptidase A (3.4.24.70 from EC) Oligoendopeptidase F ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QR4_B 3CE2_A 1Y79_1 2H1J_A 2H1N_A 2O36_A 1S4B_P 2O3E_A 1I1I_P.
Probab=29.25 E-value=77 Score=23.55 Aligned_cols=35 Identities=31% Similarity=0.455 Sum_probs=24.4
Q ss_pred HHHHhCCCCCHHHH--HHHHHHHHHHHHhhchhhcCc
Q psy2164 23 RARREATITSDHMV--QTILNEMSDIRWRLGSLIGYD 57 (68)
Q Consensus 23 ~ar~eg~I~s~~~~--~~l~~ei~~fR~~l~~L~~yD 57 (68)
+|..+..-+....+ ..+++++...|..++.+.+|+
T Consensus 16 ~a~~~~~~~~~~~~~n~~~l~~l~~~R~~~A~llGy~ 52 (458)
T PF01432_consen 16 RAYYSRYSDNQPTLDNAAILNELLKLRNELAKLLGYP 52 (458)
T ss_dssp HHHHTTTHHTHHHHHHHHHHHHHHHHHHHHHHHTT-S
T ss_pred HHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHCCCC
Confidence 33333333333445 889999999999999999986
No 40
>PF13041 PPR_2: PPR repeat family
Probab=28.21 E-value=91 Score=15.73 Aligned_cols=25 Identities=8% Similarity=0.222 Sum_probs=16.1
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHH
Q psy2164 17 ATNIINRARREATITSDHMVQTILN 41 (68)
Q Consensus 17 a~~l~~~ar~eg~I~s~~~~~~l~~ 41 (68)
|..+..+-.++|.-.+...++.+++
T Consensus 22 a~~l~~~M~~~g~~P~~~Ty~~li~ 46 (50)
T PF13041_consen 22 ALKLFKEMKKRGIKPDSYTYNILIN 46 (50)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHH
Confidence 4556666666676666666666654
No 41
>PRK01631 hypothetical protein; Provisional
Probab=27.79 E-value=1.2e+02 Score=18.37 Aligned_cols=35 Identities=11% Similarity=0.221 Sum_probs=20.8
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHH--HHHHHHhhc
Q psy2164 17 ATNIINRARREATITSDHMVQTILNE--MSDIRWRLG 51 (68)
Q Consensus 17 a~~l~~~ar~eg~I~s~~~~~~l~~e--i~~fR~~l~ 51 (68)
+..|..+++.+|+=..+..-...+.+ |..||+++.
T Consensus 8 INeLakK~K~~gLT~eE~~Eq~~LR~eYl~~fR~~~~ 44 (76)
T PRK01631 8 INELSKKEKATGLTVDEKQEQQMLRQNYTQTFRGSLD 44 (76)
T ss_pred HHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45678888888886655444433332 455666553
No 42
>COG4981 Enoyl reductase domain of yeast-type FAS1 [Lipid metabolism]
Probab=27.65 E-value=1e+02 Score=25.47 Aligned_cols=36 Identities=19% Similarity=0.440 Sum_probs=27.9
Q ss_pred cceeeHHHHHH-----HHHHHHHhCC----------CCCHHHHHHHHHHHH
Q psy2164 9 KYWLPLTWATN-----IINRARREAT----------ITSDHMVQTILNEMS 44 (68)
Q Consensus 9 kyWvPi~Wa~~-----l~~~ar~eg~----------I~s~~~~~~l~~ei~ 44 (68)
-|.=|..|..+ |+++||.+|. |.|-...+.+++|+.
T Consensus 97 ifldpylw~~qig~krLv~kara~G~~I~gvvIsAGIP~le~A~ElI~~L~ 147 (717)
T COG4981 97 IFLDPYLWKLQIGGKRLVQKARASGAPIDGVVISAGIPSLEEAVELIEELG 147 (717)
T ss_pred EEechHHhhhcCChHHHHHHHHhcCCCcceEEEecCCCcHHHHHHHHHHHh
Confidence 45568777654 8999999998 666677788888885
No 43
>PF10474 DUF2451: Protein of unknown function C-terminus (DUF2451); InterPro: IPR019514 This protein is found in eukaryotes but its function is not known. The N-terminal domain of some members is PF10475 from PFAM (DUF2450).
Probab=27.02 E-value=1.3e+02 Score=21.03 Aligned_cols=43 Identities=21% Similarity=0.292 Sum_probs=30.2
Q ss_pred eeHHHHHHHHHHHH---HhCCCCCHHHHHHHHHHHHHHHHhhchhh
Q psy2164 12 LPLTWATNIINRAR---REATITSDHMVQTILNEMSDIRWRLGSLI 54 (68)
Q Consensus 12 vPi~Wa~~l~~~ar---~eg~I~s~~~~~~l~~ei~~fR~~l~~L~ 54 (68)
+++....+.+...+ +|--..+......+++|+..|+.+|..+.
T Consensus 67 l~~~~i~~~Ia~vKWdvkev~~qhs~YVd~l~~~~~~f~~rL~~i~ 112 (234)
T PF10474_consen 67 LDLEQILNSIANVKWDVKEVMSQHSSYVDQLVQEFQQFSERLDEIS 112 (234)
T ss_pred cCHHHHHHHHHHcCCCCCCCCCccCHHHHHHHHHHHHHHHHHHHHH
Confidence 45555555555554 34444456788999999999999997666
No 44
>PHA03419 E4 protein; Provisional
Probab=26.91 E-value=77 Score=22.42 Aligned_cols=20 Identities=30% Similarity=0.523 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHhhch
Q psy2164 33 DHMVQTILNEMSDIRWRLGS 52 (68)
Q Consensus 33 ~~~~~~l~~ei~~fR~~l~~ 52 (68)
+..+++|++++.+|.++|++
T Consensus 179 ~qLV~~I~~DL~~YW~kL~t 198 (200)
T PHA03419 179 DQLVDNIVVDLRDYWQRLRT 198 (200)
T ss_pred HHHHHHHHHHHHHHHHHhcC
Confidence 57888999999999999975
No 45
>TIGR01147 V_ATP_synt_G vacuolar ATP synthase, subunit G. This model describes the vacuolar ATP synthase G subunit in eukaryotes and includes members from diverse groups e.g., fungi, plants, parasites etc. V-ATPases are multi-subunit enzymes composed of two functional domains: A transmembrane Vo domain and a peripheral catalytic domain V1. The G subunit is one of the subunits of the catalytic domain. V-ATPases are responsible for the acidification of endosomes and lysosomes, which are part of the central vacuolar system.
Probab=26.82 E-value=71 Score=20.40 Aligned_cols=32 Identities=13% Similarity=0.226 Sum_probs=19.5
Q ss_pred HHHHHHHHHH--hCCCCCHHHHHHHHHHHHHHHHhh
Q psy2164 17 ATNIINRARR--EATITSDHMVQTILNEMSDIRWRL 50 (68)
Q Consensus 17 a~~l~~~ar~--eg~I~s~~~~~~l~~ei~~fR~~l 50 (68)
|..++.+||+ ..+++ .+-...-.||..||..-
T Consensus 18 A~~IV~~AR~~r~~RLK--qAK~EA~~EI~~yr~~k 51 (113)
T TIGR01147 18 AAEKVSEARKRKTKRLK--QAKEEAQKEVEKYKQQR 51 (113)
T ss_pred HHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHH
Confidence 3456677774 33343 44456677888888754
No 46
>PF05791 Bacillus_HBL: Bacillus haemolytic enterotoxin (HBL); InterPro: IPR008414 This family consists of several Bacillus haemolytic enterotoxins (HblC, HblD, HblA, NheA, and NheB), which can cause food poisoning in humans []. Haemolysin BL (encoded by HBL) and non-haemolytic enterotoxin (encoded by NHE), represent the major enterotoxins produced by Bacillus cereus. Most of the cytotoxic activity of B. cereus isolates has been attributed to the level of Nhe, which may indicate a highly diarrheic potential []. The exact mechanism by which B. cereus causes diarrhoea is unknown. Hbl, cytotoxin K (CytK) and Nhe are all putative causes. Both Hbl and Nhe are three-component cytotoxins and maximal cytotoxicity of Nhe against epithelia is dependent on all three components. Nhe has haemolytic activity against erythrocytes from a variety of species. It is possible that the common structural and functional properties of these toxins indicate that the Hbl/Nhe and ClyA families of toxins constitute a superfamily of pore-forming cytotoxins []. The high virulence of some strains is thought to be due to the greater cytotoxic activity of CytK-1 compared to CytK-2, and to a high level of cytK expression []. Haemolysin BL and non-haemolytic enterotoxin production are both influenced by pH and micro []. This entry is found in cytotoxic proteins that form part of the enterotoxin complex and bind to erythrocytes. HblA is composed of a binding component, B, and two lytic components, L1 and L2. All three subunits act synergically to cause hemolysis.; GO: 0009405 pathogenesis, 0016020 membrane; PDB: 2NRJ_A.
Probab=26.67 E-value=63 Score=21.70 Aligned_cols=19 Identities=32% Similarity=0.552 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHhhch
Q psy2164 34 HMVQTILNEMSDIRWRLGS 52 (68)
Q Consensus 34 ~~~~~l~~ei~~fR~~l~~ 52 (68)
..+..++.||.+||.+|..
T Consensus 124 ~~~~~~i~~L~~f~~~l~~ 142 (184)
T PF05791_consen 124 DKVQALINELNDFKDKLQK 142 (184)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4567888999999998753
No 47
>PHA03418 hypothetical E4 protein; Provisional
Probab=26.13 E-value=79 Score=22.82 Aligned_cols=20 Identities=25% Similarity=0.508 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHhhch
Q psy2164 33 DHMVQTILNEMSDIRWRLGS 52 (68)
Q Consensus 33 ~~~~~~l~~ei~~fR~~l~~ 52 (68)
+..+.+|+++|.+|+++|++
T Consensus 209 ~qLV~~I~~DL~dYW~kL~t 228 (230)
T PHA03418 209 RQLVEDIQEDLDDYWRKLGI 228 (230)
T ss_pred HHHHHHHHHHHHHHHHhhcC
Confidence 57889999999999999985
No 48
>COG3969 Predicted phosphoadenosine phosphosulfate sulfotransferase [General function prediction only]
Probab=26.03 E-value=1.1e+02 Score=23.70 Aligned_cols=35 Identities=20% Similarity=0.212 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHHHHHHHHHhhchhhcC-cceecccc
Q psy2164 30 ITSDHMVQTILNEMSDIRWRLGSLIGY-DNVNLPLV 64 (68)
Q Consensus 30 I~s~~~~~~l~~ei~~fR~~l~~L~~y-DWVpIPLv 64 (68)
|+=+..+...++=+.+.|+.......+ =||++||.
T Consensus 64 iD~E~QYs~TidyV~em~~~~~dv~~~~yWvcLPl~ 99 (407)
T COG3969 64 IDWEAQYSCTIDYVQEMRESYHDVIETFYWVCLPLT 99 (407)
T ss_pred EcchhhhhhHHHHHHHHHhcccCccccceEEEeehh
Confidence 455566777788888888876666664 89999986
No 49
>PF15187 Augurin: Oesophageal cancer-related gene 4
Probab=25.23 E-value=44 Score=21.60 Aligned_cols=22 Identities=18% Similarity=0.277 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHhCCCCCHHHH
Q psy2164 15 TWATNIINRARREATITSDHMV 36 (68)
Q Consensus 15 ~Wa~~l~~~ar~eg~I~s~~~~ 36 (68)
+|..+.++...+|.++++|..+
T Consensus 52 QW~qQFlYmGFDEak~E~DlsY 73 (114)
T PF15187_consen 52 QWYQQFLYMGFDEAKFEDDLSY 73 (114)
T ss_pred HHHHHHHHhcchHHHhhhhHHH
Confidence 5999999999999999988765
No 50
>COG3943 Virulence protein [General function prediction only]
Probab=25.21 E-value=2e+02 Score=21.50 Aligned_cols=39 Identities=21% Similarity=0.366 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHhCCCCCHH---------HHHHHHHHHHHHHHhhchh
Q psy2164 15 TWATNIINRARREATITSDH---------MVQTILNEMSDIRWRLGSL 53 (68)
Q Consensus 15 ~Wa~~l~~~ar~eg~I~s~~---------~~~~l~~ei~~fR~~l~~L 53 (68)
+||.+-+.+-.-+|...+|. .++.+++-|++.|.+-..+
T Consensus 104 qwatq~lqeyl~kgfvmdderlk~~~~gdy~~emlerirdiraser~v 151 (329)
T COG3943 104 QWATQTLQEYLIKGFVMDDERLKNPPVGDYFKEMLERIRDIRASERRV 151 (329)
T ss_pred HHHHHHHHHHHHhhcccchhhccCCCcchHHHHHHHHHHHHHHHHHHH
Confidence 79999999998888877763 4678999999999876544
No 51
>PF03487 IL13: Interleukin-13; InterPro: IPR020470 Interleukin-13 (IL-13) is a pleiotropic cytokine which may be important in the regulation of the inflammatory and immune responses []. It inhibits inflammatory cytokine production and synergises with IL-2 in regulating interferon-gamma synthesis. The sequences of IL-4 and IL-13 are distantly related.; PDB: 3G6D_A 3L5W_J 3BPO_A 1GA3_A 1IK0_A 3L5X_A 3L5Y_A 1IJZ_A 3LB6_B.
Probab=25.05 E-value=81 Score=17.09 Aligned_cols=24 Identities=13% Similarity=0.328 Sum_probs=15.5
Q ss_pred HhCCCCCHHHHHHHHHHHHHHHHh
Q psy2164 26 REATITSDHMVQTILNEMSDIRWR 49 (68)
Q Consensus 26 ~eg~I~s~~~~~~l~~ei~~fR~~ 49 (68)
.-|-+.+...++.+++|+.+.-++
T Consensus 19 sPgPvp~~~alkELIeELvNITqn 42 (43)
T PF03487_consen 19 SPGPVPSSTALKELIEELVNITQN 42 (43)
T ss_dssp ----S-HHHHHHHHHHHHHHHHHS
T ss_pred CCCCCCchHHHHHHHHHHHhhccC
Confidence 345566778899999999887553
No 52
>PF05979 DUF896: Bacterial protein of unknown function (DUF896); InterPro: IPR009242 This family consists of several short, hypothetical bacterial proteins of unknown function. They may be involved in the bacterial SOS response [].; PDB: 2HEP_A 3BHP_C 2JVD_A.
Probab=25.05 E-value=75 Score=18.54 Aligned_cols=34 Identities=12% Similarity=0.287 Sum_probs=18.4
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHH--HHHHHHhh
Q psy2164 17 ATNIINRARREATITSDHMVQTILNE--MSDIRWRL 50 (68)
Q Consensus 17 a~~l~~~ar~eg~I~s~~~~~~l~~e--i~~fR~~l 50 (68)
+..|.++++.+|+-..+..-...+.. |..||+++
T Consensus 7 INeLa~K~K~~gLT~eE~~Eq~~LR~eYl~~fR~~~ 42 (65)
T PF05979_consen 7 INELAKKSKEEGLTEEEKAEQAELRQEYLQNFRGNF 42 (65)
T ss_dssp HHHHHHHHHTT---HHHHHHHHHHHHHHHHTTHHHH
T ss_pred HHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 45688889889987665555444332 44455544
No 53
>PF00458 WHEP-TRS: WHEP-TRS domain; InterPro: IPR000738 A conserved domain of 46 amino acids, called WHEP-TRS has been shown [] to exist in a number of higher eukaryote aminoacyl-transfer RNA synthetases. This domain is present one to six times in the several enzymes. There are three copies in mammalian multifunctional aminoacyl-tRNA synthetase in a region that separates the N-terminal glutamyl-tRNA synthetase domain from the C-terminal prolyl-tRNA synthetase domain, and six copies in the intercatalytic region of the Drosophila enzyme. The domain is found at the N-terminal extremity of the mammalian tryptophanyl- tRNA synthetase and histidyl-tRNA synthetase, and the mammalian, insect, nematode and plant glycyl- tRNA synthetases []. This domain could contain a central alpha-helical region and may play a role in the association of tRNA-synthetases into multienzyme complexes.; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation; PDB: 1R1B_A 1D2D_A 1X59_A 1FYJ_A 2ZT8_A 2ZXF_A 2ZT7_A 2ZT6_A 2PME_A 2ZT5_A ....
Probab=24.83 E-value=1.4e+02 Score=16.71 Aligned_cols=41 Identities=12% Similarity=0.244 Sum_probs=31.8
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhhchhhcCcceec
Q psy2164 19 NIINRARREATITSDHMVQTILNEMSDIRWRLGSLIGYDNVNL 61 (68)
Q Consensus 19 ~l~~~ar~eg~I~s~~~~~~l~~ei~~fR~~l~~L~~yDWVpI 61 (68)
+.+|+...+| .+......-++++.+.+..+..+..-||.|=
T Consensus 10 ~~VR~LKa~k--a~k~~i~~aV~~Ll~LK~~~~~~tg~~~~~~ 50 (56)
T PF00458_consen 10 DKVRKLKAEK--ADKEEIDAAVAKLLELKAELKELTGKDYKPG 50 (56)
T ss_dssp HHHHHHHHTT----HHHHHHHHHHHHHHHHHHHHHCSSSTTSS
T ss_pred HHHHHHHccC--CcHHHHHHHHHHHHHHHHHHHHhhCCCCCCC
Confidence 4566666666 3455688999999999999999999998774
No 54
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=24.48 E-value=72 Score=18.99 Aligned_cols=21 Identities=24% Similarity=0.367 Sum_probs=16.8
Q ss_pred hCCCCCHHHHHHHHHHHHHHHH
Q psy2164 27 EATITSDHMVQTILNEMSDIRW 48 (68)
Q Consensus 27 eg~I~s~~~~~~l~~ei~~fR~ 48 (68)
++.+ |+..++.|.+|+.+.|.
T Consensus 51 K~~f-S~sEm~aI~~ELG~LRK 71 (71)
T PF06569_consen 51 KDSF-SPSEMQAIAEELGQLRK 71 (71)
T ss_pred ccCC-CHHHHHHHHHHHHhhcC
Confidence 3444 78999999999998884
No 55
>PLN02350 phosphogluconate dehydrogenase (decarboxylating)
Probab=24.26 E-value=1.8e+02 Score=22.81 Aligned_cols=46 Identities=11% Similarity=0.165 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHhC-----CCCCHHHHHHHHHHHHHHHHhhchhhcCcceecc
Q psy2164 16 WATNIINRARREA-----TITSDHMVQTILNEMSDIRWRLGSLIGYDNVNLP 62 (68)
Q Consensus 16 Wa~~l~~~ar~eg-----~I~s~~~~~~l~~ei~~fR~~l~~L~~yDWVpIP 62 (68)
|++.++.+|.+++ ++.++.....+.+.....|.-...=...+ ||+|
T Consensus 381 ~lL~~i~~a~~~~~~l~~l~~~~~~~~~~~~~~~~~r~~V~~a~~~g-ip~P 431 (493)
T PLN02350 381 VFLDRIKKAYDRNPDLASLLVDPEFAKEMVERQAAWRRVVSLAINAG-ISTP 431 (493)
T ss_pred hHHHHHHHHHHcCCChhhhcCCHHHHHHHHHhhhHHHHHHHHHHHcC-CCHH
Confidence 8899999999864 24445555666677777887776665555 6665
No 56
>PF03290 Peptidase_C57: Vaccinia virus I7 processing peptidase; InterPro: IPR004970 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This is a group of cysteine peptidases which constitute MEROPS peptidase family C57 (clan CE). The type example is vaccinia virus I7 processing peptidase (vaccinia virus); protein I7 is expressed in the late phase of infection [].
Probab=24.03 E-value=49 Score=25.78 Aligned_cols=56 Identities=11% Similarity=0.249 Sum_probs=34.0
Q ss_pred CCCCcceeeHHHHHHHHHHHHHhCCCCCH-------HHH-HHHHHHHHHHHHhhchhhcCcceeccccc
Q psy2164 5 HPMTKYWLPLTWATNIINRARREATITSD-------HMV-QTILNEMSDIRWRLGSLIGYDNVNLPLVY 65 (68)
Q Consensus 5 ~~~~kyWvPi~Wa~~l~~~ar~eg~I~s~-------~~~-~~l~~ei~~fR~~l~~L~~yDWVpIPLvY 65 (68)
+.+.--.+|+.= |.+-.++|.+..+ ..+ ..++++|++=-.+...++..- .+|||+|
T Consensus 56 TaGkVScIPl~~----Llel~~~~~l~~p~~~~~~El~~K~~L~~~L~~k~~~i~d~~~~~-tsIPl~Y 119 (423)
T PF03290_consen 56 TAGKVSCIPLSI----LLELVKSGYLSAPNNSKSDELELKRYLVNYLKEKYININDIFTLP-TSIPLAY 119 (423)
T ss_pred ccCceEEeeHHH----HHHHHHcCCcCCCCCCccHHHHHHHHHHHHHHHhccCHHHHHcCC-cCCchhh
Confidence 445556788754 4444556666322 222 346666665444667777777 7999998
No 57
>PRK09282 pyruvate carboxylase subunit B; Validated
Probab=24.00 E-value=1.1e+02 Score=24.34 Aligned_cols=34 Identities=18% Similarity=0.441 Sum_probs=29.2
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhhchh
Q psy2164 17 ATNIINRARREATITSDHMVQTILNEMSDIRWRLGSL 53 (68)
Q Consensus 17 a~~l~~~ar~eg~I~s~~~~~~l~~ei~~fR~~l~~L 53 (68)
..||..++++.|.. ..+..+++|+.+-|.-+|..
T Consensus 301 ~snl~~q~~~~g~~---d~~~~vl~e~~~v~~~lG~~ 334 (592)
T PRK09282 301 ISNLVSQLKEQNAL---DKLDEVLEEIPRVREDLGYP 334 (592)
T ss_pred HHHHHHHHHHCCcH---HHHHHHHHHHHHHHHHcCCC
Confidence 57899999999984 27899999999999998853
No 58
>PLN03075 nicotianamine synthase; Provisional
Probab=23.88 E-value=1.2e+02 Score=22.19 Aligned_cols=35 Identities=20% Similarity=0.297 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhhchhhc
Q psy2164 17 ATNIINRARREATITSDHMVQTILNEMSDIRWRLGSLIG 55 (68)
Q Consensus 17 a~~l~~~ar~eg~I~s~~~~~~l~~ei~~fR~~l~~L~~ 55 (68)
+.+|+.-+..+. +.....+.+||.++|.+|..||+
T Consensus 38 f~~Lv~~c~~~~----~~~~~~l~~~i~~~~~~l~~l~~ 72 (296)
T PLN03075 38 FTQLVSTCIPPS----SIDVTKLCEEIQEMRSKLIKLCG 72 (296)
T ss_pred HHHHHHHhCCCC----cchHHHhhHHHHHHHHHHHHHHH
Confidence 344454444333 33456899999999999998886
No 59
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=23.37 E-value=75 Score=18.50 Aligned_cols=17 Identities=18% Similarity=0.477 Sum_probs=12.9
Q ss_pred HHHHHHHHHHhCCCCCH
Q psy2164 17 ATNIINRARREATITSD 33 (68)
Q Consensus 17 a~~l~~~ar~eg~I~s~ 33 (68)
+-.|+.+++++|+++-+
T Consensus 9 i~~Li~~gK~~G~lT~~ 25 (82)
T PF03979_consen 9 IKKLIEKGKKKGYLTYD 25 (82)
T ss_dssp HHHHHHHHHHHSS-BHH
T ss_pred HHHHHHHHhhcCcCCHH
Confidence 45799999999998744
No 60
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=23.34 E-value=70 Score=20.48 Aligned_cols=22 Identities=18% Similarity=0.173 Sum_probs=18.3
Q ss_pred CHHHHHHHHHHHHHHHHhhchh
Q psy2164 32 SDHMVQTILNEMSDIRWRLGSL 53 (68)
Q Consensus 32 s~~~~~~l~~ei~~fR~~l~~L 53 (68)
++..+....+|+.+||.+|+.-
T Consensus 98 e~p~y~~~~~e~~~Yr~~LE~r 119 (131)
T PF09779_consen 98 EDPEYANYEEELPEYRRSLEQR 119 (131)
T ss_pred CCccHHHHHHHHHHHHHHHHHH
Confidence 3457889999999999999864
No 61
>TIGR01987 HI0074 nucleotidyltransferase substrate binding protein, HI0074 family. The member of this family from Haemophilus influenzae, HI0074, has been shown by crystal structure to resemble nucleotidyltransferase substrate binding proteins. It forms a complex with HI0073, encoded by the adjacent gene and containing a nucleotidyltransferase nucleotide binding domain (pfam01909).
Probab=23.26 E-value=1.4e+02 Score=18.99 Aligned_cols=30 Identities=20% Similarity=0.227 Sum_probs=20.4
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhhc
Q psy2164 18 TNIINRARREATITSDHMVQTILNEMSDIRWRLG 51 (68)
Q Consensus 18 ~~l~~~ar~eg~I~s~~~~~~l~~ei~~fR~~l~ 51 (68)
-++++.|.+.|+|.+. .++-++.+=|+..+
T Consensus 63 r~~ir~A~~~glI~d~----~~W~~ml~~RN~ts 92 (123)
T TIGR01987 63 KDVLKEAFRAGLIGDE----SLWIAMLDDRNITS 92 (123)
T ss_pred HHHHHHHHHcCCcCCH----HHHHHHHHHhCccc
Confidence 3678999999999754 35555555565444
No 62
>PF08044 DUF1707: Domain of unknown function (DUF1707); InterPro: IPR012551 This domain is found in a variety of actinomycetales proteins. All of the proteins containing this domain are hypothetical and probably membrane bound or associated. Currently, it is unclear to the function of this domain.
Probab=23.06 E-value=1.4e+02 Score=16.38 Aligned_cols=17 Identities=24% Similarity=0.380 Sum_probs=14.2
Q ss_pred HHHHHHHHHHhCCCCCH
Q psy2164 17 ATNIINRARREATITSD 33 (68)
Q Consensus 17 a~~l~~~ar~eg~I~s~ 33 (68)
+..++..|..+|++..+
T Consensus 11 ~~~~L~~a~a~GrL~~~ 27 (53)
T PF08044_consen 11 AVDLLRAAFAEGRLSLD 27 (53)
T ss_pred HHHHHHHHHHCCCCCHH
Confidence 57889999999999744
No 63
>KOG0506|consensus
Probab=22.76 E-value=1.3e+02 Score=24.40 Aligned_cols=30 Identities=23% Similarity=0.378 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHHHHHHHH
Q psy2164 19 NIINRARREATITSDHMVQTILNEMSDIRW 48 (68)
Q Consensus 19 ~l~~~ar~eg~I~s~~~~~~l~~ei~~fR~ 48 (68)
.+++.-+..|+=+||+-++..|+||+++=+
T Consensus 107 KFiTALkstGLrtsDPRLk~mMd~mKd~dq 136 (622)
T KOG0506|consen 107 KFITALKSTGLRTSDPRLKDMMDEMKDVDQ 136 (622)
T ss_pred HHHHHHHHcCCCcCCchHHHHHHHHHHHHh
Confidence 455556678999999999999999999875
No 64
>KOG2351|consensus
Probab=22.65 E-value=1.1e+02 Score=20.34 Aligned_cols=21 Identities=33% Similarity=0.556 Sum_probs=17.1
Q ss_pred hCCCCCHHHHHHHHHHHHHHHH
Q psy2164 27 EATITSDHMVQTILNEMSDIRW 48 (68)
Q Consensus 27 eg~I~s~~~~~~l~~ei~~fR~ 48 (68)
+++| +|..++.++++|...|+
T Consensus 112 ~nki-dD~~le~iL~dls~lr~ 132 (134)
T KOG2351|consen 112 ENKI-DDDELEQILKDLSTLRT 132 (134)
T ss_pred cccc-CHHHHHHHHHHHHHHHh
Confidence 5777 47789999999988775
No 65
>PF08780 NTase_sub_bind: Nucleotidyltransferase substrate binding protein like; InterPro: IPR010235 The member of this family from Haemophilus influenzae, HI0074, has been shown by crystal structure to resemble nucleotidyltransferase substrate binding proteins []. It forms a complex with HI0073 (P43933 from SWISSPROT), encoded by the adjacent gene, which contains a nucleotidyltransferase nucleotide binding domain (IPR002934 from INTERPRO). Double- and single-stranded DNA binding assays showed no evidence of DNA binding to HI0074 or to HI0073/HI0074 complex despite the suggestive shape of the putative binding cleft formed by the HI0074 dimer []. ; PDB: 1WWP_A 1JOG_A 1WTY_C 2YWA_B.
Probab=22.61 E-value=2.1e+02 Score=17.96 Aligned_cols=32 Identities=19% Similarity=0.166 Sum_probs=21.5
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHhhchh
Q psy2164 18 TNIINRARREATITSDHMVQTILNEMSDIRWRLGSL 53 (68)
Q Consensus 18 ~~l~~~ar~eg~I~s~~~~~~l~~ei~~fR~~l~~L 53 (68)
=.++++|.+.|+|. |. .++-++.+=|+..+..
T Consensus 63 r~~~r~A~~~glI~-d~---e~Wl~m~~~RN~tsHt 94 (124)
T PF08780_consen 63 RDVFREAFKAGLID-DG---EIWLDMLEDRNLTSHT 94 (124)
T ss_dssp HHHHHHHHHTTSSS-HH---HHHHHHHHHHHHGGGT
T ss_pred HHHHHHHHHcCCCC-CH---HHHHHHHHHhccccCC
Confidence 36789999999994 44 2355666666655543
No 66
>PF06547 DUF1117: Protein of unknown function (DUF1117); InterPro: IPR010543 This entry represents the C terminus of a number of hypothetical plant proteins.
Probab=22.30 E-value=30 Score=22.55 Aligned_cols=8 Identities=63% Similarity=1.140 Sum_probs=6.5
Q ss_pred cccccccC
Q psy2164 61 LPLVYTQK 68 (68)
Q Consensus 61 IPLvYtQv 68 (68)
+|+|||++
T Consensus 30 lPvVyTEm 37 (117)
T PF06547_consen 30 LPVVYTEM 37 (117)
T ss_pred CCEEEEEe
Confidence 69999974
No 67
>PRK01546 hypothetical protein; Provisional
Probab=22.24 E-value=1.6e+02 Score=17.79 Aligned_cols=34 Identities=15% Similarity=0.256 Sum_probs=19.6
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHH--HHHHHHhh
Q psy2164 17 ATNIINRARREATITSDHMVQTILNE--MSDIRWRL 50 (68)
Q Consensus 17 a~~l~~~ar~eg~I~s~~~~~~l~~e--i~~fR~~l 50 (68)
+..|..+++.+|+=..+..-..-+.+ |..||.++
T Consensus 10 INeLakK~K~~gLT~eEk~Eq~~LR~eYl~~fR~~~ 45 (79)
T PRK01546 10 INFLAKKAKAEGLTEEEQRERQSLREQYLKGFRQNM 45 (79)
T ss_pred HHHHHHhhcccCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 45688888888986655443333322 34455443
No 68
>PF11458 Mistic: Membrane-integrating protein Mistic; InterPro: IPR021078 Mistic is an integral membrane protein that folds autonomously into the membrane []. It is conserved in the Bacilli bacteria. The protein forms a helical bundle with a polar lipid-facing surface. Mistic can be used for high-level production of other membrane proteins in their native conformations [].
Probab=22.12 E-value=78 Score=19.40 Aligned_cols=29 Identities=17% Similarity=0.382 Sum_probs=20.7
Q ss_pred HHHHHHHHHh-CCCCCHHHHHHHHHHHHHH
Q psy2164 18 TNIINRARRE-ATITSDHMVQTILNEMSDI 46 (68)
Q Consensus 18 ~~l~~~ar~e-g~I~s~~~~~~l~~ei~~f 46 (68)
..|+++||.. |--.-+.-+++++.||.+|
T Consensus 46 ael~~~A~~~yG~e~~n~klN~iIkqiLs~ 75 (84)
T PF11458_consen 46 AELIRQAREKYGQEKLNEKLNAIIKQILSI 75 (84)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHcc
Confidence 4578888864 5555567788888888764
No 69
>PF11900 DUF3420: Domain of unknown function (DUF3420); InterPro: IPR024228 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes and is about 50 amino acids in length.
Probab=21.43 E-value=95 Score=17.07 Aligned_cols=16 Identities=13% Similarity=0.381 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHhhch
Q psy2164 37 QTILNEMSDIRWRLGS 52 (68)
Q Consensus 37 ~~l~~ei~~fR~~l~~ 52 (68)
..++.+|+..|.+++.
T Consensus 13 ~eVv~kIk~lR~k~~~ 28 (49)
T PF11900_consen 13 PEVVKKIKDLRLKSQL 28 (49)
T ss_pred HHHHHHHHHHHHHcCC
Confidence 3688999999999886
No 70
>cd01055 Nonheme_Ferritin nonheme-containing ferritins. Nonheme Ferritin domain, found in archaea and bacteria, is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The ferritin protein shell is composed of 24 protein subunits arranged in 432 symmetry. Each protein subunit, a four-helix bundle with a fifth short terminal helix, contains a dinuclear ferroxidase center (H type). Unique to this group of proteins is a third metal site in the ferroxidase center. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite.
Probab=21.17 E-value=1.9e+02 Score=18.04 Aligned_cols=38 Identities=21% Similarity=0.110 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHH----HHHHHHhhchhhcC
Q psy2164 19 NIINRARREATITSDHMVQTILNE----MSDIRWRLGSLIGY 56 (68)
Q Consensus 19 ~l~~~ar~eg~I~s~~~~~~l~~e----i~~fR~~l~~L~~y 56 (68)
.+...|.++|-...-..+..++++ ++.+.+-++.|...
T Consensus 101 ~l~~~A~~~~D~~~~~~l~~~l~~q~e~~~~~~~~l~~l~~~ 142 (156)
T cd01055 101 NLVDLALEEKDYATFNFLQWFVKEQVEEEALARDILDKLKLA 142 (156)
T ss_pred HHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456667777765554555555554 67777777766544
No 71
>PF10625 UspB: Universal stress protein B (UspB); InterPro: IPR019598 Universal stress protein B (UspB) in Escherichia coli is a 14kDa protein which is predicted to be an integral membrane protein. Over expression of UspB results in cell death in stationary phase, and mutants of UspB are sensitive to ethanol exposure during stationary phase [].
Probab=20.75 E-value=2.3e+02 Score=18.23 Aligned_cols=29 Identities=28% Similarity=0.340 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHhhchhhcCcceecccccccC
Q psy2164 36 VQTILNEMSDIRWRLGSLIGYDNVNLPLVYTQK 68 (68)
Q Consensus 36 ~~~l~~ei~~fR~~l~~L~~yDWVpIPLvYtQv 68 (68)
...++.=+.+.|.=+-.+...| ||-|-||
T Consensus 16 ~vNm~RY~SsLR~LL~imR~~d----PLLYQ~V 44 (107)
T PF10625_consen 16 IVNMARYFSSLRALLYIMREAD----PLLYQQV 44 (107)
T ss_pred HHHHHHHHHHHHHHHHHHhcCC----cHHHHhc
Confidence 3445556677777777777777 8888876
No 72
>PF09454 Vps23_core: Vps23 core domain; InterPro: IPR017916 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ]. This entry represents the Steadiness box domain.; PDB: 2CAZ_A 2F66_D 2F6M_A 2P22_A.
Probab=20.70 E-value=1.4e+02 Score=17.03 Aligned_cols=21 Identities=19% Similarity=0.365 Sum_probs=14.3
Q ss_pred HHHHHHHHHHhCCCCCHHHHH
Q psy2164 17 ATNIINRARREATITSDHMVQ 37 (68)
Q Consensus 17 a~~l~~~ar~eg~I~s~~~~~ 37 (68)
++..+.+|.+.|.|.-|..++
T Consensus 27 tiy~L~~al~~g~I~~d~~lK 47 (65)
T PF09454_consen 27 TIYYLDRALQRGSIDLDTFLK 47 (65)
T ss_dssp HHHHHHHHHHTTSS-HHHHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHH
Confidence 456788999999997554443
No 73
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=20.68 E-value=1.9e+02 Score=17.69 Aligned_cols=26 Identities=19% Similarity=0.297 Sum_probs=16.2
Q ss_pred HHHHHHHhCCCCCHHHHHHHHHHHHH
Q psy2164 20 IINRARREATITSDHMVQTILNEMSD 45 (68)
Q Consensus 20 l~~~ar~eg~I~s~~~~~~l~~ei~~ 45 (68)
++.+|++.|.--+|..++..++++.+
T Consensus 56 ~~q~ak~~gI~vsd~evd~~i~~ia~ 81 (118)
T PF09312_consen 56 QLQEAKRLGIKVSDEEVDEAIANIAK 81 (118)
T ss_dssp HHHHHHHCT----HHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 35677888888888888888777653
No 74
>COG3784 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.51 E-value=2e+02 Score=18.52 Aligned_cols=28 Identities=18% Similarity=0.430 Sum_probs=22.8
Q ss_pred HHHHHHhCC-----------CCCHHHHHHHHHHHHHHHH
Q psy2164 21 INRARREAT-----------ITSDHMVQTILNEMSDIRW 48 (68)
Q Consensus 21 ~~~ar~eg~-----------I~s~~~~~~l~~ei~~fR~ 48 (68)
+.+||.+|+ +..|-....++.+|+.=|.
T Consensus 26 ld~A~tqGrVGEt~~GYL~~v~~daet~alv~~IN~aR~ 64 (109)
T COG3784 26 LDEARTQGRVGETLDGYLVAVSTDAETQALVADINAARA 64 (109)
T ss_pred HHHHHhccchhccccceeeeecCcHHHHHHHHHHHHHHH
Confidence 578888887 4567889999999998875
No 75
>PF07751 Abi_2: Abi-like protein; InterPro: IPR011664 Bacteria have numerous mechanisms to resist bacteriophage infection. While most are based on preventing infection in the first place, the abortive infection (Abi) systems provide protection by the abortion of an existing phage infection []. Typically, these Abi systems target a crucial step of phage multiplication such as replication, transcription or translation, and lead to the death of the infected cell. These protein sequences, found in various bacterial species, are similar to those of the AbiD and AbiF proteins from Lactococcus species [, ]. The proteins are thought to have helix-turn-helix motifs, found in many DNA-binding proteins, allowing them to perform their function [].
Probab=20.18 E-value=2e+02 Score=18.11 Aligned_cols=20 Identities=30% Similarity=0.453 Sum_probs=17.0
Q ss_pred CHHHHHHHHHHHHHHHHhhc
Q psy2164 32 SDHMVQTILNEMSDIRWRLG 51 (68)
Q Consensus 32 s~~~~~~l~~ei~~fR~~l~ 51 (68)
+...+...++.|+.+|+.|+
T Consensus 164 ~~~~~~~~l~~i~~lRN~~A 183 (191)
T PF07751_consen 164 SRKDLSNWLNSIRDLRNRIA 183 (191)
T ss_pred ChhHHHHHHHHHHHHHhHhc
Confidence 46678889999999999886
Done!