Query psy5489
Match_columns 94
No_of_seqs 101 out of 483
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 18:48:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5489.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5489hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08441 Integrin_alpha2: Inte 99.8 3.8E-20 8.2E-25 142.6 9.6 91 4-94 168-266 (457)
2 KOG3637|consensus 99.7 8.9E-17 1.9E-21 135.0 10.3 90 4-94 642-738 (1030)
3 PF01345 DUF11: Domain of unkn 95.2 0.13 2.7E-06 30.5 6.2 50 4-58 24-74 (76)
4 TIGR01451 B_ant_repeat conserv 94.3 0.17 3.7E-06 28.5 4.9 37 20-58 8-45 (53)
5 PF07705 CARDB: CARDB; InterP 90.1 2 4.4E-05 25.7 6.2 44 5-53 3-47 (101)
6 PF00207 A2M: Alpha-2-macroglo 82.7 7.7 0.00017 23.6 5.9 38 5-48 55-92 (92)
7 PF10633 NPCBM_assoc: NPCBM-as 80.4 5.1 0.00011 23.6 4.4 31 25-55 4-35 (78)
8 PF04597 Ribophorin_I: Ribopho 75.2 39 0.00084 26.7 9.6 73 20-93 11-99 (432)
9 cd08523 Reeler_cohesin_like Do 69.2 13 0.00029 24.6 4.5 28 26-53 13-40 (124)
10 PF05753 TRAP_beta: Translocon 67.8 8.1 0.00017 27.1 3.4 28 25-52 37-66 (181)
11 PF00963 Cohesin: Cohesin doma 58.6 36 0.00078 22.0 5.1 38 24-61 12-50 (141)
12 COG1952 SecB Preprotein transl 56.1 35 0.00076 23.7 4.8 25 27-51 43-67 (157)
13 cd08547 Type_II_cohesin Type I 54.9 38 0.00083 21.4 4.7 39 22-61 12-51 (132)
14 PRK05751 preprotein translocas 51.8 25 0.00054 24.3 3.5 39 14-52 27-68 (156)
15 TIGR01624 LRP1_Cterm LRP1 C-te 48.0 23 0.0005 19.9 2.4 20 30-49 15-37 (50)
16 PF07919 Gryzun: Gryzun, putat 47.4 63 0.0014 25.5 5.6 31 18-50 184-214 (554)
17 KOG0250|consensus 46.9 14 0.0003 32.7 1.9 23 24-46 106-128 (1074)
18 PF00927 Transglut_C: Transglu 46.4 69 0.0015 19.7 5.7 32 19-52 10-47 (107)
19 COG1470 Predicted membrane pro 42.8 73 0.0016 26.1 5.3 37 20-56 278-315 (513)
20 PRK13031 preprotein translocas 40.2 40 0.00086 23.2 3.1 38 15-52 24-65 (149)
21 TIGR00809 secB protein-export 37.2 46 0.001 22.6 3.0 37 16-52 23-62 (140)
22 PF07987 DUF1775: Domain of un 36.7 56 0.0012 22.2 3.4 35 28-62 15-49 (145)
23 PF00553 CBM_2: Cellulose bind 36.4 1E+02 0.0023 18.9 5.7 34 27-60 14-48 (101)
24 cd08545 YcnI_like Reeler-like 35.7 65 0.0014 22.1 3.6 38 23-62 15-52 (152)
25 PF05142 DUF702: Domain of unk 33.9 37 0.0008 23.5 2.1 28 30-60 117-146 (154)
26 PF00345 PapD_N: Pili and flag 32.2 82 0.0018 19.7 3.5 22 29-50 17-38 (122)
27 cd08546 cohesin_like Cohesin d 32.1 1.3E+02 0.0028 18.7 4.6 37 24-61 13-50 (135)
28 PLN03080 Probable beta-xylosid 31.8 80 0.0017 27.0 4.2 26 27-52 685-712 (779)
29 PF11611 DUF4352: Domain of un 31.5 57 0.0012 20.1 2.6 20 24-43 34-53 (123)
30 KOG3865|consensus 29.9 89 0.0019 24.5 3.8 33 1-38 190-222 (402)
31 PF12690 BsuPI: Intracellular 28.5 1.3E+02 0.0028 18.1 3.8 25 28-56 2-26 (82)
32 KOG0415|consensus 28.4 68 0.0015 25.5 3.0 26 31-56 93-118 (479)
33 COG2017 GalM Galactose mutarot 27.8 1.5E+02 0.0033 22.0 4.8 33 20-53 138-172 (308)
34 cd09025 Aldose_epim_Slr1438 Al 27.0 2.4E+02 0.0052 20.3 5.6 22 20-42 124-145 (271)
35 PRK15098 beta-D-glucoside gluc 25.2 1.3E+02 0.0029 25.5 4.4 28 25-52 666-695 (765)
36 cd01081 Aldose_epim aldose 1-e 24.3 2.2E+02 0.0048 19.9 4.9 20 20-40 119-138 (284)
37 cd05853 Ig6_Contactin-4 Sixth 23.8 1.1E+02 0.0023 18.5 2.8 20 33-52 65-85 (85)
38 PF12215 GBA2_N: beta-Glucocer 23.5 1.6E+02 0.0034 21.8 4.1 30 28-57 113-142 (299)
39 COG1470 Predicted membrane pro 23.2 1.9E+02 0.0042 23.7 4.7 39 17-56 388-428 (513)
40 PF14016 DUF4232: Protein of u 23.2 2.1E+02 0.0046 18.2 4.4 34 2-43 2-35 (131)
41 cd00557 Translocase_SecB Prepr 22.0 1.1E+02 0.0024 20.3 2.7 23 29-51 33-56 (131)
42 PHA00692 hypothetical protein 20.9 73 0.0016 18.7 1.5 17 43-59 30-46 (74)
43 PF08033 Sec23_BS: Sec23/Sec24 20.5 1.2E+02 0.0025 18.4 2.5 22 41-62 1-22 (96)
44 cd09020 D-hex-6-P-epi_like D-h 20.3 2.3E+02 0.0049 20.5 4.4 21 20-41 115-135 (269)
No 1
>PF08441 Integrin_alpha2: Integrin alpha; InterPro: IPR013649 This domain is found in integrin alpha and integrin alpha precursors to the C terminus of a number of IPR013517 from INTERPRO repeats and to the N terminus of the IPR013513 from INTERPRO cytoplasmic region. ; PDB: 1M1X_A 1U8C_A 1L5G_A 3IJE_A 1JV2_A 2VDN_A 2VC2_A 3NIF_A 3NIG_C 2VDM_A ....
Probab=99.82 E-value=3.8e-20 Score=142.57 Aligned_cols=91 Identities=35% Similarity=0.523 Sum_probs=70.5
Q ss_pred cceEEEEEeccCC-ceEEEecccceEEEEEEeEeCCCCCcceEEEEEeCCCceeeeEeec----cceeeccC-C--CceE
Q psy5489 4 QSLSVRESTEMVG-SYELLLGQHQEVLLNVSTHNAGESAYEAQLFIAHHPHLSYIGLEGQ----RGALCNPY-N--TSLV 75 (94)
Q Consensus 4 ~dL~l~~~~~~~~-~~~l~vG~~~~l~l~v~v~N~gEdAY~t~L~v~~P~~L~y~~v~~~----~~~~C~~~-~--~~~v 75 (94)
-||+|+++..... ...++||+.+.|.|+|+|+|.|||||+|+|+++||++|+|+++... ..+.|+.. + ...+
T Consensus 168 ~dL~l~~~~~~~~~~~~l~lg~~~~l~l~v~v~N~GE~AY~a~l~v~~P~~l~~~~v~~~~~~~~~~~C~~~~~~~~~~~ 247 (457)
T PF08441_consen 168 SDLQLSASFSNSESSDVLVLGSDNTLNLNVTVTNKGEDAYEAKLTVTYPSGLSYSKVEKKQNSDSPISCSQPESNSSSTV 247 (457)
T ss_dssp --EEEEEEETS-CS---EECSS-EEEEEEEEEEESSS-BSSEEEEEEEETTEEEEEEE-SSSSSC--EEEEEESSSSCEE
T ss_pred cCeEEEEEecCccceeEEEECCCCEEEEEEEEEECCCCCCceeEEEECCCCccccccccccccccceecccCCCCCceEE
Confidence 4899999976532 1249999999999999999999999999999999999999999822 25799975 2 2289
Q ss_pred EEEeCCCcCCCCEEEEEEC
Q psy5489 76 VCALGNPFKKNASSHLKLR 94 (94)
Q Consensus 76 ~C~lGnP~~~~~~~~f~l~ 94 (94)
.|+|||||++++++.|.|+
T Consensus 248 ~C~lgnPl~~~~~~~~~l~ 266 (457)
T PF08441_consen 248 SCSLGNPLKRGSQVTFSLR 266 (457)
T ss_dssp EEEEETSBBTTEEEEEEEE
T ss_pred EEECChhhhcCCcceEEEE
Confidence 9999999999988888764
No 2
>KOG3637|consensus
Probab=99.70 E-value=8.9e-17 Score=135.00 Aligned_cols=90 Identities=37% Similarity=0.622 Sum_probs=76.3
Q ss_pred cceEEEEEeccCCceEEEecccceEEEEEEeEeCCCCCcceEEEEEeCCCceeeeEeecc----ceeeccCC---CceEE
Q psy5489 4 QSLSVRESTEMVGSYELLLGQHQEVLLNVSTHNAGESAYEAQLFIAHHPHLSYIGLEGQR----GALCNPYN---TSLVV 76 (94)
Q Consensus 4 ~dL~l~~~~~~~~~~~l~vG~~~~l~l~v~v~N~gEdAY~t~L~v~~P~~L~y~~v~~~~----~~~C~~~~---~~~v~ 76 (94)
-||+|+++.... ..+++++.+..|.++|+++|.||+||+|+|+|++|++|+|+++.... .++|.... ...+.
T Consensus 642 ~dLqL~~~~~~~-~~~~~~~~~~~L~l~vt~~N~gE~AYea~l~v~~p~~L~~~~v~~~~~~~~~i~C~~~~~~~~~~~~ 720 (1030)
T KOG3637|consen 642 SDLQLSASFDSE-NKYLLVSGDNELSLNVTLTNSGEDAYEAQLYVTFPAGLSFAGVEELGKVPSSISCDPNENNGAKQVS 720 (1030)
T ss_pred cCcEEEEEecCC-CceEEEecCcEEEEEEEEeeCCCcceeeeEEEecCCCccccccccccCCCccceeccCCCCcceEEE
Confidence 489999986552 14667776679999999999999999999999999999999999764 57999752 23799
Q ss_pred EEeCCCcCCCCEEEEEEC
Q psy5489 77 CALGNPFKKNASSHLKLR 94 (94)
Q Consensus 77 C~lGnP~~~~~~~~f~l~ 94 (94)
|+|||||+++++++|.++
T Consensus 721 C~lgnP~~~~~~~~~~l~ 738 (1030)
T KOG3637|consen 721 CDLGNPFKRGSQVTFSLR 738 (1030)
T ss_pred cCCCCCccCCcEEEEEEE
Confidence 999999999999999874
No 3
>PF01345 DUF11: Domain of unknown function DUF11; InterPro: IPR001434 This group of sequences is represented by a conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis (Streptococcus faecalis), and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydia trachomatis outer membrane proteins. In C. trachomatis, three cysteine-rich proteins (also believed to be lipoproteins), MOMP, OMP6 and OMP3, make up the extracellular matrix of the outer membrane []. They are involved in the essential structural integrity of both the elementary body (EB) and recticulate body (RB) phase. They are thought to be involved in porin formation and, as these bacteria lack the peptidoglycan layer common to most Gram-negative microbes, such proteins are highly important in the pathogenicity of the organism.; GO: 0005727 extrachromosomal circular DNA
Probab=95.25 E-value=0.13 Score=30.52 Aligned_cols=50 Identities=16% Similarity=0.231 Sum_probs=37.6
Q ss_pred cceEEEEEeccCCceEEEecccceEEEEEEeEeCCCC-CcceEEEEEeCCCceeee
Q psy5489 4 QSLSVRESTEMVGSYELLLGQHQEVLLNVSTHNAGES-AYEAQLFIAHHPHLSYIG 58 (94)
Q Consensus 4 ~dL~l~~~~~~~~~~~l~vG~~~~l~l~v~v~N~gEd-AY~t~L~v~~P~~L~y~~ 58 (94)
.+|.+..+... ....+| +.+..+|+|+|.|.. |.+..+.=.+|+++.|..
T Consensus 24 ~~~~~~k~~~~---~~~~~G--d~v~ytitvtN~G~~~a~nv~v~D~lp~g~~~v~ 74 (76)
T PF01345_consen 24 PDLSITKTVNP---STANPG--DTVTYTITVTNTGPAPATNVVVTDTLPAGLTFVS 74 (76)
T ss_pred CCEEEEEecCC---CcccCC--CEEEEEEEEEECCCCeeEeEEEEEcCCCCCEEeC
Confidence 45555554332 356666 889999999999776 777889999999999964
No 4
>TIGR01451 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins.
Probab=94.35 E-value=0.17 Score=28.53 Aligned_cols=37 Identities=11% Similarity=0.232 Sum_probs=31.5
Q ss_pred EEecccceEEEEEEeEeCCC-CCcceEEEEEeCCCceeee
Q psy5489 20 LLLGQHQEVLLNVSTHNAGE-SAYEAQLFIAHHPHLSYIG 58 (94)
Q Consensus 20 l~vG~~~~l~l~v~v~N~gE-dAY~t~L~v~~P~~L~y~~ 58 (94)
..+| +.+..+++++|.|. +|.+..+.=.+|+++.|..
T Consensus 8 ~~~G--d~v~Yti~v~N~g~~~a~~v~v~D~lP~g~~~v~ 45 (53)
T TIGR01451 8 ATIG--DTITYTITVTNNGNVPATNVVVTDILPSGTTFVS 45 (53)
T ss_pred cCCC--CEEEEEEEEEECCCCceEeEEEEEcCCCCCEEEe
Confidence 4455 88999999999986 5888999999999999964
No 5
>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=90.11 E-value=2 Score=25.66 Aligned_cols=44 Identities=18% Similarity=0.258 Sum_probs=26.6
Q ss_pred ceEEEEEeccCCceEEEecccceEEEEEEeEeCCCC-CcceEEEEEeCCC
Q psy5489 5 SLSVRESTEMVGSYELLLGQHQEVLLNVSTHNAGES-AYEAQLFIAHHPH 53 (94)
Q Consensus 5 dL~l~~~~~~~~~~~l~vG~~~~l~l~v~v~N~gEd-AY~t~L~v~~P~~ 53 (94)
||.+...... .....| +.+.++++|.|.|+. |....+.+.....
T Consensus 3 DL~v~~~~~~---~~~~~g--~~~~i~~~V~N~G~~~~~~~~v~~~~~~~ 47 (101)
T PF07705_consen 3 DLTVSITVSP---SNVVPG--EPVTITVTVKNNGTADAENVTVRLYLDGN 47 (101)
T ss_dssp -EEE-EEEC----SEEETT--SEEEEEEEEEE-SSS-BEEEEEEEEETTE
T ss_pred CEEEEEeeCC---CcccCC--CEEEEEEEEEECCCCCCCCEEEEEEECCc
Confidence 7888333322 245555 888889999999887 5666666655443
No 6
>PF00207 A2M: Alpha-2-macroglobulin family; InterPro: IPR001599 This entry contains serum complement C3 and C4 precursors and alpha-macrogrobulins. The alpha-macroglobulin (aM) family of proteins includes protease inhibitors [], typified by the human tetrameric a2-macroglobulin (a2M); they belong to the MEROPS proteinase inhibitor family I39, clan IL. These protease inhibitors share several defining properties, which include (i) the ability to inhibit proteases from all catalytic classes, (ii) the presence of a 'bait region' and a thiol ester, (iii) a similar protease inhibitory mechanism and (iv) the inactivation of the inhibitory capacity by reaction of the thiol ester with small primary amines. aM protease inhibitors inhibit by steric hindrance []. The mechanism involves protease cleavage of the bait region, a segment of the aM that is particularly susceptible to proteolytic cleavage, which initiates a conformational change such that the aM collapses about the protease. In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. Two additional events occur as a consequence of bait region cleavage, namely (i) the h-cysteinyl-g-glutamyl thiol ester becomes highly reactive and (ii) a major conformational change exposes a conserved COOH-terminal receptor binding domain [] (RBD). RBD exposure allows the aM protease complex to bind to clearance receptors and be removed from circulation []. Tetrameric, dimeric, and, more recently, monomeric aM protease inhibitors have been identified [, ].; GO: 0004866 endopeptidase inhibitor activity; PDB: 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 2PN5_A 3FRP_G 3HRZ_B ....
Probab=82.67 E-value=7.7 Score=23.64 Aligned_cols=38 Identities=13% Similarity=0.207 Sum_probs=23.7
Q ss_pred ceEEEEEeccCCceEEEecccceEEEEEEeEeCCCCCcceEEEE
Q psy5489 5 SLSVRESTEMVGSYELLLGQHQEVLLNVSTHNAGESAYEAQLFI 48 (94)
Q Consensus 5 dL~l~~~~~~~~~~~l~vG~~~~l~l~v~v~N~gEdAY~t~L~v 48 (94)
++-+..+... .+..| +.+.+.++|.|..++..+.++.+
T Consensus 55 p~~i~~~lP~----~l~~G--D~~~i~v~v~N~~~~~~~v~V~l 92 (92)
T PF00207_consen 55 PFFIQLNLPR----SLRRG--DQIQIPVTVFNYTDKDQEVTVTL 92 (92)
T ss_dssp SEEEEEE--S----EEETT--SEEEEEEEEEE-SSS-EEEEEEE
T ss_pred eEEEEcCCCc----EEecC--CEEEEEEEEEeCCCCCEEEEEEC
Confidence 4444544432 34445 88899999999999988877654
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=80.39 E-value=5.1 Score=23.64 Aligned_cols=31 Identities=13% Similarity=0.203 Sum_probs=21.6
Q ss_pred cceEEEEEEeEeCCCC-CcceEEEEEeCCCce
Q psy5489 25 HQEVLLNVSTHNAGES-AYEAQLFIAHHPHLS 55 (94)
Q Consensus 25 ~~~l~l~v~v~N~gEd-AY~t~L~v~~P~~L~ 55 (94)
.+...++++|+|.|.. +-...+.+..|+|..
T Consensus 4 G~~~~~~~tv~N~g~~~~~~v~~~l~~P~GW~ 35 (78)
T PF10633_consen 4 GETVTVTLTVTNTGTAPLTNVSLSLSLPEGWT 35 (78)
T ss_dssp TEEEEEEEEEE--SSS-BSS-EEEEE--TTSE
T ss_pred CCEEEEEEEEEECCCCceeeEEEEEeCCCCcc
Confidence 3677888999999865 578999999999988
No 8
>PF04597 Ribophorin_I: Ribophorin I; InterPro: IPR007676 Ribophorin I is an essential subunit of oligosaccharyltransferase (OST), which is also known as dolichyl-diphosphooligosaccharide--protein glycosyltransferase, (2.4.1.119 from EC). OST catalyses the transfer of an oligosaccharide from dolichol pyrophosphate to selected asparagine residues of nascent polypeptides as they are translocated into the lumen of the rough endoplasmic reticulum. Ribophorin I and OST48 are thought to be responsible for OST catalytic activity []. Both yeast and mammalian proteins are glycosylated but the sites are not conserved. Glycosylation may contribute towards general solubility but is unlikely to be involved in a specific biochemical function []. Most family members are predicted to have a transmembrane helix at the C terminus of this region.; GO: 0004579 dolichyl-diphosphooligosaccharide-protein glycotransferase activity, 0006486 protein glycosylation, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=75.18 E-value=39 Score=26.68 Aligned_cols=73 Identities=16% Similarity=0.277 Sum_probs=48.4
Q ss_pred EEec-ccceEEEEEEeEeCCCCCcceEEEEEeCC----CceeeeEeecc---ceee----ccCC----CceEEEEeCCCc
Q psy5489 20 LLLG-QHQEVLLNVSTHNAGESAYEAQLFIAHHP----HLSYIGLEGQR---GALC----NPYN----TSLVVCALGNPF 83 (94)
Q Consensus 20 l~vG-~~~~l~l~v~v~N~gEdAY~t~L~v~~P~----~L~y~~v~~~~---~~~C----~~~~----~~~v~C~lGnP~ 83 (94)
+-++ +--...++++++|.|+++ .....+.+|. .+++..+...+ ...+ ...+ .....-.+..|+
T Consensus 11 idl~~~~vk~~~~i~i~N~g~~p-~~~y~~~l~~~~~~~ls~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~pl 89 (432)
T PF04597_consen 11 IDLSKSYVKETIEITIKNIGDEP-VSEYYFALPNDEADHLSYVSAKDKDKKKKLKVSKEITEVNSGSEIKYYEITLPKPL 89 (432)
T ss_pred EEccCcEEEEEEEEEEEECCCCC-ceEEEEEECchhhccEEEEEEEECCCccccccccccccccCCCCcceEEEECCCCC
Confidence 3443 335678889999999998 7888888888 56665555432 2223 1111 124667788999
Q ss_pred CCCCEEEEEE
Q psy5489 84 KKNASSHLKL 93 (94)
Q Consensus 84 ~~~~~~~f~l 93 (94)
..++++++.+
T Consensus 90 ~~~~~~~l~v 99 (432)
T PF04597_consen 90 APGEKVTLTV 99 (432)
T ss_pred CCCCEEEEEE
Confidence 8888888765
No 9
>cd08523 Reeler_cohesin_like Domains similar to the eukaryotic reeler domain and bacterial cohesins. This diverse family summarizes a set of distantly related domains, as revealed by structural similarity.
Probab=69.17 E-value=13 Score=24.63 Aligned_cols=28 Identities=11% Similarity=0.106 Sum_probs=23.6
Q ss_pred ceEEEEEEeEeCCCCCcceEEEEEeCCC
Q psy5489 26 QEVLLNVSTHNAGESAYEAQLFIAHHPH 53 (94)
Q Consensus 26 ~~l~l~v~v~N~gEdAY~t~L~v~~P~~ 53 (94)
....|++.|.|..+.|+.+++.|.+|.+
T Consensus 13 s~~~vtf~Vp~e~~~a~ttk~~v~lp~~ 40 (124)
T cd08523 13 TNLEVTLSIDEPVNFAPEIEFTVNLKSN 40 (124)
T ss_pred ceEEEEEECCCCccCcceEEEEEEcCCC
Confidence 4455667778988899999999999999
No 10
>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=67.80 E-value=8.1 Score=27.10 Aligned_cols=28 Identities=29% Similarity=0.452 Sum_probs=23.7
Q ss_pred cceEEEEEEeEeCCCC-CcceEEEE-EeCC
Q psy5489 25 HQEVLLNVSTHNAGES-AYEAQLFI-AHHP 52 (94)
Q Consensus 25 ~~~l~l~v~v~N~gEd-AY~t~L~v-~~P~ 52 (94)
.+++.++++|.|.|+. ||+-+|.= .+|+
T Consensus 37 g~~v~V~~~iyN~G~~~A~dV~l~D~~fp~ 66 (181)
T PF05753_consen 37 GEDVTVTYTIYNVGSSAAYDVKLTDDSFPP 66 (181)
T ss_pred CcEEEEEEEEEECCCCeEEEEEEECCCCCc
Confidence 4899999999999887 99988877 5663
No 11
>PF00963 Cohesin: Cohesin domain; InterPro: IPR002102 Cohesin domains interact with a complementary domain, termed the dockerin domain (see IPR002105 from INTERPRO). The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome []. The scaffoldin component of the cellulolytic bacterium Clostridium thermocellum is a non-hydrolytic protein which organises the hydrolytic enzymes in a large complex, called the cellulosome. Scaffoldin comprises a series of functional domains, amongst which is a single cellulose-binding domain and nine cohesin domains which are responsible for integrating the individual enzymatic subunits into the complex.; GO: 0030246 carbohydrate binding, 0000272 polysaccharide catabolic process; PDB: 2BM3_A 3P0D_I 3KCP_A 2B59_A 3L8Q_B 3FNK_C 3GHP_B 2CCL_A 1ANU_A 1OHZ_A ....
Probab=58.55 E-value=36 Score=22.03 Aligned_cols=38 Identities=18% Similarity=0.248 Sum_probs=31.3
Q ss_pred ccceEEEEEEeEeCCCCCcceEEEEEe-CCCceeeeEee
Q psy5489 24 QHQEVLLNVSTHNAGESAYEAQLFIAH-HPHLSYIGLEG 61 (94)
Q Consensus 24 ~~~~l~l~v~v~N~gEdAY~t~L~v~~-P~~L~y~~v~~ 61 (94)
..+.+.+.|.+.|....=+..++.+.| |.-|.|..+..
T Consensus 12 ~G~tv~V~V~v~~~~~~i~~~~~~l~yDp~~Le~~~v~~ 50 (141)
T PF00963_consen 12 PGETVTVPVNVSNVSNSIAGMQFTLSYDPSVLEFVSVEP 50 (141)
T ss_dssp TTSEEEEEEEEESCTTTEEEEEEEEEE-TTTEEEEECEC
T ss_pred CCCEEEEEEEEEcCCCcEEEEEEEEEeCCceEEEEeecc
Confidence 348899999999987767888899999 55699988864
No 12
>COG1952 SecB Preprotein translocase subunit SecB [Intracellular trafficking and secretion]
Probab=56.10 E-value=35 Score=23.70 Aligned_cols=25 Identities=20% Similarity=0.325 Sum_probs=19.2
Q ss_pred eEEEEEEeEeCCCCCcceEEEEEeC
Q psy5489 27 EVLLNVSTHNAGESAYEAQLFIAHH 51 (94)
Q Consensus 27 ~l~l~v~v~N~gEdAY~t~L~v~~P 51 (94)
.+++++.....+|+.|+..|.++.-
T Consensus 43 ~l~l~~~~~~l~e~~feVvL~itv~ 67 (157)
T COG1952 43 NLDLNTNANQLAENVFEVVLTVTVT 67 (157)
T ss_pred eeeeeeccccCCCCceEEEEEEEEE
Confidence 4566667777899999998888753
No 13
>cd08547 Type_II_cohesin Type II cohesin domain, interaction partner of dockerin. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent interactions between cohesins and dockerins appear to be essential for cellulosome assembly. This subfamily represents type II cohesins; their interactions with dockerin mediate attachment of the cellulosome complex to the bacterial cell wall.
Probab=54.86 E-value=38 Score=21.45 Aligned_cols=39 Identities=13% Similarity=0.183 Sum_probs=30.9
Q ss_pred ecccceEEEEEEeEeCCCCCcceEEEEEe-CCCceeeeEee
Q psy5489 22 LGQHQEVLLNVSTHNAGESAYEAQLFIAH-HPHLSYIGLEG 61 (94)
Q Consensus 22 vG~~~~l~l~v~v~N~gEdAY~t~L~v~~-P~~L~y~~v~~ 61 (94)
+...+.+.+.+.+.|.. +.|...+.+.| |.-|.|.++..
T Consensus 12 v~~G~~~~v~v~~~~~~-~~~~~~~~l~YD~~~l~~~~~~~ 51 (132)
T cd08547 12 VKVGETFTVTVKVNNAT-NLAGYQFTLSYDPSVLEFVSVTS 51 (132)
T ss_pred cCCCCEEEEEEEEeccC-ceEEEEEEEEECcceEEEEeccc
Confidence 34458888889988877 88899999999 55699988754
No 14
>PRK05751 preprotein translocase subunit SecB; Validated
Probab=51.78 E-value=25 Score=24.28 Aligned_cols=39 Identities=23% Similarity=0.264 Sum_probs=24.0
Q ss_pred cCCceEEEec-ccceEEEEEEe--EeCCCCCcceEEEEEeCC
Q psy5489 14 MVGSYELLLG-QHQEVLLNVST--HNAGESAYEAQLFIAHHP 52 (94)
Q Consensus 14 ~~~~~~l~vG-~~~~l~l~v~v--~N~gEdAY~t~L~v~~P~ 52 (94)
..+.+..... ...++.+++.+ .+.+|+-||..|.++.-.
T Consensus 27 ~PnaP~if~~~~~P~i~v~l~~~~~~l~~~~~EV~L~v~v~a 68 (156)
T PRK05751 27 NPNAPAIFQEEWQPEVNLNLDTNANKLAEDVYEVVLTVTVTA 68 (156)
T ss_pred CCCCccccccccCCceeEEeccCceEcCCCeEEEEEEEEEEE
Confidence 3344454443 34455555444 447999999999888763
No 15
>TIGR01624 LRP1_Cterm LRP1 C-terminal domain. This model represents a tightly conserved small domain found in LRP1 and related plant proteins. This family also contains a well-conserved putative zinc finger domain (TIGR01623). The rest of the sequence of most members consists of highly divergent, low-complexity sequence.
Probab=48.00 E-value=23 Score=19.95 Aligned_cols=20 Identities=35% Similarity=0.602 Sum_probs=12.8
Q ss_pred EEEEeEeCCCC---CcceEEEEE
Q psy5489 30 LNVSTHNAGES---AYEAQLFIA 49 (94)
Q Consensus 30 l~v~v~N~gEd---AY~t~L~v~ 49 (94)
+.|+--+.||+ ||+|.+.|.
T Consensus 15 vRvs~idd~~~~e~aYQt~V~Ig 37 (50)
T TIGR01624 15 VRVTAIDDGEQAEYAYQATVTIG 37 (50)
T ss_pred EEEeccCCCCCceEEEEEEEEEC
Confidence 33444455666 899988763
No 16
>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=47.37 E-value=63 Score=25.52 Aligned_cols=31 Identities=13% Similarity=0.087 Sum_probs=24.5
Q ss_pred eEEEecccceEEEEEEeEeCCCCCcceEEEEEe
Q psy5489 18 YELLLGQHQEVLLNVSTHNAGESAYEAQLFIAH 50 (94)
Q Consensus 18 ~~l~vG~~~~l~l~v~v~N~gEdAY~t~L~v~~ 50 (94)
.++++| +.+.+.++|.|..+.+.+..+.+..
T Consensus 184 ~~~l~g--E~~~i~i~I~n~e~~~~~~~~~~~~ 214 (554)
T PF07919_consen 184 PPALTG--EFYPIPITISNNEDEEASGVLEVRL 214 (554)
T ss_pred CCeEcC--CEEEEEEEEEcCCCccceeEEEEEE
Confidence 467887 8899999999998888777665554
No 17
>KOG0250|consensus
Probab=46.92 E-value=14 Score=32.71 Aligned_cols=23 Identities=13% Similarity=0.372 Sum_probs=18.7
Q ss_pred ccceEEEEEEeEeCCCCCcceEE
Q psy5489 24 QHQEVLLNVSTHNAGESAYEAQL 46 (94)
Q Consensus 24 ~~~~l~l~v~v~N~gEdAY~t~L 46 (94)
+.....+.|+++|.|++||.+.+
T Consensus 106 G~~~A~IsItL~N~G~~Afk~ei 128 (1074)
T KOG0250|consen 106 GCSSAKISITLSNSGLDAFKPEI 128 (1074)
T ss_pred CCcceEEEEEEecCCcccCChhh
Confidence 44567888999999999999654
No 18
>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=46.40 E-value=69 Score=19.70 Aligned_cols=32 Identities=16% Similarity=0.252 Sum_probs=22.2
Q ss_pred EEEecccceEEEEEEeEeCCCCC-cc-----eEEEEEeCC
Q psy5489 19 ELLLGQHQEVLLNVSTHNAGESA-YE-----AQLFIAHHP 52 (94)
Q Consensus 19 ~l~vG~~~~l~l~v~v~N~gEdA-Y~-----t~L~v~~P~ 52 (94)
...+| +.+.+.++++|.-... +. ..+.+.|+-
T Consensus 10 ~~~vG--~d~~v~v~~~N~~~~~l~~v~~~l~~~~v~ytG 47 (107)
T PF00927_consen 10 DPVVG--QDFTVSVSFTNPSSEPLRNVSLNLCAFTVEYTG 47 (107)
T ss_dssp EEBTT--SEEEEEEEEEE-SSS-EECEEEEEEEEEEECTT
T ss_pred CccCC--CCEEEEEEEEeCCcCccccceeEEEEEEEEECC
Confidence 35577 8889999999997777 99 445557653
No 19
>COG1470 Predicted membrane protein [Function unknown]
Probab=42.79 E-value=73 Score=26.06 Aligned_cols=37 Identities=19% Similarity=0.153 Sum_probs=31.8
Q ss_pred EEecccceEEEEEEeEeCCCCCcceEEEEE-eCCCcee
Q psy5489 20 LLLGQHQEVLLNVSTHNAGESAYEAQLFIA-HHPHLSY 56 (94)
Q Consensus 20 l~vG~~~~l~l~v~v~N~gEdAY~t~L~v~-~P~~L~y 56 (94)
+.+......+++|+++|+|..+-+-.|.+. +|++-.+
T Consensus 278 ~~i~~~~t~sf~V~IeN~g~~~d~y~Le~~g~pe~w~~ 315 (513)
T COG1470 278 LEISPSTTASFTVSIENRGKQDDEYALELSGLPEGWTA 315 (513)
T ss_pred eEEccCCceEEEEEEccCCCCCceeEEEeccCCCCcce
Confidence 555567788999999999999999999999 9998666
No 20
>PRK13031 preprotein translocase subunit SecB; Provisional
Probab=40.17 E-value=40 Score=23.19 Aligned_cols=38 Identities=16% Similarity=0.173 Sum_probs=23.6
Q ss_pred CCceEEEe-cccceEEEEEEeEe--C-CCCCcceEEEEEeCC
Q psy5489 15 VGSYELLL-GQHQEVLLNVSTHN--A-GESAYEAQLFIAHHP 52 (94)
Q Consensus 15 ~~~~~l~v-G~~~~l~l~v~v~N--~-gEdAY~t~L~v~~P~ 52 (94)
.+.+.... +....+.+++.+.. . +|+.||..|.++...
T Consensus 24 PnaP~if~~~~~P~i~v~ln~~a~~l~~e~~yEV~L~vtvta 65 (149)
T PRK13031 24 PNSDKIWTTNWKPELHTDLKVEATKLPEENTYETVLTLEVKV 65 (149)
T ss_pred CCCchhhCcCCCCceeEEeccCccccCCCCcEEEEEEEEEEE
Confidence 33444333 34555666666555 5 578899998888763
No 21
>TIGR00809 secB protein-export chaperone SecB. The archaeal Methanococcus jannaschii homolog MJ0357 has been shown (PubMed:14985117) to share many properties, including chaperone-like activity, and scores between trusted and noise.
Probab=37.24 E-value=46 Score=22.56 Aligned_cols=37 Identities=19% Similarity=0.190 Sum_probs=22.1
Q ss_pred CceEEEec-ccceEEEE--EEeEeCCCCCcceEEEEEeCC
Q psy5489 16 GSYELLLG-QHQEVLLN--VSTHNAGESAYEAQLFIAHHP 52 (94)
Q Consensus 16 ~~~~l~vG-~~~~l~l~--v~v~N~gEdAY~t~L~v~~P~ 52 (94)
+.+.+... ....+.++ +.....+|+.||..|.++...
T Consensus 23 naP~if~~~~~P~i~v~l~~~a~~l~e~~~EV~L~~~vta 62 (140)
T TIGR00809 23 NAPHIFQLDWRPEVDLDLDTNSTQLSDDFYEVVLNITVTA 62 (140)
T ss_pred CCchhhccccCCceEEEEecCceecCCCeEEEEEEEEEEE
Confidence 34443333 33444444 444446899999998888764
No 22
>PF07987 DUF1775: Domain of unkown function (DUF1775); InterPro: IPR012533 GLE1 is an essential nuclear export factor involved in RNA export.; PDB: 3ESM_A.
Probab=36.72 E-value=56 Score=22.19 Aligned_cols=35 Identities=6% Similarity=0.061 Sum_probs=21.4
Q ss_pred EEEEEEeEeCCCCCcceEEEEEeCCCceeeeEeec
Q psy5489 28 VLLNVSTHNAGESAYEAQLFIAHHPHLSYIGLEGQ 62 (94)
Q Consensus 28 l~l~v~v~N~gEdAY~t~L~v~~P~~L~y~~v~~~ 62 (94)
..+.+.|.|-.|.|=-+++.|.+|.++...+....
T Consensus 15 ~~~tf~Vp~e~d~a~Tt~v~v~lP~gv~~v~~~p~ 49 (145)
T PF07987_consen 15 YKLTFRVPHECDGAATTKVRVTLPEGVTSVSPQPK 49 (145)
T ss_dssp EEEEEEEE---SS--EEEEEEEEEE-ESEEEE---
T ss_pred EEEEEEecCCCCCCCceEEEEECCCcccccceeeC
Confidence 35567777999999999999999999888776643
No 23
>PF00553 CBM_2: Cellulose binding domain; InterPro: IPR001919 The microbial degradation of cellulose and xylans requires several types of enzyme such as endoglucanases (3.2.1.4 from EC), cellobiohydrolases (3.2.1.91 from EC) (exoglucanases), or xylanases (3.2.1.8 from EC) []. Structurally, cellulases and xylanases generally consist of a catalytic domain joined to a cellulose-binding domain (CBD) by a short linker sequence rich in proline and/or hydroxy-amino acids. The CBD domain is found either at the N-terminal or at the C-terminal extremity of these enzymes. As it is shown in the following schematic representation, there are two conserved cysteines in this CBD domain - one at each extremity of the domain - which have been shown [] to be involved in a disulphide bond. There are also four conserved tryptophan, two are involved in cellulose binding. The CBD of a number of bacterial cellulases has been shown to consist of about 105 amino acid residues [, ]. +-------------------------------------------------+ | | xCxxxxWxxxxxNxxxWxxxxxxxWxxxxxxxxWNxxxxxGxxxxxxxxxxCx 'C': conserved cysteine involved in a disulphide bond. ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process; PDB: 2CZN_A 2CWR_A 1HEH_C 1HEJ_C 3NDZ_E 3NDY_E 2XBD_A 1E5C_A 1XBD_A 1E5B_A ....
Probab=36.41 E-value=1e+02 Score=18.95 Aligned_cols=34 Identities=12% Similarity=-0.023 Sum_probs=27.0
Q ss_pred eEEEEEEeEeCCCCC-cceEEEEEeCCCceeeeEe
Q psy5489 27 EVLLNVSTHNAGESA-YEAQLFIAHHPHLSYIGLE 60 (94)
Q Consensus 27 ~l~l~v~v~N~gEdA-Y~t~L~v~~P~~L~y~~v~ 60 (94)
-+..+|+|+|.++.+ -.=+|.+.+|.+.....+.
T Consensus 14 Gf~~~v~v~N~~~~~i~~W~v~~~~~~~~~i~~~W 48 (101)
T PF00553_consen 14 GFQGEVTVTNNGSSPINGWTVTFTFPSGQTITSSW 48 (101)
T ss_dssp EEEEEEEEEESSSSTEESEEEEEEESTTEEEEEEE
T ss_pred CeEEEEEEEECCCCccCCEEEEEEeCCCCEEeeee
Confidence 366689999998876 4568999999888887766
No 24
>cd08545 YcnI_like Reeler-like domain of YcnI and similar proteins. YcnI is a copper-responsive gene of Bacillus subtilis. It is homologous to an uncharacterized protein from Nocardia farcinica, which shares a conserved three-dimensional structure with cohesins and the reeler domain. Some members in this YcnI_like family have C-terminal domains (DUF461) that may bind copper.
Probab=35.65 E-value=65 Score=22.05 Aligned_cols=38 Identities=8% Similarity=0.071 Sum_probs=29.3
Q ss_pred cccceEEEEEEeEeCCCCCcceEEEEEeCCCceeeeEeec
Q psy5489 23 GQHQEVLLNVSTHNAGESAYEAQLFIAHHPHLSYIGLEGQ 62 (94)
Q Consensus 23 G~~~~l~l~v~v~N~gEdAY~t~L~v~~P~~L~y~~v~~~ 62 (94)
|+.. .+.+.|-|--+.+--++|.|.+|.++.+.+....
T Consensus 15 Gs~~--~~tfrVPhecdg~~Ttkv~V~lP~gv~~v~p~p~ 52 (152)
T cd08545 15 GSYY--KLTFRVPHGCDGAATTKVRVKLPEGVASVKPQPK 52 (152)
T ss_pred CceE--EEEEEccCCCCCCCceEEEEEcCCCccccceecC
Confidence 5444 4455666877779999999999999999887654
No 25
>PF05142 DUF702: Domain of unknown function (DUF702) ; InterPro: IPR007818 This is a family of plant proteins of unknown function.
Probab=33.86 E-value=37 Score=23.52 Aligned_cols=28 Identities=29% Similarity=0.482 Sum_probs=16.5
Q ss_pred EEEEeEeCCCC--CcceEEEEEeCCCceeeeEe
Q psy5489 30 LNVSTHNAGES--AYEAQLFIAHHPHLSYIGLE 60 (94)
Q Consensus 30 l~v~v~N~gEd--AY~t~L~v~~P~~L~y~~v~ 60 (94)
+.|+--+.||| ||+|.+.|- |=-|.++.
T Consensus 117 VRVssiDdgedE~AYQTaV~IG---GHVFKGiL 146 (154)
T PF05142_consen 117 VRVSSIDDGEDEYAYQTAVNIG---GHVFKGIL 146 (154)
T ss_pred EEEecccCcccceeeEEeEEEC---CEEeeeee
Confidence 44444445666 999988773 44454543
No 26
>PF00345 PapD_N: Pili and flagellar-assembly chaperone, PapD N-terminal domain; InterPro: IPR016147 Most Gram-negative bacteria possess a supramolecular structure - the pili - on their surface, which mediates attachment to specific receptors. Many interactive subunits are required to assemble pili, but their assembly only takes place after translocation across the cytoplasmic membrane. Periplasmic chaperones assist pili assembly by binding to the subunits, thereby preventing premature aggregation [, ]. Pili chaperones are structurally, and possibly evolutionarily, related to the immunoglobulin superfamily [, ]: they contain two globular domains, with a topology identical to an immunoglobulin fold. This entry represents the N-terminal domain of pili assembly chaperone, and has a beta-sandwich fold consisting of seven strands in two sheets with a Greek key topology.; GO: 0007047 cellular cell wall organization, 0030288 outer membrane-bounded periplasmic space; PDB: 2CO6_B 2CO7_B 1L4I_B 3GFU_A 3F65_F 3F6L_A 3F6I_A 3GEW_B 3DSN_D 2OS7_B ....
Probab=32.23 E-value=82 Score=19.74 Aligned_cols=22 Identities=14% Similarity=0.357 Sum_probs=15.3
Q ss_pred EEEEEeEeCCCCCcceEEEEEe
Q psy5489 29 LLNVSTHNAGESAYEAQLFIAH 50 (94)
Q Consensus 29 ~l~v~v~N~gEdAY~t~L~v~~ 50 (94)
...++|.|.++..|.-++.+.-
T Consensus 17 ~~~i~v~N~~~~~~~vq~~v~~ 38 (122)
T PF00345_consen 17 SASITVTNNSDQPYLVQVWVYD 38 (122)
T ss_dssp EEEEEEEESSSSEEEEEEEEEE
T ss_pred EEEEEEEcCCCCcEEEEEEEEc
Confidence 4456677887777777777765
No 27
>cd08546 cohesin_like Cohesin domain, interaction parter of dockerin. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent interactions between cohesins and dockerins appear to be essential for cellulosome assembly. Cohesin modules are phylogenetically distributed into three groups: type I cohesin-dockerin interactions mediate assembly of a range of dockerin-borne enzymes to the complex, while type-II interactions mediate attachment of the cellulosome complex to the bacterial cell wall. Recently discovered type-III cohesins, such as found in the anchoring scaffoldin ScaE, appears to contribute to increased stability of the elaborate cellulosome complex. While the p
Probab=32.14 E-value=1.3e+02 Score=18.72 Aligned_cols=37 Identities=16% Similarity=0.283 Sum_probs=30.5
Q ss_pred ccceEEEEEEeEeCCCCCcceEEEEEeC-CCceeeeEee
Q psy5489 24 QHQEVLLNVSTHNAGESAYEAQLFIAHH-PHLSYIGLEG 61 (94)
Q Consensus 24 ~~~~l~l~v~v~N~gEdAY~t~L~v~~P-~~L~y~~v~~ 61 (94)
..+.+.+.|.+.|.. +.+...+.+.|. .-|.|..+..
T Consensus 13 ~G~~~~v~v~~~~~~-~~~~~~~~l~yD~~~l~~~~~~~ 50 (135)
T cd08546 13 VGETVTVTVKVNNVP-NVAAADFTLSYDPSVLEFVSVEA 50 (135)
T ss_pred CCCEEEEEEEEecCC-CeEEEEEEEEECcccEEEEeccc
Confidence 347888889998888 888899999997 6788888764
No 28
>PLN03080 Probable beta-xylosidase; Provisional
Probab=31.79 E-value=80 Score=26.95 Aligned_cols=26 Identities=27% Similarity=0.377 Sum_probs=21.6
Q ss_pred eEEEEEEeEeCCCC--CcceEEEEEeCC
Q psy5489 27 EVLLNVSTHNAGES--AYEAQLFIAHHP 52 (94)
Q Consensus 27 ~l~l~v~v~N~gEd--AY~t~L~v~~P~ 52 (94)
.+.++|+|+|.|+- ++-.||++..|.
T Consensus 685 ~~~v~v~VtNtG~~~G~evvQlYv~~p~ 712 (779)
T PLN03080 685 RFNVHISVSNVGEMDGSHVVMLFSRSPP 712 (779)
T ss_pred eEEEEEEEEECCcccCcEEEEEEEecCc
Confidence 58999999999876 577788988775
No 29
>PF11611 DUF4352: Domain of unknown function (DUF4352); InterPro: IPR021652 This entry is represented by Bacteriophage A118, Gp32. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a group of putative lipoproteins of unknown function.; PDB: 3CFU_A.
Probab=31.47 E-value=57 Score=20.10 Aligned_cols=20 Identities=20% Similarity=0.476 Sum_probs=14.3
Q ss_pred ccceEEEEEEeEeCCCCCcc
Q psy5489 24 QHQEVLLNVSTHNAGESAYE 43 (94)
Q Consensus 24 ~~~~l~l~v~v~N~gEdAY~ 43 (94)
..+-+.|+++|+|.|++...
T Consensus 34 g~~fv~v~v~v~N~~~~~~~ 53 (123)
T PF11611_consen 34 GNKFVVVDVTVKNNGDEPLD 53 (123)
T ss_dssp -SEEEEEEEEEEE-SSS-EE
T ss_pred CCEEEEEEEEEEECCCCcEE
Confidence 35668999999999888765
No 30
>KOG3865|consensus
Probab=29.93 E-value=89 Score=24.49 Aligned_cols=33 Identities=21% Similarity=0.245 Sum_probs=25.2
Q ss_pred CCCcceEEEEEeccCCceEEEecccceEEEEEEeEeCC
Q psy5489 1 MKPQSLSVRESTEMVGSYELLLGQHQEVLLNVSTHNAG 38 (94)
Q Consensus 1 ~~~~dL~l~~~~~~~~~~~l~vG~~~~l~l~v~v~N~g 38 (94)
|.++-|+|.++.+.+ -+.=| +.+.++|.|+|.-
T Consensus 190 mS~~~lhLevsLDkE---iYyHG--E~isvnV~V~NNs 222 (402)
T KOG3865|consen 190 MSDGPLHLEVSLDKE---IYYHG--EPISVNVHVTNNS 222 (402)
T ss_pred cCCCceEEEEEecch---heecC--CceeEEEEEecCC
Confidence 678889999998763 23335 8899999999953
No 31
>PF12690 BsuPI: Intracellular proteinase inhibitor; InterPro: IPR020481 BsuPI is a intracellular proteinase inhibitor that directly regulates the major intracellular proteinase (ISP-1) activity in vivo. It inhibits ISP-1 in the early stages of sporulation and then may be inactivated by a membrane-bound proteinase [].; PDB: 3ISY_A.
Probab=28.51 E-value=1.3e+02 Score=18.13 Aligned_cols=25 Identities=12% Similarity=0.219 Sum_probs=16.5
Q ss_pred EEEEEEeEeCCCCCcceEEEEEeCCCcee
Q psy5489 28 VLLNVSTHNAGESAYEAQLFIAHHPHLSY 56 (94)
Q Consensus 28 l~l~v~v~N~gEdAY~t~L~v~~P~~L~y 56 (94)
+.+.++|.|.++.+. .+.||++=.|
T Consensus 2 v~~~l~v~N~s~~~v----~l~f~sgq~~ 26 (82)
T PF12690_consen 2 VEFTLTVTNNSDEPV----TLQFPSGQRY 26 (82)
T ss_dssp EEEEEEEEE-SSS-E----EEEESSS--E
T ss_pred EEEEEEEEeCCCCeE----EEEeCCCCEE
Confidence 567888999988764 6788888776
No 32
>KOG0415|consensus
Probab=28.44 E-value=68 Score=25.53 Aligned_cols=26 Identities=38% Similarity=0.534 Sum_probs=23.8
Q ss_pred EEEeEeCCCCCcceEEEEEeCCCcee
Q psy5489 31 NVSTHNAGESAYEAQLFIAHHPHLSY 56 (94)
Q Consensus 31 ~v~v~N~gEdAY~t~L~v~~P~~L~y 56 (94)
.|+..|.|++-.-+|++|++-++|.|
T Consensus 93 ~vsmvs~g~n~~gSQF~iTlgenLdy 118 (479)
T KOG0415|consen 93 TVSMVSAGENLNGSQFFITLGENLDY 118 (479)
T ss_pred eEEeecCCcccccceEEEEccccccc
Confidence 46777999999999999999999999
No 33
>COG2017 GalM Galactose mutarotase and related enzymes [Carbohydrate transport and metabolism]
Probab=27.75 E-value=1.5e+02 Score=22.03 Aligned_cols=33 Identities=9% Similarity=0.111 Sum_probs=23.0
Q ss_pred EEecccceEEEEEEeEeCC--CCCcceEEEEEeCCC
Q psy5489 20 LLLGQHQEVLLNVSTHNAG--ESAYEAQLFIAHHPH 53 (94)
Q Consensus 20 l~vG~~~~l~l~v~v~N~g--EdAY~t~L~v~~P~~ 53 (94)
+.+..+. |.+++++.|.| +=.+....+-.|+-.
T Consensus 138 Y~L~~~~-L~v~~~~~n~~~~~~p~~~g~HpYFnl~ 172 (308)
T COG2017 138 YTLNEDG-LTVTYEVTNDGDEPTPFNLGNHPYFNLP 172 (308)
T ss_pred EEEcCCC-EEEEEEEEeCCCCcceecccccceEecC
Confidence 4555445 99999999998 446777766655544
No 34
>cd09025 Aldose_epim_Slr1438 Aldose 1-epimerase, similar to Synechocystis Slr1438. Proteins similar to Synechocystis Slr1438 are uncharacterized members of aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen.
Probab=27.01 E-value=2.4e+02 Score=20.30 Aligned_cols=22 Identities=18% Similarity=0.297 Sum_probs=16.5
Q ss_pred EEecccceEEEEEEeEeCCCCCc
Q psy5489 20 LLLGQHQEVLLNVSTHNAGESAY 42 (94)
Q Consensus 20 l~vG~~~~l~l~v~v~N~gEdAY 42 (94)
+.+. ...|.++++++|.|+.+.
T Consensus 124 y~L~-~~~L~i~~~v~N~~~~~~ 145 (271)
T cd09025 124 YRLA-GNTLEIAQRVHNLGDQPM 145 (271)
T ss_pred EEEe-CCEEEEEEEEEECCCCcE
Confidence 4443 388999999999887643
No 35
>PRK15098 beta-D-glucoside glucohydrolase; Provisional
Probab=25.23 E-value=1.3e+02 Score=25.48 Aligned_cols=28 Identities=25% Similarity=0.366 Sum_probs=21.6
Q ss_pred cceEEEEEEeEeCCCC--CcceEEEEEeCC
Q psy5489 25 HQEVLLNVSTHNAGES--AYEAQLFIAHHP 52 (94)
Q Consensus 25 ~~~l~l~v~v~N~gEd--AY~t~L~v~~P~ 52 (94)
...+.++|+|+|.|+- +.-.||++..|.
T Consensus 666 ~~~i~v~v~V~NtG~~~G~EVvQlYv~~~~ 695 (765)
T PRK15098 666 DGKVTASVTVTNTGKREGATVVQLYLQDVT 695 (765)
T ss_pred CCeEEEEEEEEECCCCCccEEEEEeccCCC
Confidence 4579999999999776 455678887765
No 36
>cd01081 Aldose_epim aldose 1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism; they catalyze the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate and the histidine as the active site acid to protonate the C-5 ring oxygen.
Probab=24.27 E-value=2.2e+02 Score=19.89 Aligned_cols=20 Identities=15% Similarity=0.345 Sum_probs=15.2
Q ss_pred EEecccceEEEEEEeEeCCCC
Q psy5489 20 LLLGQHQEVLLNVSTHNAGES 40 (94)
Q Consensus 20 l~vG~~~~l~l~v~v~N~gEd 40 (94)
+.+.. ..|.++.+|+|.|+.
T Consensus 119 y~L~~-~~L~i~~~v~N~~~~ 138 (284)
T cd01081 119 YTLDA-DTLTITFTVTNLGDE 138 (284)
T ss_pred EEEeC-CeEEEEEEEEeCCCC
Confidence 44443 899999999998764
No 37
>cd05853 Ig6_Contactin-4 Sixth Ig domain of contactin-4. Ig6_Contactin-4: sixth Ig domain of the neural cell adhesion molecule contactin-4. Contactins are neural cell adhesion molecules, and are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The different contactins show different expression patterns in the central nervous system. Highest expresson of contactin-4 is in testes, thyroid, small intestine, uterus and brain. Contactin-4 plays a role in the response of neuroblastoma cells to differentiating agents, such as retinoids. The contactin 4 gene is associated with cerebellar degeneration in spinocerebellar ataxia type 16.
Probab=23.79 E-value=1.1e+02 Score=18.50 Aligned_cols=20 Identities=15% Similarity=0.258 Sum_probs=14.1
Q ss_pred EeEeC-CCCCcceEEEEEeCC
Q psy5489 33 STHNA-GESAYEAQLFIAHHP 52 (94)
Q Consensus 33 ~v~N~-gEdAY~t~L~v~~P~ 52 (94)
.+.|. ++..+.|+|.|.-||
T Consensus 65 ~a~n~~~~~~a~a~L~V~~pP 85 (85)
T cd05853 65 MVQTSVDKLSAAADLIVRGPP 85 (85)
T ss_pred EEEcccCceEEEEEEEEecCC
Confidence 34453 667888888888775
No 38
>PF12215 GBA2_N: beta-Glucocerebrosidase 2 N terminal; InterPro: IPR024462 This entry represents a domain found in beta-glucosidase 2 (also known as beta-glucocerebrosidase 2, acid beta-glucosidase, D-glucosyl-N-acylsphingosine glucohydrolase, or GCase), which is typically between 320 to 354 amino acids in length. It is found just after the extreme N terminus. This protein is located in the ER. The N-terminal is thought to be the luminal domain while the C-terminal is the cytosolic domain []. The catalytic domain of GBA-2 is unknown.
Probab=23.46 E-value=1.6e+02 Score=21.79 Aligned_cols=30 Identities=7% Similarity=0.178 Sum_probs=26.4
Q ss_pred EEEEEEeEeCCCCCcceEEEEEeCCCceee
Q psy5489 28 VLLNVSTHNAGESAYEAQLFIAHHPHLSYI 57 (94)
Q Consensus 28 l~l~v~v~N~gEdAY~t~L~v~~P~~L~y~ 57 (94)
..++++|+|.++++.+..|.++++-.+...
T Consensus 113 ~vf~~~v~N~~~~~~~vsi~~s~~N~vG~~ 142 (299)
T PF12215_consen 113 AVFEWTVENTSDEPVEVSIAFSWPNGVGWD 142 (299)
T ss_pred EEEEEEEEcCCCCcEEEEEEEEeeCCcCcc
Confidence 678999999999999999999999876653
No 39
>COG1470 Predicted membrane protein [Function unknown]
Probab=23.24 E-value=1.9e+02 Score=23.72 Aligned_cols=39 Identities=21% Similarity=0.272 Sum_probs=27.6
Q ss_pred ceEEEecccceEEEEEEeEeCCCCCcceE--EEEEeCCCcee
Q psy5489 17 SYELLLGQHQEVLLNVSTHNAGESAYEAQ--LFIAHHPHLSY 56 (94)
Q Consensus 17 ~~~l~vG~~~~l~l~v~v~N~gEdAY~t~--L~v~~P~~L~y 56 (94)
...+.+-+.++..+.+.|+|.| +|=.+. |.|.-|++.+-
T Consensus 388 ~~~lt~taGee~~i~i~I~NsG-na~LtdIkl~v~~PqgWei 428 (513)
T COG1470 388 PYRLTITAGEEKTIRISIENSG-NAPLTDIKLTVNGPQGWEI 428 (513)
T ss_pred cEEEEecCCccceEEEEEEecC-CCccceeeEEecCCccceE
Confidence 3455555778888999999999 554444 66777888543
No 40
>PF14016 DUF4232: Protein of unknown function (DUF4232)
Probab=23.19 E-value=2.1e+02 Score=18.24 Aligned_cols=34 Identities=18% Similarity=0.187 Sum_probs=21.4
Q ss_pred CCcceEEEEEeccCCceEEEecccceEEEEEEeEeCCCCCcc
Q psy5489 2 KPQSLSVRESTEMVGSYELLLGQHQEVLLNVSTHNAGESAYE 43 (94)
Q Consensus 2 ~~~dL~l~~~~~~~~~~~l~vG~~~~l~l~v~v~N~gEdAY~ 43 (94)
+..||++++..... |.... .+.++++|.+..+..
T Consensus 2 ~~~~L~~~~~~~~~-------~~g~~-~~~l~~tN~s~~~C~ 35 (131)
T PF14016_consen 2 TAADLSVTVGPVDA-------GAGQR-HATLTFTNTSDTPCT 35 (131)
T ss_pred CcccEEEEEecccC-------CCCcc-EEEEEEEECCCCcEE
Confidence 35688888864321 32222 667788899887654
No 41
>cd00557 Translocase_SecB Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent polypeptides across the cytoplasmic membrane. SecB has been shown to function as export-specific molecular chaperone that selectively binds preproteins, maintains them in a translocation competent state and delivers them to SecA, the membrane-bound ATPase, that drives the translocation reaction. In solution, SecB exists as homotetramer, which is organized as a dimer of dimers.
Probab=21.97 E-value=1.1e+02 Score=20.29 Aligned_cols=23 Identities=22% Similarity=0.239 Sum_probs=13.5
Q ss_pred EEEEEeEeCC-CCCcceEEEEEeC
Q psy5489 29 LLNVSTHNAG-ESAYEAQLFIAHH 51 (94)
Q Consensus 29 ~l~v~v~N~g-EdAY~t~L~v~~P 51 (94)
.+++.....+ |+.|+..|.++.-
T Consensus 33 ~l~~~~~~~~~~~~~EV~L~i~v~ 56 (131)
T cd00557 33 DLDTEITQLKNDNKYEVVLNITAG 56 (131)
T ss_pred EecccccccCCCCcEEEEEEEEEE
Confidence 3334444455 6678887776654
No 42
>PHA00692 hypothetical protein
Probab=20.86 E-value=73 Score=18.73 Aligned_cols=17 Identities=18% Similarity=0.446 Sum_probs=13.7
Q ss_pred ceEEEEEeCCCceeeeE
Q psy5489 43 EAQLFIAHHPHLSYIGL 59 (94)
Q Consensus 43 ~t~L~v~~P~~L~y~~v 59 (94)
.+..++.||+++.|-+-
T Consensus 30 rthyfveyppgfrfggc 46 (74)
T PHA00692 30 RTHYFVEYPPGFRFGGC 46 (74)
T ss_pred ceeEeEecCCCccccce
Confidence 35678999999999664
No 43
>PF08033 Sec23_BS: Sec23/Sec24 beta-sandwich domain; InterPro: IPR012990 COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger (IPR006895 from INTERPRO), an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes part of the Sec23/24 beta-barrel domain, which is formed from approximately 180 residues from three segments of the polypeptide. The strands of the barrel are oriented roughly parallel to the membrane such that one end of the barrel forms part of the inner surface of the coat and the other end part of the membrane-distal surface. The barrel is constructed from two opposed sheets: a six-stranded beta sheet facing partly towards the zinc finger domain and partly towards the solvent, and a five-stranded beta sheet facing the helical domain.; PDB: 3EFO_B 3EG9_B 1PD0_A 1PD1_A 1M2V_B 1PCX_A 3EH2_C 3EGD_A 2NUP_A 3EGX_A ....
Probab=20.50 E-value=1.2e+02 Score=18.42 Aligned_cols=22 Identities=23% Similarity=0.312 Sum_probs=18.1
Q ss_pred CcceEEEEEeCCCceeeeEeec
Q psy5489 41 AYEAQLFIAHHPHLSYIGLEGQ 62 (94)
Q Consensus 41 AY~t~L~v~~P~~L~y~~v~~~ 62 (94)
||++.+.|.-++++...++...
T Consensus 1 g~~~~l~vr~S~gl~v~~~~G~ 22 (96)
T PF08033_consen 1 GFNAVLRVRCSKGLKVSGVIGP 22 (96)
T ss_dssp EEEEEEEEEE-TTEEEEEEESS
T ss_pred CceEEEEEEECCCeEEEEEEcC
Confidence 6899999999999999887643
No 44
>cd09020 D-hex-6-P-epi_like D-hexose-6-phosphate epimerase-like. D-Hexose-6-phosphate epimerase Ymr099c from Saccharomyces cerevisiae belongs to the large superfamily of aldose-1-epimerases. Its active site is very similar to the catalytic site of galactose mutarotase, the best studied member of the superfamily. It also contains the conserved glutamate and histidine residues that have been shown in galactose mutarotase to be critical for catalysis, the glutamate serving as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen. In addition Ymr099c contains 2 conserved arginine residues which are involved in phosphate binding, and exhibits hexose-6-phosphate mutarotase activity on glucose-6-P, galactose-6-P and mannose-6-P.
Probab=20.28 E-value=2.3e+02 Score=20.51 Aligned_cols=21 Identities=24% Similarity=0.521 Sum_probs=16.3
Q ss_pred EEecccceEEEEEEeEeCCCCC
Q psy5489 20 LLLGQHQEVLLNVSTHNAGESA 41 (94)
Q Consensus 20 l~vG~~~~l~l~v~v~N~gEdA 41 (94)
+.++ .+.|.++++|+|.|+.+
T Consensus 115 ~~L~-~~~L~~~l~v~N~g~~~ 135 (269)
T cd09020 115 VTLG-FDTLELELTVTNTGDKP 135 (269)
T ss_pred EEEc-CCcEEEEEEEECCCCCC
Confidence 4554 47899999999998763
Done!