Query 033895
Match_columns 109
No_of_seqs 103 out of 627
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 07:30:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033895.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033895hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3342 Signal peptidase I [In 100.0 1.8E-32 4E-37 197.5 6.5 107 2-109 74-180 (180)
2 TIGR02228 sigpep_I_arch signal 99.9 2.1E-23 4.5E-28 150.9 11.2 91 3-103 58-149 (158)
3 cd06530 S26_SPase_I The S26 Ty 99.0 9.8E-10 2.1E-14 70.5 5.5 52 5-72 31-85 (85)
4 TIGR02754 sod_Ni_protease nick 97.9 5.2E-05 1.1E-09 49.0 6.5 58 6-73 30-89 (90)
5 cd06462 Peptidase_S24_S26 The 96.8 0.0044 9.6E-08 38.4 5.6 40 6-51 29-68 (84)
6 TIGR02227 sigpep_I_bact signal 96.8 0.0061 1.3E-07 43.7 7.0 69 4-76 50-159 (163)
7 KOG0171 Mitochondrial inner me 96.6 0.0042 9E-08 45.9 4.5 65 5-75 65-154 (176)
8 PF00717 Peptidase_S24: Peptid 96.0 0.014 3.1E-07 35.3 4.2 38 4-47 23-60 (70)
9 KOG1568 Mitochondrial inner me 95.6 0.015 3.2E-07 43.0 3.6 65 5-75 68-147 (174)
10 TIGR02771 TraF_Ti conjugative 95.5 0.063 1.4E-06 39.2 6.4 30 3-32 44-93 (171)
11 PRK13838 conjugal transfer pil 94.0 0.26 5.6E-06 36.2 6.5 29 41-73 141-169 (176)
12 PF05582 Peptidase_U57: YabG p 88.1 1.6 3.5E-05 34.7 5.7 37 6-46 1-37 (287)
13 PRK10861 signal peptidase I; P 83.1 1.7 3.7E-05 35.0 3.8 30 4-33 124-154 (324)
14 cd06529 S24_LexA-like Peptidas 83.0 5.5 0.00012 24.2 5.4 41 5-53 27-67 (81)
15 COG0681 LepB Signal peptidase 80.2 1.2 2.6E-05 30.9 1.7 24 6-29 85-109 (166)
16 TIGR02855 spore_yabG sporulati 76.9 7.2 0.00016 31.0 5.3 36 7-46 1-36 (283)
17 cd04451 S1_IF1 S1_IF1: Transla 72.3 4.4 9.6E-05 24.4 2.6 22 5-26 40-64 (64)
18 PRK12423 LexA repressor; Provi 71.5 26 0.00057 25.7 7.0 11 66-76 189-199 (202)
19 cd04712 BAH_DCM_I BAH, or Brom 70.5 15 0.00033 25.5 5.3 31 3-33 3-44 (130)
20 cd06555 ASCH_PF0470_like ASC-1 69.4 11 0.00025 25.7 4.3 30 4-33 30-59 (109)
21 COG2000 Predicted Fe-S protein 69.3 2.7 5.9E-05 32.0 1.3 21 3-25 107-127 (226)
22 cd04466 S1_YloQ_GTPase S1_YloQ 68.5 12 0.00026 22.2 3.9 26 4-29 36-61 (68)
23 PRK00215 LexA repressor; Valid 68.5 33 0.00072 24.9 7.0 11 66-76 192-202 (205)
24 PF10502 Peptidase_S26: Signal 66.7 7.9 0.00017 27.0 3.2 30 4-33 20-62 (138)
25 PF06890 Phage_Mu_Gp45: Bacter 64.5 9.1 0.0002 27.9 3.2 30 2-31 71-102 (162)
26 PF14594 Sipho_Gp37: Siphoviru 60.2 31 0.00067 27.5 5.9 30 4-33 292-321 (335)
27 PF06940 DUF1287: Domain of un 57.9 6.7 0.00015 28.9 1.6 16 3-18 104-119 (164)
28 PF14085 DUF4265: Domain of un 55.7 31 0.00067 23.4 4.5 43 4-52 24-66 (117)
29 TIGR02219 phage_NlpC_fam putat 54.2 12 0.00027 25.8 2.4 22 3-25 74-95 (134)
30 TIGR00498 lexA SOS regulatory 53.6 81 0.0018 22.7 7.3 11 66-76 185-195 (199)
31 COG3837 Uncharacterized conser 52.1 24 0.00052 25.9 3.7 46 5-58 85-130 (161)
32 CHL00010 infA translation init 51.0 18 0.0004 22.9 2.6 24 6-29 47-73 (78)
33 PRK00276 infA translation init 50.0 20 0.00042 22.3 2.6 22 6-27 47-71 (72)
34 COG1188 Ribosome-associated he 50.0 31 0.00067 23.4 3.7 29 2-32 45-73 (100)
35 PF06107 DUF951: Bacterial pro 47.9 23 0.00049 21.7 2.5 23 5-27 1-26 (57)
36 COG1974 LexA SOS-response tran 45.6 1.1E+02 0.0025 22.9 6.5 58 3-76 138-197 (201)
37 COG3895 Predicted periplasmic 45.5 50 0.0011 22.9 4.2 46 6-52 49-96 (112)
38 PRK13884 conjugal transfer pep 42.5 69 0.0015 23.3 4.9 31 3-33 48-98 (178)
39 PF04225 OapA: Opacity-associa 40.9 88 0.0019 20.0 4.7 40 4-48 41-80 (85)
40 PRK10276 DNA polymerase V subu 40.8 1.2E+02 0.0026 20.8 7.0 10 67-76 126-135 (139)
41 COG3738 Uncharacterized protei 40.7 28 0.00061 26.1 2.6 17 3-19 138-154 (200)
42 cd04714 BAH_BAHCC1 BAH, or Bro 40.3 95 0.0021 21.0 5.1 31 4-34 2-33 (121)
43 TIGR03024 arch_pef_cterm PEF-C 40.1 33 0.00072 17.8 2.1 16 93-108 8-23 (26)
44 PF00877 NLPC_P60: NlpC/P60 fa 39.0 24 0.00052 22.7 1.8 25 3-30 49-73 (105)
45 cd00320 cpn10 Chaperonin 10 Kd 38.5 73 0.0016 20.8 4.1 15 3-17 55-69 (93)
46 PF13640 2OG-FeII_Oxy_3: 2OG-F 35.7 1.1E+02 0.0024 19.1 4.6 31 6-43 66-96 (100)
47 PRK09570 rpoH DNA-directed RNA 34.9 66 0.0014 20.8 3.3 24 5-28 51-76 (79)
48 PTZ00414 10 kDa heat shock pro 34.0 89 0.0019 21.0 4.0 14 3-16 60-73 (100)
49 PRK00364 groES co-chaperonin G 33.9 94 0.002 20.4 4.1 14 4-17 57-70 (95)
50 PF00166 Cpn10: Chaperonin 10 33.7 89 0.0019 20.2 3.9 15 3-17 55-69 (93)
51 PF07039 DUF1325: SGF29 tudor- 31.2 1.8E+02 0.0039 20.1 6.1 27 7-33 1-30 (130)
52 PF00278 Orn_DAP_Arg_deC: Pyri 31.2 28 0.0006 22.6 1.2 15 4-18 81-95 (116)
53 PLN00036 40S ribosomal protein 31.1 1.2E+02 0.0026 23.9 4.9 37 4-47 152-188 (261)
54 TIGR03784 marine_sortase sorta 30.5 94 0.002 22.6 4.0 28 4-32 107-134 (174)
55 PF00122 E1-E2_ATPase: E1-E2 A 30.2 38 0.00083 24.5 1.9 42 3-45 49-95 (230)
56 cd06541 ASCH ASC-1 homology or 29.9 1.4E+02 0.0031 19.5 4.5 29 4-33 29-57 (105)
57 TIGR01451 B_ant_repeat conserv 29.9 51 0.0011 19.2 2.0 14 3-16 5-18 (53)
58 PF10125 NADHdeh_related: NADH 29.4 90 0.0019 23.9 3.7 27 66-93 3-29 (219)
59 COG1531 Uncharacterized protei 29.4 1.6E+02 0.0034 19.1 4.4 29 4-33 39-67 (77)
60 PRK04313 30S ribosomal protein 29.2 1.3E+02 0.0028 23.3 4.7 37 4-47 149-185 (237)
61 PTZ00223 40S ribosomal protein 28.9 1.5E+02 0.0032 23.6 5.0 37 4-47 149-185 (273)
62 PTZ00118 40S ribosomal protein 28.9 1.5E+02 0.0032 23.4 5.0 37 4-47 152-188 (262)
63 PRK06033 hypothetical protein; 28.8 65 0.0014 20.7 2.6 13 5-17 27-39 (83)
64 PF13275 S4_2: S4 domain; PDB: 28.7 45 0.00097 20.7 1.7 13 2-14 45-57 (65)
65 cd03470 Rieske_cytochrome_bc1 28.4 48 0.001 22.8 2.0 23 4-26 7-29 (126)
66 TIGR02594 conserved hypothetic 27.9 47 0.001 23.0 1.9 15 4-18 72-86 (129)
67 cd03703 aeIF5B_II aeIF5B_II: T 27.8 71 0.0015 21.9 2.7 38 4-45 25-62 (110)
68 PF07313 DUF1460: Protein of u 27.0 2E+02 0.0042 21.9 5.3 30 4-33 152-181 (216)
69 PRK10838 spr outer membrane li 26.6 47 0.001 24.7 1.8 15 2-16 125-139 (190)
70 PF01191 RNA_pol_Rpb5_C: RNA p 26.4 1.2E+02 0.0025 19.4 3.4 24 5-28 48-73 (74)
71 PF05708 DUF830: Orthopoxvirus 26.4 47 0.001 22.8 1.7 29 5-33 1-38 (158)
72 PF04970 LRAT: Lecithin retino 26.1 70 0.0015 21.4 2.5 24 4-31 5-28 (125)
73 cd04717 BAH_polybromo BAH, or 26.1 2E+02 0.0043 19.1 4.7 30 5-34 3-33 (121)
74 PF01272 GreA_GreB: Transcript 26.1 1.7E+02 0.0036 18.0 4.2 24 6-31 53-76 (77)
75 PRK05610 rpsQ 30S ribosomal pr 25.4 2E+02 0.0042 18.6 4.8 29 3-32 51-81 (84)
76 COG4043 Preprotein translocase 25.2 49 0.0011 22.8 1.5 25 4-32 32-56 (111)
77 PRK14533 groES co-chaperonin G 25.2 1.7E+02 0.0036 19.2 4.1 13 4-16 52-64 (91)
78 cd05829 Sortase_E Sortase E (S 25.2 1.5E+02 0.0033 20.5 4.1 25 4-30 71-96 (144)
79 PF02559 CarD_CdnL_TRCF: CarD- 25.1 90 0.0019 20.0 2.8 24 5-33 1-24 (98)
80 COG0234 GroS Co-chaperonin Gro 24.9 48 0.001 22.3 1.4 14 3-16 56-69 (96)
81 PF12436 USP7_ICP0_bdg: ICP0-b 24.4 51 0.0011 25.2 1.7 14 4-17 139-152 (249)
82 PF02839 CBM_5_12: Carbohydrat 24.2 34 0.00074 18.5 0.5 12 4-15 8-19 (41)
83 cd04760 BAH_Dnmt1_I BAH, or Br 23.1 1.6E+02 0.0035 20.5 3.9 31 4-34 2-33 (124)
84 PF13793 Pribosyltran_N: N-ter 22.6 41 0.0009 22.8 0.8 15 70-84 80-94 (116)
85 PF13759 2OG-FeII_Oxy_5: Putat 22.4 1.2E+02 0.0027 19.3 3.0 24 5-33 69-92 (101)
86 PF05257 CHAP: CHAP domain; I 22.3 59 0.0013 21.5 1.5 12 4-15 61-72 (124)
87 PF02298 Cu_bind_like: Plastoc 22.1 99 0.0022 19.7 2.5 26 4-33 17-42 (85)
88 PLN03148 Blue copper-like prot 21.9 1.1E+02 0.0024 22.4 3.0 26 4-33 44-69 (167)
89 PF08909 DUF1854: Domain of un 21.6 1.6E+02 0.0036 20.8 3.7 27 21-47 58-93 (133)
90 PF06605 Prophage_tail: Propha 21.2 1.7E+02 0.0036 22.7 4.1 30 3-32 261-290 (327)
91 PF01878 EVE: EVE domain; Int 21.2 2.4E+02 0.0051 19.2 4.4 25 5-32 39-63 (143)
92 cd03688 eIF2_gamma_II eIF2_gam 21.0 2.9E+02 0.0064 19.0 4.9 63 4-75 38-111 (113)
93 PF03120 DNA_ligase_OB: NAD-de 21.0 1.2E+02 0.0026 19.7 2.7 26 4-29 48-73 (82)
94 PRK05467 Fe(II)-dependent oxyg 20.9 1.2E+02 0.0025 23.2 3.0 22 6-32 145-166 (226)
95 PF02038 ATP1G1_PLM_MAT8: ATP1 20.5 1.2E+02 0.0025 18.1 2.3 16 93-108 21-36 (50)
96 TIGR02480 fliN flagellar motor 20.3 1.1E+02 0.0023 19.0 2.4 13 5-17 28-40 (77)
97 COG0361 InfA Translation initi 20.2 1.3E+02 0.0029 19.2 2.8 22 6-27 47-71 (75)
No 1
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.97 E-value=1.8e-32 Score=197.52 Aligned_cols=107 Identities=61% Similarity=1.060 Sum_probs=102.2
Q ss_pred CCCCCCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCCCCCCCChhhhccCccccccceEeceEEEEcccccE
Q 033895 2 SKDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDRLLYAQGQLWLKRQHIMGRAVGFLPYVGW 81 (109)
Q Consensus 2 ~~~~~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD~N~~~D~~~y~~~~~~V~~~~v~G~v~~~IP~lG~ 81 (109)
.++.+++|||++|+.+|+++||+|||++.++.. +|+..|+||||||..+|..+|++||.|+++++|+|++.+++||+|+
T Consensus 74 ~~~p~~vGdivVf~vegR~IPiVHRviK~he~~-~~~~~~LTKGDNN~~dD~~Ly~~gq~~L~r~~Ivg~~~G~~Py~G~ 152 (180)
T KOG3342|consen 74 NEDPIRVGDIVVFKVEGREIPIVHRVIKQHEKS-NGHIKFLTKGDNNAVDDRGLYAQGQNWLERKDIVGRVRGYLPYVGM 152 (180)
T ss_pred CCCcceeccEEEEEECCccCchhHHHHHHhccc-CCcEEEEecCCCCcccchhcccccccceeccceeeEEeeccccceE
Confidence 357799999999999999999999999999864 5888899999999999999999999999999999999999999999
Q ss_pred EEEEeccchhHHHHHHHHHHHHhhhcCC
Q 033895 82 VTIIMTEKPIIKYILIGALGLLVITSKD 109 (109)
Q Consensus 82 v~~~~~~~~~~~~~i~~~l~~~~l~~~e 109 (109)
+++|+++.|.+|+++++.+|+++|++||
T Consensus 153 itI~mnd~p~~KyalL~~lGl~vL~~rE 180 (180)
T KOG3342|consen 153 ITIWMNDYPKLKYALLGGLGLSVLLHRE 180 (180)
T ss_pred EEEEecCCcchHHHHHHHHHHheeeccC
Confidence 9999999999999999999999999998
No 2
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=99.90 E-value=2.1e-23 Score=150.92 Aligned_cols=91 Identities=25% Similarity=0.503 Sum_probs=76.1
Q ss_pred CCCCCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCCCCCCCChhhhccCccccccceEeceEE-EEcccccE
Q 033895 3 KDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDRLLYAQGQLWLKRQHIMGRAV-GFLPYVGW 81 (109)
Q Consensus 3 ~~~~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD~N~~~D~~~y~~~~~~V~~~~v~G~v~-~~IP~lG~ 81 (109)
+++++.||||+|+.++++.+++|||+++.++ +|+.+|+||||||..+|+++ ++++|++|++. +++||+||
T Consensus 58 ~~~~~~GDIVvf~~~~~~~~iihRVi~v~~~--~g~~~~~tkGDnN~~~D~~~-------v~~~~IiG~v~~~~iP~~G~ 128 (158)
T TIGR02228 58 PNDIQVGDVITYKSPGFNTPVTHRVIEINNS--GGELGFITKGDNNPAPDGEP-------VPSENVIGKYLGFTIPFAGY 128 (158)
T ss_pred cCCCCCCCEEEEEECCCCccEEEEEEEEECC--CCcEEEEEEecCCCCCCccc-------CCHHHEEEEEEEeccCcccE
Confidence 4689999999999887557999999999876 36788999999999999876 88999999998 88999999
Q ss_pred EEEEeccchhHHHHHHHHHHHH
Q 033895 82 VTIIMTEKPIIKYILIGALGLL 103 (109)
Q Consensus 82 v~~~~~~~~~~~~~i~~~l~~~ 103 (109)
+..++++..+.. +++++.+++
T Consensus 129 ~~~~~~~~~~~~-~~~~~p~~~ 149 (158)
T TIGR02228 129 VLVFAPQAIGAA-ALLIIPGIG 149 (158)
T ss_pred EEEEeecCchhh-hhHHhHHHH
Confidence 999999977644 333443333
No 3
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=98.99 E-value=9.8e-10 Score=70.50 Aligned_cols=52 Identities=35% Similarity=0.570 Sum_probs=43.8
Q ss_pred CCCcCcEEEEeeCCc-cccEEEEEEEEEecCCCCeeEEEEeCCC--CCCCChhhhccCccccccceEeceE
Q 033895 5 PIRAGEIVVFNVDGR-EIPIVHRVIKVHERQDTGEVEVLTKGDN--NYGDDRLLYAQGQLWLKRQHIMGRA 72 (109)
Q Consensus 5 ~~~~GDIIvf~~~g~-~~~itHRVi~v~~~~~~g~~~~iTKGD~--N~~~D~~~y~~~~~~V~~~~v~G~v 72 (109)
+++.||+|+|+.++. +.+++||+++ |.||||| |..+|+...+ ++.++++|++
T Consensus 31 ~~~~GDiv~~~~~~~~~~~~vkRv~~-----------~~~~gDn~~ns~d~~~~g~-----~~~~~i~G~~ 85 (85)
T cd06530 31 EPKRGDVVVFKSPGDPGKPIIKRVIG-----------YFVLGDNRNNSLDSRYWGP-----VPEDDIVGKV 85 (85)
T ss_pred CCCCCCEEEEeCCCCCCCEEEEEEEE-----------EEEeeCCCCCCCccCCcCC-----CcHHHeEEeC
Confidence 689999999998764 4689999988 7899999 9898887644 6788999874
No 4
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=97.91 E-value=5.2e-05 Score=49.04 Aligned_cols=58 Identities=21% Similarity=0.261 Sum_probs=41.2
Q ss_pred CCcCcEEEEeeCC-ccccEEEEEEEEEecCCCCeeEEEEeCCCCCC-CChhhhccCccccccceEeceEE
Q 033895 6 IRAGEIVVFNVDG-REIPIVHRVIKVHERQDTGEVEVLTKGDNNYG-DDRLLYAQGQLWLKRQHIMGRAV 73 (109)
Q Consensus 6 ~~~GDIIvf~~~g-~~~~itHRVi~v~~~~~~g~~~~iTKGD~N~~-~D~~~y~~~~~~V~~~~v~G~v~ 73 (109)
.+.||+++|+.++ .+..++||++..... .+...|||+.. .|+..+. +++..+|+|+++
T Consensus 30 ~~~Gdivv~~~~~~~~~~~vkRv~~~~~~------~~~l~~dN~~~~~d~~~~g----~v~~~~I~G~v~ 89 (90)
T TIGR02754 30 PPIGNVVVVRHPLQPYGLIIKRLAAVDDN------GLFLLGDNPKASTDSRQLG----PVPRSLLLGKVL 89 (90)
T ss_pred CCCCeEEEEecCCCCcceEEEEeeEEcCC------eEEEeCCCCCCCCcccccC----CCcHHHEEEEEE
Confidence 4569999998764 236899999988643 25567998754 4443333 378899999985
No 5
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=96.84 E-value=0.0044 Score=38.38 Aligned_cols=40 Identities=33% Similarity=0.423 Sum_probs=30.7
Q ss_pred CCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCCCCCCC
Q 033895 6 IRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGD 51 (109)
Q Consensus 6 ~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD~N~~~ 51 (109)
++.||++++..++ +.+++||+...... ..+..++||.+.+
T Consensus 29 ~~~G~iv~~~~~~-~~~~ikrl~~~~~~-----~~~~l~~~N~~~~ 68 (84)
T cd06462 29 PKRGDIVVFRLPG-GELTVKRVIGLPGE-----GHYFLLGDNPNSP 68 (84)
T ss_pred CcCCEEEEEEcCC-CcEEEEEEEEECCC-----CEEEEECCCCCCC
Confidence 7889999998776 35999999987541 2589999993333
No 6
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=96.84 E-value=0.0061 Score=43.75 Aligned_cols=69 Identities=23% Similarity=0.339 Sum_probs=45.7
Q ss_pred CCCCcCcEEEEeeCC-ccccEEEEEEEEEecC----C-----C------------------------------CeeEEEE
Q 033895 4 DPIRAGEIVVFNVDG-REIPIVHRVIKVHERQ----D-----T------------------------------GEVEVLT 43 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g-~~~~itHRVi~v~~~~----~-----~------------------------------g~~~~iT 43 (109)
.+++.||||+|+.++ .+...++||++.-.+. + | .+..|--
T Consensus 50 ~~~~rGDiVvf~~~~~~~~~~iKRVig~pGd~v~i~~~~l~vNg~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~g~~fv 129 (163)
T TIGR02227 50 SDPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKVEFRDGKLYINGKKIDEPYLKPNGSLDTSGFNTTDFKPVTVPPGHYFV 129 (163)
T ss_pred CCCCCCcEEEEecCCCCCceeEEEEEecCCCEEEEECCEEEECCEECcccccccccccccccccccccCceEECCCCEEE
Confidence 678999999999763 3358999999642110 0 0 0112334
Q ss_pred eCCC-CCCCChhhhccCccccccceEeceEEEEc
Q 033895 44 KGDN-NYGDDRLLYAQGQLWLKRQHIMGRAVGFL 76 (109)
Q Consensus 44 KGD~-N~~~D~~~y~~~~~~V~~~~v~G~v~~~I 76 (109)
-||| +++.|.-.+. +|+.++|+|++.+.+
T Consensus 130 lGDnr~~S~DSR~~G----~V~~~~I~Gk~~~~~ 159 (163)
T TIGR02227 130 LGDNRDNSLDSRYFG----FVPIDDIIGKVSFVF 159 (163)
T ss_pred ECCCCCCCcccCCcC----cCCHHHeEEEEEEEE
Confidence 4887 5777876543 389999999998753
No 7
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=96.56 E-value=0.0042 Score=45.86 Aligned_cols=65 Identities=26% Similarity=0.315 Sum_probs=47.6
Q ss_pred CCCcCcEEEEeeC-CccccEEEEEEEEEec--C-----C----------------CCeeEEEEeCCC-CCCCChhhhccC
Q 033895 5 PIRAGEIVVFNVD-GREIPIVHRVIKVHER--Q-----D----------------TGEVEVLTKGDN-NYGDDRLLYAQG 59 (109)
Q Consensus 5 ~~~~GDIIvf~~~-g~~~~itHRVi~v~~~--~-----~----------------~g~~~~iTKGD~-N~~~D~~~y~~~ 59 (109)
..++||||+++.| .....++-||++.+.+ . . .|+ .| -.||| |+.-|.--|.+
T Consensus 65 ~~~~gDIVi~~sP~~~~~~~cKRIva~eGD~v~v~~~~~~~n~~~e~~~~~i~VP~Gh-Vf-v~GDN~~nS~DSr~yGp- 141 (176)
T KOG0171|consen 65 KPQVGDIVIAKSPPDPKEHICKRIVAMEGDLVEVHDGPLVVNDLVEKFSTPIRVPEGH-VF-VEGDNRNNSLDSRNYGP- 141 (176)
T ss_pred CCCCCCEEEEeCCCCchhhhhheeeccCCceEEEecCCcccchhhhhccceeeccCce-EE-EecCCCCCcccccccCC-
Confidence 4589999999876 3335799999987765 0 0 011 13 34898 88889877765
Q ss_pred ccccccceEeceEEEE
Q 033895 60 QLWLKRQHIMGRAVGF 75 (109)
Q Consensus 60 ~~~V~~~~v~G~v~~~ 75 (109)
++...|.||+++.
T Consensus 142 ---lP~glI~gRvv~r 154 (176)
T KOG0171|consen 142 ---LPMGLIQGRVVFR 154 (176)
T ss_pred ---CchhheeeeEEEE
Confidence 8999999999976
No 8
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=96.03 E-value=0.014 Score=35.32 Aligned_cols=38 Identities=29% Similarity=0.438 Sum_probs=26.0
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCCC
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDN 47 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD~ 47 (109)
.+++.||+|+|..++.....+||++.... ..++.+.+|
T Consensus 23 ~~~~~gdivv~~~~~~~~~~iKrv~~~~~------~~~~~~~~n 60 (70)
T PF00717_consen 23 SEPKDGDIVVVKIDGDEELYIKRVVGEPG------GIILISSNN 60 (70)
T ss_dssp S---TTSEEEEEETTEESEEEEEEEEETT------EEEEE-SST
T ss_pred CCCccCeEEEEEECCceeeEEEEEEEeCC------CEEEEeccC
Confidence 46789999999988765689999996542 257777666
No 9
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=95.64 E-value=0.015 Score=42.95 Aligned_cols=65 Identities=25% Similarity=0.377 Sum_probs=42.2
Q ss_pred CCCcCcEEEEeeC-CccccEEEEEEEEEecC-----C--------CCeeEEEEeCCCC-CCCChhhhccCccccccceEe
Q 033895 5 PIRAGEIVVFNVD-GREIPIVHRVIKVHERQ-----D--------TGEVEVLTKGDNN-YGDDRLLYAQGQLWLKRQHIM 69 (109)
Q Consensus 5 ~~~~GDIIvf~~~-g~~~~itHRVi~v~~~~-----~--------~g~~~~iTKGD~N-~~~D~~~y~~~~~~V~~~~v~ 69 (109)
.+..||||+|++| ..+..++-||.+++.+. . .| .|.+. |||- ..-|...|.| |+-..|.
T Consensus 68 ~~~rGDiVvl~sP~~p~~~~iKRv~alegd~~~t~~~k~~~v~vpkg-hcWVe-gDn~~hs~DSntFGP----VS~gli~ 141 (174)
T KOG1568|consen 68 KVSRGDIVVLKSPNDPDKVIIKRVAALEGDIMVTEDEKEEPVVVPKG-HCWVE-GDNQKHSYDSNTFGP----VSTGLIV 141 (174)
T ss_pred eeccCCEEEEeCCCChhheeeeeeecccccEeccCCCCCCceecCCC-cEEEe-cCCcccccccCccCC----cchhhee
Confidence 3668999999987 44468999999987641 0 12 23433 6652 3445555443 7777788
Q ss_pred ceEEEE
Q 033895 70 GRAVGF 75 (109)
Q Consensus 70 G~v~~~ 75 (109)
|+++..
T Consensus 142 grai~i 147 (174)
T KOG1568|consen 142 GRAIYI 147 (174)
T ss_pred eeEEEE
Confidence 888753
No 10
>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems.
Probab=95.45 E-value=0.063 Score=39.21 Aligned_cols=30 Identities=27% Similarity=0.553 Sum_probs=22.9
Q ss_pred CCCCCcCcEEEEeeCCccc--------------------cEEEEEEEEEe
Q 033895 3 KDPIRAGEIVVFNVDGREI--------------------PIVHRVIKVHE 32 (109)
Q Consensus 3 ~~~~~~GDIIvf~~~g~~~--------------------~itHRVi~v~~ 32 (109)
..+++.||+|+|+.+.... ..+-||+.+-.
T Consensus 44 ~~~~~rGDiVvf~~p~~~~~~~~~~rg~l~~g~~p~~~~~~vKRViglpG 93 (171)
T TIGR02771 44 SKPVERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPG 93 (171)
T ss_pred CCCCCCCcEEEEeCCCchhhhchhhcCcccccccCcCccceEEEEEEeCC
Confidence 4689999999999764321 68999998643
No 11
>PRK13838 conjugal transfer pilin processing protease TraF; Provisional
Probab=93.99 E-value=0.26 Score=36.21 Aligned_cols=29 Identities=10% Similarity=0.082 Sum_probs=21.7
Q ss_pred EEEeCCCCCCCChhhhccCccccccceEeceEE
Q 033895 41 VLTKGDNNYGDDRLLYAQGQLWLKRQHIMGRAV 73 (109)
Q Consensus 41 ~iTKGD~N~~~D~~~y~~~~~~V~~~~v~G~v~ 73 (109)
|..-||++.+-|.-.+. +|+.++|+|++.
T Consensus 141 ~fvlgd~~~S~DSRy~G----~V~~~~I~G~a~ 169 (176)
T PRK13838 141 LFLHSSFAGSYDSRYFG----PVPASGLLGLAR 169 (176)
T ss_pred EEEECCCCCCCcccccC----cccHHHeEEEEE
Confidence 34448888888886654 388999999985
No 12
>PF05582 Peptidase_U57: YabG peptidase U57; InterPro: IPR008764 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. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This is a group of peptidases belong to MEROPS peptidase family U57 (clan U-). The type example is the YabG protein of Bacillus subtilis. This is a protease involved in the synthesis and maturation of the spore coat proteins SpoIVA and YrbA of B. subtilis [].
Probab=88.06 E-value=1.6 Score=34.71 Aligned_cols=37 Identities=30% Similarity=0.547 Sum_probs=31.4
Q ss_pred CCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCC
Q 033895 6 IRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGD 46 (109)
Q Consensus 6 ~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD 46 (109)
+++||||+=++-+. =|+.||+++.+. +|+..++-||-
T Consensus 1 mkiGDIV~RKSYg~--DI~FrIidI~~~--~g~~~aiLkG~ 37 (287)
T PF05582_consen 1 MKIGDIVARKSYGK--DILFRIIDIKEE--NGKKIAILKGL 37 (287)
T ss_pred CCCCCEEEeeecCC--ceEEEEEEEEcC--CCceEEEEeCC
Confidence 57999999987665 489999999985 47889999994
No 13
>PRK10861 signal peptidase I; Provisional
Probab=83.09 E-value=1.7 Score=34.99 Aligned_cols=30 Identities=23% Similarity=0.433 Sum_probs=23.3
Q ss_pred CCCCcCcEEEEeeCC-ccccEEEEEEEEEec
Q 033895 4 DPIRAGEIVVFNVDG-REIPIVHRVIKVHER 33 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g-~~~~itHRVi~v~~~ 33 (109)
.+.+.||||+|+.|. .+...+-|||..-.+
T Consensus 124 ~~p~RGDIVVF~~P~~~~~~yIKRVIGlPGD 154 (324)
T PRK10861 124 GHPKRGDIVVFKYPEDPKLDYIKRVVGLPGD 154 (324)
T ss_pred CCCCCCCEEEEecCCCCCCcEEEEeeecCCc
Confidence 567899999998764 346799999986543
No 14
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=83.03 E-value=5.5 Score=24.16 Aligned_cols=41 Identities=27% Similarity=0.212 Sum_probs=26.5
Q ss_pred CCCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCCCCCCCCh
Q 033895 5 PIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDR 53 (109)
Q Consensus 5 ~~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD~N~~~D~ 53 (109)
.++.||++++..++ ...+.|+..... ..+.-+.||...++.
T Consensus 27 ~~~~g~i~~~~~~~--~~~ikr~~~~~~------~~~~L~s~N~~~~~~ 67 (81)
T cd06529 27 TPRDGDIVVARLDG--ELTVKRLQRRGG------GRLRLISDNPAYPPI 67 (81)
T ss_pred CCCCCCEEEEEECC--EEEEEEEEECCC------CcEEEEeCCCCCCCE
Confidence 46667777776655 367888776442 247788998655543
No 15
>COG0681 LepB Signal peptidase I [Intracellular trafficking and secretion]
Probab=80.23 E-value=1.2 Score=30.88 Aligned_cols=24 Identities=42% Similarity=0.549 Sum_probs=16.4
Q ss_pred CCcCcEEEEeeCCcc-ccEEEEEEE
Q 033895 6 IRAGEIVVFNVDGRE-IPIVHRVIK 29 (109)
Q Consensus 6 ~~~GDIIvf~~~g~~-~~itHRVi~ 29 (109)
...||+|+|+.+... .+.+||...
T Consensus 85 ~~~GD~i~~~~~~~~~~~~~~~~~~ 109 (166)
T COG0681 85 GLRGDIVVFKDDRLYVVPIIPRVYG 109 (166)
T ss_pred cCCCCEEEEECCEEEeecccCcchh
Confidence 467999999875321 356777654
No 16
>TIGR02855 spore_yabG sporulation peptidase YabG. Members of this family are the protein YabG, demonstrated for Bacillus subtilis to be an endopeptidase able to release N-terminal peptides from a number of sporulation proteins, including CotT, CotF, and SpoIVA. It appears to be expressed under control of sigma-K.
Probab=76.94 E-value=7.2 Score=31.04 Aligned_cols=36 Identities=28% Similarity=0.471 Sum_probs=28.5
Q ss_pred CcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCC
Q 033895 7 RAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGD 46 (109)
Q Consensus 7 ~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD 46 (109)
++||||+=++-+. =|+-||+++... +|...++-||-
T Consensus 1 ~iGDIV~RKSYg~--DI~FkIidI~~~--~G~~~aiLkGi 36 (283)
T TIGR02855 1 KIGDIVARKSYGC--DILFRIIDIIEN--KGGDIAILHGE 36 (283)
T ss_pred CCCCEEEeeecCC--ccEEEEEEEEcc--CCceEEEEecc
Confidence 5899999988766 478999999433 36778999994
No 17
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=72.30 E-value=4.4 Score=24.43 Aligned_cols=22 Identities=27% Similarity=0.285 Sum_probs=15.7
Q ss_pred CCCcCcEEEEeeC--C-ccccEEEE
Q 033895 5 PIRAGEIVVFNVD--G-REIPIVHR 26 (109)
Q Consensus 5 ~~~~GDIIvf~~~--g-~~~~itHR 26 (109)
.+.+||.|.|... . ..-.||||
T Consensus 40 ~~~vGD~V~~~~~~~~~~~g~I~~~ 64 (64)
T cd04451 40 RILPGDRVKVELSPYDLTKGRIVYR 64 (64)
T ss_pred ccCCCCEEEEEEeecCCCEEEEEEC
Confidence 4789999999842 2 23478887
No 18
>PRK12423 LexA repressor; Provisional
Probab=71.49 E-value=26 Score=25.68 Aligned_cols=11 Identities=27% Similarity=0.374 Sum_probs=8.5
Q ss_pred ceEeceEEEEc
Q 033895 66 QHIMGRAVGFL 76 (109)
Q Consensus 66 ~~v~G~v~~~I 76 (109)
-.|+|++++.+
T Consensus 189 ~~I~Gvv~g~~ 199 (202)
T PRK12423 189 FAIEGVFCGLI 199 (202)
T ss_pred EEEEEEEEEEE
Confidence 47899998765
No 19
>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=70.48 E-value=15 Score=25.51 Aligned_cols=31 Identities=26% Similarity=0.432 Sum_probs=23.8
Q ss_pred CCCCCcCcEEEEeeCCcc-----------ccEEEEEEEEEec
Q 033895 3 KDPIRAGEIVVFNVDGRE-----------IPIVHRVIKVHER 33 (109)
Q Consensus 3 ~~~~~~GDIIvf~~~g~~-----------~~itHRVi~v~~~ 33 (109)
...+++||+|....++.+ .+.+=||....+.
T Consensus 3 ~~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~ 44 (130)
T cd04712 3 GLTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKG 44 (130)
T ss_pred CCEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeec
Confidence 467899999999876543 5678888887665
No 20
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=69.40 E-value=11 Score=25.69 Aligned_cols=30 Identities=17% Similarity=0.400 Sum_probs=22.3
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEec
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHER 33 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~ 33 (109)
..+++||.|+|..-..+.-+.=+|+++..-
T Consensus 30 ~~ikvGD~I~f~~~~~~~~l~v~V~~i~~Y 59 (109)
T cd06555 30 QQIKVGDKILFNDLDTGQQLLVKVVDIRKY 59 (109)
T ss_pred hcCCCCCEEEEEEcCCCcEEEEEEEEEEec
Confidence 369999999997532234678888888875
No 21
>COG2000 Predicted Fe-S protein [General function prediction only]
Probab=69.32 E-value=2.7 Score=31.97 Aligned_cols=21 Identities=29% Similarity=0.618 Sum_probs=16.7
Q ss_pred CCCCCcCcEEEEeeCCccccEEE
Q 033895 3 KDPIRAGEIVVFNVDGREIPIVH 25 (109)
Q Consensus 3 ~~~~~~GDIIvf~~~g~~~~itH 25 (109)
..++++||||-|++-|. ||+|
T Consensus 107 ~~~lekgdiiRyRp~Gc--pi~h 127 (226)
T COG2000 107 SKELEKGDIIRYRPLGC--PITH 127 (226)
T ss_pred ccccccccEEEeccCCC--cchh
Confidence 35689999999987675 6666
No 22
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=68.53 E-value=12 Score=22.20 Aligned_cols=26 Identities=15% Similarity=0.397 Sum_probs=17.0
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEE
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIK 29 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~ 29 (109)
+.+.+||-|.+..++.+..++|++..
T Consensus 36 ~~~~VGD~V~~~~~~~~~~~I~~vl~ 61 (68)
T cd04466 36 NPPAVGDRVEFEPEDDGEGVIEEILP 61 (68)
T ss_pred CCCCCCcEEEEEECCCCcEEEEEEec
Confidence 45689999999765444445555544
No 23
>PRK00215 LexA repressor; Validated
Probab=68.46 E-value=33 Score=24.86 Aligned_cols=11 Identities=36% Similarity=0.739 Sum_probs=8.3
Q ss_pred ceEeceEEEEc
Q 033895 66 QHIMGRAVGFL 76 (109)
Q Consensus 66 ~~v~G~v~~~I 76 (109)
-.|+|+|+..+
T Consensus 192 ~~IiG~Vv~~~ 202 (205)
T PRK00215 192 VTIEGKVVGLI 202 (205)
T ss_pred EEEEEEEEEEE
Confidence 57889888654
No 24
>PF10502 Peptidase_S26: Signal peptidase, peptidase S26 ; InterPro: IPR019533 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents a conserved region found in the S26A family of serine endopeptidases, which function in the processing of newly-synthesised secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal signal peptides as proteins are translocated across membranes. ; PDB: 3S04_B 1KN9_C 1B12_D 3IIQ_B 1T7D_A.
Probab=66.68 E-value=7.9 Score=27.03 Aligned_cols=30 Identities=33% Similarity=0.555 Sum_probs=0.0
Q ss_pred CCCCcCcEEEEeeCC-------------ccccEEEEEEEEEec
Q 033895 4 DPIRAGEIVVFNVDG-------------REIPIVHRVIKVHER 33 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g-------------~~~~itHRVi~v~~~ 33 (109)
+.++.||+|+|..+. .+.+++=||+.+-.+
T Consensus 20 ~~~~rGd~V~f~~p~~~~~~~~~~gy~~~~~~~iKrV~a~pGD 62 (138)
T PF10502_consen 20 DKIERGDLVVFCPPAEVAFFAAERGYLPEGQPLIKRVAAVPGD 62 (138)
T ss_dssp -------------------------------------------
T ss_pred ccccccccccccccccccccccccccccccccccccccccccc
Confidence 347899999998753 124667777775543
No 25
>PF06890 Phage_Mu_Gp45: Bacteriophage Mu Gp45 protein; InterPro: IPR014462 This entry is represented by the Bacteriophage Mu, Gp45. The characteristics of the protein distribution suggest prophage matches.
Probab=64.53 E-value=9.1 Score=27.94 Aligned_cols=30 Identities=23% Similarity=0.625 Sum_probs=22.2
Q ss_pred CCCCCCcCcEEEEeeCCccccEEE--EEEEEE
Q 033895 2 SKDPIRAGEIVVFNVDGREIPIVH--RVIKVH 31 (109)
Q Consensus 2 ~~~~~~~GDIIvf~~~g~~~~itH--RVi~v~ 31 (109)
|+..|+.|+++.|...|..+..+- |+|++.
T Consensus 71 R~~~L~~GEvalY~~~G~~I~L~~~G~ii~~~ 102 (162)
T PF06890_consen 71 RPKGLKPGEVALYDDEGQKIHLKRDGRIIEVT 102 (162)
T ss_pred cccCCCCCcEEEEcCCCCEEEEEecceEEecc
Confidence 677899999999998787555553 566554
No 26
>PF14594 Sipho_Gp37: Siphovirus ReqiPepy6 Gp37-like protein
Probab=60.23 E-value=31 Score=27.52 Aligned_cols=30 Identities=23% Similarity=0.276 Sum_probs=24.6
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEec
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHER 33 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~ 33 (109)
.++..||+|+.+.+.-+..+..||.++...
T Consensus 292 ~D~~LGDiVt~~~~~~G~~~~~~Itev~~~ 321 (335)
T PF14594_consen 292 KDYDLGDIVTVRDKKWGITMDARITEVIET 321 (335)
T ss_pred cccccccEEEEEecccceEEeeeEeeEEEE
Confidence 468899999999875557889999998765
No 27
>PF06940 DUF1287: Domain of unknown function (DUF1287); InterPro: IPR009706 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=57.88 E-value=6.7 Score=28.86 Aligned_cols=16 Identities=25% Similarity=0.619 Sum_probs=13.8
Q ss_pred CCCCCcCcEEEEeeCC
Q 033895 3 KDPIRAGEIVVFNVDG 18 (109)
Q Consensus 3 ~~~~~~GDIIvf~~~g 18 (109)
+++.+.||||+|..++
T Consensus 104 ~~~~q~GDIVtw~l~~ 119 (164)
T PF06940_consen 104 PEDWQPGDIVTWRLPG 119 (164)
T ss_pred hhhcCCCCEEEEeCCC
Confidence 4789999999998775
No 28
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=55.68 E-value=31 Score=23.42 Aligned_cols=43 Identities=21% Similarity=0.167 Sum_probs=26.1
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCCCCCCCC
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDD 52 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD~N~~~D 52 (109)
..+..||+|....+.....+.+||.+ + |+.+++--=++....|
T Consensus 24 ~glA~gDvV~~~~~~g~~~~~~~v~~----s--GnsTiRv~~~~~~~~~ 66 (117)
T PF14085_consen 24 YGLALGDVVRAEPDDGELWFQKVVES----S--GNSTIRVIFDDPGPDD 66 (117)
T ss_pred CCCCCCCEEEEEeCCCeEEEEEEEec----C--CCEEEEEEEcCCcchh
Confidence 46789999999876543455555443 2 5666655544433333
No 29
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=54.22 E-value=12 Score=25.79 Aligned_cols=22 Identities=23% Similarity=0.389 Sum_probs=15.1
Q ss_pred CCCCCcCcEEEEeeCCccccEEE
Q 033895 3 KDPIRAGEIVVFNVDGREIPIVH 25 (109)
Q Consensus 3 ~~~~~~GDIIvf~~~g~~~~itH 25 (109)
.+++++||+|.|+.... ..+.|
T Consensus 74 ~~~~qpGDlvff~~~~~-~~~~H 95 (134)
T TIGR02219 74 CDAAQPGDVLVFRWRPG-AAAKH 95 (134)
T ss_pred hhcCCCCCEEEEeeCCC-CCCcE
Confidence 46899999999975322 23556
No 30
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=53.59 E-value=81 Score=22.65 Aligned_cols=11 Identities=36% Similarity=0.827 Sum_probs=8.4
Q ss_pred ceEeceEEEEc
Q 033895 66 QHIMGRAVGFL 76 (109)
Q Consensus 66 ~~v~G~v~~~I 76 (109)
-.|+|+|+..+
T Consensus 185 ~~IiG~Vv~~~ 195 (199)
T TIGR00498 185 VTILGKVVGVI 195 (199)
T ss_pred EEEEEEEEEEE
Confidence 57899988664
No 31
>COG3837 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=52.14 E-value=24 Score=25.91 Aligned_cols=46 Identities=20% Similarity=0.290 Sum_probs=34.6
Q ss_pred CCCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCCCCCCCChhhhcc
Q 033895 5 PIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDRLLYAQ 58 (109)
Q Consensus 5 ~~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD~N~~~D~~~y~~ 58 (109)
.+++||++.|.... ..-|-.+..... -..|+.=||-++. |.--|+.
T Consensus 85 ~lrpGD~~gFpAG~---~~aHhliN~s~~----~~~yL~vG~r~~~-d~i~YPd 130 (161)
T COG3837 85 RLRPGDSAGFPAGV---GNAHHLINRSDV----ILRYLEVGTREPD-DIITYPD 130 (161)
T ss_pred EecCCceeeccCCC---cceeEEeecCCc----eEEEEEecccccc-ceeecCC
Confidence 47899999997633 688999987765 3468888998777 7655553
No 32
>CHL00010 infA translation initiation factor 1
Probab=50.97 E-value=18 Score=22.95 Aligned_cols=24 Identities=21% Similarity=0.194 Sum_probs=16.4
Q ss_pred CCcCcEEEEee-C--CccccEEEEEEE
Q 033895 6 IRAGEIVVFNV-D--GREIPIVHRVIK 29 (109)
Q Consensus 6 ~~~GDIIvf~~-~--g~~~~itHRVi~ 29 (109)
+.+||.|.|.. + ...-.||||--.
T Consensus 47 ~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 47 ILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred cCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 56899999983 1 222478888644
No 33
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=50.01 E-value=20 Score=22.31 Aligned_cols=22 Identities=23% Similarity=0.129 Sum_probs=15.1
Q ss_pred CCcCcEEEEee--C-CccccEEEEE
Q 033895 6 IRAGEIVVFNV--D-GREIPIVHRV 27 (109)
Q Consensus 6 ~~~GDIIvf~~--~-g~~~~itHRV 27 (109)
+.+||+|.|.. . .+.-.|+||-
T Consensus 47 i~vGD~V~ve~~~~~~~~g~Iv~r~ 71 (72)
T PRK00276 47 ILPGDKVTVELSPYDLTKGRITYRH 71 (72)
T ss_pred cCCCCEEEEEEcccCCCeEEEEEEe
Confidence 67899999983 1 2224788873
No 34
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=49.97 E-value=31 Score=23.39 Aligned_cols=29 Identities=14% Similarity=0.428 Sum_probs=21.6
Q ss_pred CCCCCCcCcEEEEeeCCccccEEEEEEEEEe
Q 033895 2 SKDPIRAGEIVVFNVDGREIPIVHRVIKVHE 32 (109)
Q Consensus 2 ~~~~~~~GDIIvf~~~g~~~~itHRVi~v~~ 32 (109)
+..++++||+++...... ..+=+|.+...
T Consensus 45 pS~~VK~GD~l~i~~~~~--~~~v~Vl~~~~ 73 (100)
T COG1188 45 PSKEVKVGDILTIRFGNK--EFTVKVLALGE 73 (100)
T ss_pred cccccCCCCEEEEEeCCc--EEEEEEEeccc
Confidence 347899999999987654 67777776543
No 35
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=47.90 E-value=23 Score=21.70 Aligned_cols=23 Identities=22% Similarity=0.287 Sum_probs=16.3
Q ss_pred CCCcCcEEEEeeC---CccccEEEEE
Q 033895 5 PIRAGEIVVFNVD---GREIPIVHRV 27 (109)
Q Consensus 5 ~~~~GDIIvf~~~---g~~~~itHRV 27 (109)
++++||||..+-+ |+..+-+=|+
T Consensus 1 ~~~vgDiV~mKK~HPCG~~~Wei~R~ 26 (57)
T PF06107_consen 1 EYEVGDIVEMKKPHPCGSNEWEIIRI 26 (57)
T ss_pred CccCCCEEEEcCCCCCCCCEEEEEEc
Confidence 5789999999744 6656655554
No 36
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=45.60 E-value=1.1e+02 Score=22.87 Aligned_cols=58 Identities=29% Similarity=0.486 Sum_probs=28.8
Q ss_pred CCCCCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCCCCCCCChhhhccCccccc--cceEeceEEEEc
Q 033895 3 KDPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNNYGDDRLLYAQGQLWLK--RQHIMGRAVGFL 76 (109)
Q Consensus 3 ~~~~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD~N~~~D~~~y~~~~~~V~--~~~v~G~v~~~I 76 (109)
.++++.||||+-..+| +...+-|... + |+. +.-+- .|+.-.|-. ++ .-.|+|++++++
T Consensus 138 ~~~a~~GdiVvA~i~g-~e~TvKrl~~---~---g~~-i~L~p-~Np~~~~i~-------~~~~~~~I~G~vvgv~ 197 (201)
T COG1974 138 TEDAENGDIVVALIDG-EEATVKRLYR---D---GNQ-ILLKP-ENPAYPPIP-------VDADSVTILGKVVGVI 197 (201)
T ss_pred CCCCCCCCEEEEEcCC-CcEEEEEEEE---e---CCE-EEEEe-CCCCCCCcc-------cCccceEEEEEEEEEE
Confidence 3455666666666555 2233333322 2 111 22222 355555544 34 357899988754
No 37
>COG3895 Predicted periplasmic protein [General function prediction only]
Probab=45.47 E-value=50 Score=22.89 Aligned_cols=46 Identities=30% Similarity=0.402 Sum_probs=32.3
Q ss_pred CCcCcE-EEEeeCCccccEEEEEEEEEecC-CCCeeEEEEeCCCCCCCC
Q 033895 6 IRAGEI-VVFNVDGREIPIVHRVIKVHERQ-DTGEVEVLTKGDNNYGDD 52 (109)
Q Consensus 6 ~~~GDI-Ivf~~~g~~~~itHRVi~v~~~~-~~g~~~~iTKGD~N~~~D 52 (109)
+..||+ ++|-.+++ .++.-.||+-...- .+|...+=||||.-...|
T Consensus 49 ~n~gd~sv~~v~Dg~-tlv~~nviSaSGAkYa~G~YvwWsKG~~A~lyd 96 (112)
T COG3895 49 NNAGDISVSFVLDGK-TLVLSNVISASGAKYADGIYVWWSKGDEATLYD 96 (112)
T ss_pred ecCCCceEEEEecCC-EEEEeeeeeccCccccCcEEEEEeCCCceEEEe
Confidence 357999 99987765 67778888754321 147778899998755554
No 38
>PRK13884 conjugal transfer peptidase TraF; Provisional
Probab=42.52 E-value=69 Score=23.33 Aligned_cols=31 Identities=23% Similarity=0.371 Sum_probs=22.6
Q ss_pred CCCCCcCcEEEEeeCCcc--------------------ccEEEEEEEEEec
Q 033895 3 KDPIRAGEIVVFNVDGRE--------------------IPIVHRVIKVHER 33 (109)
Q Consensus 3 ~~~~~~GDIIvf~~~g~~--------------------~~itHRVi~v~~~ 33 (109)
...++.||+|.|..+... .+.+-||+..-.+
T Consensus 48 ~~~~~~Gd~V~f~~p~~~~~~~a~~rgyl~~g~~p~~~~~liKRVva~pGD 98 (178)
T PRK13884 48 SAPVEKGAYVLFCPPQRGVFDDAKERGYIGAGFCPGGYGYMMKRVLAAKGD 98 (178)
T ss_pred CCCCCCCCEEEEeCCchHHHHHHHhCCccccCcCCCCCCceEEEEEeeCCc
Confidence 356899999999865311 2688999997644
No 39
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=40.92 E-value=88 Score=20.04 Aligned_cols=40 Identities=13% Similarity=0.152 Sum_probs=19.6
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCCCC
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDNN 48 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD~N 48 (109)
..+++||-+.|..+..+.+..=|+. . +. .+..|..+.|.+
T Consensus 41 ~~L~pGq~l~f~~d~~g~L~~L~~~-~--~~--~~~~~~R~~DG~ 80 (85)
T PF04225_consen 41 TRLKPGQTLEFQLDEDGQLTALRYE-R--SP--KTTLYTRQSDGS 80 (85)
T ss_dssp GG--TT-EEEEEE-TTS-EEEEEEE-E--ET--TEEEEEE-TTS-
T ss_pred hhCCCCCEEEEEECCCCCEEEEEEE-c--CC--cEEEEEEeCCCC
Confidence 4689999999998755444433322 2 21 255676767753
No 40
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=40.77 E-value=1.2e+02 Score=20.81 Aligned_cols=10 Identities=10% Similarity=0.375 Sum_probs=7.3
Q ss_pred eEeceEEEEc
Q 033895 67 HIMGRAVGFL 76 (109)
Q Consensus 67 ~v~G~v~~~I 76 (109)
+|+|+|++.+
T Consensus 126 ~IiG~V~~~~ 135 (139)
T PRK10276 126 DVFGVVTHIV 135 (139)
T ss_pred EEEEEEEEEE
Confidence 6889887554
No 41
>COG3738 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.71 E-value=28 Score=26.06 Aligned_cols=17 Identities=29% Similarity=0.548 Sum_probs=14.2
Q ss_pred CCCCCcCcEEEEeeCCc
Q 033895 3 KDPIRAGEIVVFNVDGR 19 (109)
Q Consensus 3 ~~~~~~GDIIvf~~~g~ 19 (109)
+++++.|||++.+.++.
T Consensus 138 ~s~y~aGDIvsWRLdng 154 (200)
T COG3738 138 PSDYQAGDIVSWRLDNG 154 (200)
T ss_pred ccccCCCceEEEEcCCC
Confidence 47899999999997643
No 42
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=40.35 E-value=95 Score=21.00 Aligned_cols=31 Identities=35% Similarity=0.662 Sum_probs=24.9
Q ss_pred CCCCcCcEEEEeeCCc-cccEEEEEEEEEecC
Q 033895 4 DPIRAGEIVVFNVDGR-EIPIVHRVIKVHERQ 34 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~-~~~itHRVi~v~~~~ 34 (109)
+.+++||-|.++.++. ..+.+=||.++.++.
T Consensus 2 ~~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~ 33 (121)
T cd04714 2 EIIRVGDCVLFKSPGRPSLPYVARIESLWEDP 33 (121)
T ss_pred CEEEcCCEEEEeCCCCCCCCEEEEEEEEEEcC
Confidence 4578999999997654 568899999988763
No 43
>TIGR03024 arch_pef_cterm PEF-C-terminal archaeal protein sorting domain. This domain, distantly related to the PEP-Cterm domain described in model TIGR02595, is found in Methanosarcina mazei in four different proteins, as well as in other archaea such as Methanococcoides burtonii. Several proteins with this domain have their genes only a short distance from a distant homology of EpsH, a proposed integral membrane transpeptidase.
Probab=40.08 E-value=33 Score=17.75 Aligned_cols=16 Identities=25% Similarity=0.455 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHhhhcC
Q 033895 93 KYILIGALGLLVITSK 108 (109)
Q Consensus 93 ~~~i~~~l~~~~l~~~ 108 (109)
.+.+++++++++++.|
T Consensus 8 ~l~I~all~i~~i~~r 23 (26)
T TIGR03024 8 ALPIIALLAIIVILRR 23 (26)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 4566777888777754
No 44
>PF00877 NLPC_P60: NlpC/P60 family; InterPro: IPR000064 The Escherichia coli NLPC/Listeria P60 domain occurs at the C terminus of a number of different bacterial and viral proteins. The viral proteins are either described as tail assembly proteins or Gp19. In bacteria, the proteins are variously described as being putative tail component of prophage, invasin, invasion associated protein, putative lipoprotein, cell wall hydrolase, or putative endopeptidase. The E. coli NLPC/Listeria P60 domain is contained within the boundaries of the cysteine peptidase domain that defines the MEROPS peptidase family C40 (clan C-). A type example being dipeptidyl-peptidase VI from Bacillus sphaericus and gamma-glutamyl-diamino acid-endopeptidase precursor from Lactococcus lactis 3.4.19.11 from EC. This group also contains proteins classified as non-peptidase homologues in that they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the C40 family. ; PDB: 3PVQ_B 3GT2_A 3NPF_B 2K1G_A 3I86_A 3S0Q_A 2XIV_A 3PBC_A 3NE0_A 3M1U_B ....
Probab=38.98 E-value=24 Score=22.68 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=17.9
Q ss_pred CCCCCcCcEEEEeeCCccccEEEEEEEE
Q 033895 3 KDPIRAGEIVVFNVDGREIPIVHRVIKV 30 (109)
Q Consensus 3 ~~~~~~GDIIvf~~~g~~~~itHRVi~v 30 (109)
.+++++||++.|+. + ..+.|=.+-+
T Consensus 49 ~~~~~pGDlif~~~-~--~~~~Hvgiy~ 73 (105)
T PF00877_consen 49 ISELQPGDLIFFKG-G--GGISHVGIYL 73 (105)
T ss_dssp GGG-TTTEEEEEEG-T--GGEEEEEEEE
T ss_pred hhcCCcccEEEEeC-C--ccCCEeEEEE
Confidence 46789999999987 2 3677766655
No 45
>cd00320 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface.
Probab=38.53 E-value=73 Score=20.79 Aligned_cols=15 Identities=20% Similarity=0.350 Sum_probs=12.0
Q ss_pred CCCCCcCcEEEEeeC
Q 033895 3 KDPIRAGEIVVFNVD 17 (109)
Q Consensus 3 ~~~~~~GDIIvf~~~ 17 (109)
+.++++||.|.|..-
T Consensus 55 ~~~vk~GD~Vl~~~~ 69 (93)
T cd00320 55 PLSVKVGDKVLFPKY 69 (93)
T ss_pred cccccCCCEEEECCC
Confidence 457999999999753
No 46
>PF13640 2OG-FeII_Oxy_3: 2OG-Fe(II) oxygenase superfamily; PDB: 3DKQ_B 3GZE_D 3HQR_A 2Y34_A 2G1M_A 2G19_A 3OUI_A 3OUJ_A 2HBU_A 2Y33_A ....
Probab=35.74 E-value=1.1e+02 Score=19.07 Aligned_cols=31 Identities=32% Similarity=0.438 Sum_probs=20.9
Q ss_pred CCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEE
Q 033895 6 IRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLT 43 (109)
Q Consensus 6 ~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iT 43 (109)
.+.|+.|+|.. . -.-|+|..+... +.+..++
T Consensus 66 p~~g~~v~F~~-~---~~~H~v~~v~~~---~~R~~l~ 96 (100)
T PF13640_consen 66 PKPGRLVIFPS-D---NSLHGVTPVGEG---GRRYSLT 96 (100)
T ss_dssp -BTTEEEEEES-C---TCEEEEEEE-EE---SEEEEEE
T ss_pred CCCCEEEEEeC-C---CCeecCcccCCC---CCEEEEE
Confidence 57899999986 3 489999999222 4554443
No 47
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=34.86 E-value=66 Score=20.84 Aligned_cols=24 Identities=8% Similarity=0.266 Sum_probs=16.1
Q ss_pred CCCcCcEEEE--eeCCccccEEEEEE
Q 033895 5 PIRAGEIVVF--NVDGREIPIVHRVI 28 (109)
Q Consensus 5 ~~~~GDIIvf--~~~g~~~~itHRVi 28 (109)
.+++||||-- +++..+..++=|++
T Consensus 51 g~k~GdVvkI~R~S~taG~~v~YR~V 76 (79)
T PRK09570 51 GAKPGDVIKIVRKSPTAGEAVYYRLV 76 (79)
T ss_pred CCCCCCEEEEEECCCCCCccEEEEEE
Confidence 5789999854 33444457888876
No 48
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=34.01 E-value=89 Score=21.05 Aligned_cols=14 Identities=14% Similarity=0.441 Sum_probs=10.8
Q ss_pred CCCCCcCcEEEEee
Q 033895 3 KDPIRAGEIVVFNV 16 (109)
Q Consensus 3 ~~~~~~GDIIvf~~ 16 (109)
|-++|+||.|.|..
T Consensus 60 ~~~Vk~GD~Vl~~~ 73 (100)
T PTZ00414 60 TPTVKVGDTVLLPE 73 (100)
T ss_pred cceecCCCEEEEcC
Confidence 45688999999964
No 49
>PRK00364 groES co-chaperonin GroES; Reviewed
Probab=33.90 E-value=94 Score=20.37 Aligned_cols=14 Identities=21% Similarity=0.394 Sum_probs=11.0
Q ss_pred CCCCcCcEEEEeeC
Q 033895 4 DPIRAGEIVVFNVD 17 (109)
Q Consensus 4 ~~~~~GDIIvf~~~ 17 (109)
-++++||.|.|...
T Consensus 57 ~~vk~GD~Vlf~~~ 70 (95)
T PRK00364 57 LDVKVGDKVLFGKY 70 (95)
T ss_pred cccCCCCEEEEcCC
Confidence 46899999999643
No 50
>PF00166 Cpn10: Chaperonin 10 Kd subunit; InterPro: IPR020818 The chaperonins are `helper' molecules required for correct folding and subsequent assembly of some proteins []. These are required for normal cell growth [], and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10) []. The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits []. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg2+-ATP dependent manner []. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL []. Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.; GO: 0006457 protein folding, 0005737 cytoplasm; PDB: 1PF9_Q 1AON_P 1SX4_T 1SVT_R 2C7D_P 1PCQ_O 2C7C_Q 1GRU_Q 1WNR_F 1P3H_I ....
Probab=33.74 E-value=89 Score=20.19 Aligned_cols=15 Identities=20% Similarity=0.348 Sum_probs=11.1
Q ss_pred CCCCCcCcEEEEeeC
Q 033895 3 KDPIRAGEIVVFNVD 17 (109)
Q Consensus 3 ~~~~~~GDIIvf~~~ 17 (109)
|.++++||.|.|...
T Consensus 55 ~~~vk~GD~Vl~~~~ 69 (93)
T PF00166_consen 55 PMDVKVGDKVLFPKY 69 (93)
T ss_dssp ETSS-TTSEEEEETT
T ss_pred eeeeeeccEEecccc
Confidence 457899999999754
No 51
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=31.24 E-value=1.8e+02 Score=20.14 Aligned_cols=27 Identities=26% Similarity=0.319 Sum_probs=20.6
Q ss_pred CcCcEEEEeeC---CccccEEEEEEEEEec
Q 033895 7 RAGEIVVFNVD---GREIPIVHRVIKVHER 33 (109)
Q Consensus 7 ~~GDIIvf~~~---g~~~~itHRVi~v~~~ 33 (109)
|+||-|+|+.. +.+.+|.=+|++...+
T Consensus 1 q~G~~VAak~~~~~~~~~WIla~Vv~~~~~ 30 (130)
T PF07039_consen 1 QPGDQVAAKVKQGNEEEEWILAEVVKYNSD 30 (130)
T ss_dssp -TT-EEEEEECTTTTTCEEEEEEEEEEETT
T ss_pred CCCCEEEEEcCCCCCCCCEEEEEEEEEeCC
Confidence 58999999864 4557999999998876
No 52
>PF00278 Orn_DAP_Arg_deC: Pyridoxal-dependent decarboxylase, C-terminal sheet domain; InterPro: IPR022643 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region []. This entry represents the C-terminal region of the Orn/DAP/Arg decarboxylases.; GO: 0003824 catalytic activity; PDB: 1TWI_B 1TUF_A 3MT1_A 3N2B_C 2O0T_A 1HKW_A 1HKV_A 3VAB_A 3N2O_A 7ODC_A ....
Probab=31.19 E-value=28 Score=22.61 Aligned_cols=15 Identities=27% Similarity=0.563 Sum_probs=10.8
Q ss_pred CCCCcCcEEEEeeCC
Q 033895 4 DPIRAGEIVVFNVDG 18 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g 18 (109)
.++++||.++|..-|
T Consensus 81 ~~l~~GD~l~f~~~G 95 (116)
T PF00278_consen 81 KELEVGDWLVFENMG 95 (116)
T ss_dssp STTTTT-EEEESS-S
T ss_pred CCCCCCCEEEEecCc
Confidence 489999999997555
No 53
>PLN00036 40S ribosomal protein S4; Provisional
Probab=31.13 E-value=1.2e+02 Score=23.87 Aligned_cols=37 Identities=16% Similarity=0.397 Sum_probs=25.7
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCCC
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDN 47 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD~ 47 (109)
.++++||-|.++.+.+. |++..+-+ .|+.+++|.|-|
T Consensus 152 ~~~k~~Dtv~i~l~~~k------I~~~ikfe-~G~l~~vtgG~n 188 (261)
T PLN00036 152 PLIKANDTIKIDLETNK------IVDFIKFD-VGNLVMVTGGRN 188 (261)
T ss_pred CccccCCEEEEeCCCCc------eeeEEecC-CCCEEEEECCee
Confidence 37899999999876543 34444443 378889998864
No 54
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=30.50 E-value=94 Score=22.63 Aligned_cols=28 Identities=11% Similarity=0.162 Sum_probs=19.0
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEe
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHE 32 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~ 32 (109)
+++++||.|....... ...+-||.++..
T Consensus 107 ~~L~~GD~I~v~~~~g-~~~~Y~V~~~~i 134 (174)
T TIGR03784 107 QELRPGDVIRLQTPDG-QWQSYQVTATRV 134 (174)
T ss_pred hhCCCCCEEEEEECCC-eEEEEEEeEEEE
Confidence 5799999999975432 345666666544
No 55
>PF00122 E1-E2_ATPase: E1-E2 ATPase p-type cation-transporting ATPase superfamily signature H+-transporting ATPase (proton pump) signature sodium/potassium-transporting ATPase signature; InterPro: IPR008250 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the actuator (A) domain, and some transmembrane helices found in P-type ATPases []. It contains the TGES-loop which is essential for the metal ion binding which results in tight association between the A and P (phosphorylation) domains []. It does not contain the phosphorylation site. It is thought that the large movement of the actuator domain, which is transmitted to the transmembrane helices, is essential to the long distance coupling between formation/decomposition of the acyl phosphate in the cytoplasmic P-domain and the changes in the ion-binding sites buried deep in the membranous region []. This domain has a modulatory effect on the phosphoenzyme processing steps through its nucleotide binding [],[]. P-type (or E1-E2-type) ATPases that form an aspartyl phosphate intermediate in the course of ATP hydrolysis, can be divided into 4 major groups []: (1) Ca2+-transporting ATPases; (2) Na+/K+- and gastric H+/K+-transporting ATPases; (3) plasma membrane H+-transporting ATPases (proton pumps) of plants, fungi and lower eukaryotes; and (4) all bacterial P-type ATPases, except the g2+-ATPase of Salmonella typhimurium, which is more similar to the eukaryotic sequences. However, great variety of sequence analysis methods results in diversity of classification. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000166 nucleotide binding, 0046872 metal ion binding; PDB: 2XZB_A 1MHS_B 3TLM_A 3A3Y_A 2ZXE_A 3NAL_A 3NAM_A 3NAN_A 2YJ6_B 2IYE_A ....
Probab=30.20 E-value=38 Score=24.52 Aligned_cols=42 Identities=26% Similarity=0.465 Sum_probs=22.2
Q ss_pred CCCCCcCcEEEEeeCCcccc----EEE-EEEEEEecCCCCeeEEEEeC
Q 033895 3 KDPIRAGEIVVFNVDGREIP----IVH-RVIKVHERQDTGEVEVLTKG 45 (109)
Q Consensus 3 ~~~~~~GDIIvf~~~g~~~~----itH-RVi~v~~~~~~g~~~~iTKG 45 (109)
.+++++||||..+. |+..| ++. --..+++...+|+..-+.|-
T Consensus 49 ~~~L~~GDiI~l~~-g~~vPaD~~ll~~g~~~vd~s~ltGes~pv~k~ 95 (230)
T PF00122_consen 49 SSELVPGDIIILKA-GDIVPADGILLESGSAYVDESALTGESEPVKKT 95 (230)
T ss_dssp GGGT-TTSEEEEET-TEBESSEEEEEESSEEEEECHHHHSBSSEEEES
T ss_pred Hhhccceeeeeccc-ccccccCccceeccccccccccccccccccccc
Confidence 47899999999974 43333 333 33333332112445566665
No 56
>cd06541 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery.
Probab=29.90 E-value=1.4e+02 Score=19.49 Aligned_cols=29 Identities=17% Similarity=0.193 Sum_probs=21.6
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEec
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHER 33 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~ 33 (109)
..+++||.++|...+ ....+=|++++..-
T Consensus 29 ~~~k~Gd~~i~~~~~-~~~~~i~v~~V~~~ 57 (105)
T cd06541 29 QLPKAGDYLIILDGQ-QPLAIAEVVKVEIM 57 (105)
T ss_pred cCCCCCCEEEEecCC-CcEEEEEEEEEEEE
Confidence 468999999996434 44568888888765
No 57
>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=29.86 E-value=51 Score=19.17 Aligned_cols=14 Identities=14% Similarity=0.479 Sum_probs=11.8
Q ss_pred CCCCCcCcEEEEee
Q 033895 3 KDPIRAGEIVVFNV 16 (109)
Q Consensus 3 ~~~~~~GDIIvf~~ 16 (109)
+...++||.|+|..
T Consensus 5 ~~~~~~Gd~v~Yti 18 (53)
T TIGR01451 5 KTVATIGDTITYTI 18 (53)
T ss_pred ccccCCCCEEEEEE
Confidence 56789999999975
No 58
>PF10125 NADHdeh_related: NADH dehydrogenase I, subunit N related protein; InterPro: IPR017059 This group contains membrane proteins that are predicted to be transmembrane subunits (EhaH) of multisubunit membrane-bound [NiFe]-hydrogenase Eha complexes. The energy-converting hydrogenase A (eha) operon encodes a putative multisubunit membrane-bound [NiFe]-hydrogenase Eha in Methanobacterium thermoautotrophicum (strain Marburg / DSM 2133). Sequence analysis of the eha operon indicates that it encodes at least 20 proteins, including the [NiFe]-hydrogenase large subunit (IPR014363 from INTERPRO), the [NiFe]-hydrogenase small subunit (PIRSF002913 from PIRSF), and two broadly conserved integral membrane proteins (this entry and PIRSF000215 from PIRSF). These four proteins show high sequence similarity to subunits of the Ech hydrogenase from Methanosarcina barkeri, Escherichia coli hydrogenases 3 and 4 (Hyc and Hyf), and CO-induced hydrogenase from Rhodospirillum rubrum (Coo), all of which form a distinct group of multisubunit membrane-bound [NiFe]-hydrogenases (together called hydrogenase-3-type hydrogenases). In addition to these four subunits, the eha operon encodes a 6[4Fe-4S] polyferredoxin, a 10[4Fe-4S] polyferredoxin, ten other predicted integral membrane proteins (PIRSF005019 from PIRSF, PIRSF019706 from PIRSF, PIRSF036534 from PIRSF, PIRSF006581 from PIRSF, PIRSF036535 from PIRSF, PIRSF019373 from PIRSF, PIRSF019136 from PIRSF, PIRSF036537 from PIRSF, PIRSF036538 from PIRSF, PIRSF004953 from PIRSF), and four hydrophilic subunits (PIRSF005292 from PIRSF, PIRSF019370 from PIRSF, PIRSF006414 from PIRSF, PIRSF000536 from PIRSF) (the latter two hydrophilic subunits are members of well-characterised enzyme families but lack the essential amino acids assumed to form the active site []). All of these proteins are expressed and therefore thought to be functional subunits of the Eha hydrogenase complex []. Note, however, that the ten additional predicted integral membrane proteins are absent from Ech, Coo, Hyc, and Hyf complexes (and therefore from corresponding organisms), indicating that those complexes have a simpler membrane component than Eha []. Members of this group are homologous to the N-terminal domain of PIRSF006542 from PIRSF members (e.g., EhbF, HyfF of E. coli hydrogenase 4, amongst others). Therefore, this type of membrane subunit of Eha complex is conserved across the various hydrogenase-3-type hydrogenases (that is, they are not limited to the Eha subgroup). A protein with sequence similarity to the C-terminal part of EhbF (PIRSF006542 from PIRSF) is not present in the Eha complex (not encoded by the eha operon). Based on sequence similarity and genome context analysis, other organisms such as Methanopyrus kandleri,Methanocaldococcus jannaschii, and M. thermoautotrophicum also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar eha operon structure.
Probab=29.45 E-value=90 Score=23.89 Aligned_cols=27 Identities=22% Similarity=0.517 Sum_probs=20.4
Q ss_pred ceEeceEEEEcccccEEEEEeccchhHH
Q 033895 66 QHIMGRAVGFLPYVGWVTIIMTEKPIIK 93 (109)
Q Consensus 66 ~~v~G~v~~~IP~lG~v~~~~~~~~~~~ 93 (109)
+++-|...+.||+ |-+..+++......
T Consensus 3 ~~i~G~~l~~ipf-GDIV~Y~s~~~~~~ 29 (219)
T PF10125_consen 3 ESIGGNLLGIIPF-GDIVFYFSPFSLIL 29 (219)
T ss_pred cccCCcEEEEEEc-CcEEEEecchHHHH
Confidence 5677999999995 88888887755433
No 59
>COG1531 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.45 E-value=1.6e+02 Score=19.07 Aligned_cols=29 Identities=17% Similarity=0.287 Sum_probs=18.5
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEec
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHER 33 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~ 33 (109)
++++.++...+-..+. ..=.|||+++...
T Consensus 39 ~di~~~~~~~~~~~~~-~IP~HRIveIr~~ 67 (77)
T COG1531 39 DDIEEVGRFYLLYQGT-YIPYHRIVEIRKK 67 (77)
T ss_pred hhheecceEEEEecCc-eeeeEEEEEEEec
Confidence 5667777733333343 4567999999944
No 60
>PRK04313 30S ribosomal protein S4e; Validated
Probab=29.19 E-value=1.3e+02 Score=23.32 Aligned_cols=37 Identities=16% Similarity=0.454 Sum_probs=26.4
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCCC
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDN 47 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD~ 47 (109)
.++++||-|.+..+.+. |++..+-+ .|+.+++|.|-|
T Consensus 149 ~~~k~~Dtv~i~l~~~k------I~~~i~fe-~G~l~~itgG~n 185 (237)
T PRK04313 149 DDYKTGDSLLISLPEQE------IVDHIPFE-EGNLAIITGGKH 185 (237)
T ss_pred cccccCCEEEEECCCCc------eeEEEecC-CCCEEEEECCee
Confidence 47899999999976553 44444443 378899998865
No 61
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=28.95 E-value=1.5e+02 Score=23.60 Aligned_cols=37 Identities=27% Similarity=0.551 Sum_probs=25.7
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCCC
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDN 47 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD~ 47 (109)
.++++||-|.+..+.+. |++..+-+ .|+.+++|.|-|
T Consensus 149 ~~~k~~Dtv~i~l~~~k------I~~~ikfe-~G~l~~vtgG~n 185 (273)
T PTZ00223 149 PRTSRGDTLVYNVKEKK------VVDLIKNR-NGKVVMVTGGAN 185 (273)
T ss_pred ccccCCCEEEEECCCCe------eeEEEecC-CCCEEEEECCee
Confidence 36899999999876542 34444443 378888888864
No 62
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=28.94 E-value=1.5e+02 Score=23.43 Aligned_cols=37 Identities=16% Similarity=0.442 Sum_probs=25.8
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeCCC
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKGDN 47 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKGD~ 47 (109)
.++++||-|.++.+.+. |++..+-+ .|+.+++|.|-|
T Consensus 152 ~~ik~~Dtv~i~l~~~k------I~~~ikfe-~G~l~~vtgG~n 188 (262)
T PTZ00118 152 PDVKVGDSLRLDLETGK------VLEFLKFE-VGNLVMITGGHN 188 (262)
T ss_pred CcccCCCEEEEECCCCc------eeeEEecC-CCCEEEEECCee
Confidence 47899999999876543 34444443 378889998864
No 63
>PRK06033 hypothetical protein; Validated
Probab=28.85 E-value=65 Score=20.72 Aligned_cols=13 Identities=8% Similarity=0.394 Sum_probs=10.8
Q ss_pred CCCcCcEEEEeeC
Q 033895 5 PIRAGEIVVFNVD 17 (109)
Q Consensus 5 ~~~~GDIIvf~~~ 17 (109)
++++||||.+..+
T Consensus 27 ~L~~GDVI~L~~~ 39 (83)
T PRK06033 27 RMGRGAVIPLDAT 39 (83)
T ss_pred CCCCCCEEEeCCC
Confidence 5789999999754
No 64
>PF13275 S4_2: S4 domain; PDB: 1P9K_A.
Probab=28.67 E-value=45 Score=20.73 Aligned_cols=13 Identities=23% Similarity=0.547 Sum_probs=7.6
Q ss_pred CCCCCCcCcEEEE
Q 033895 2 SKDPIRAGEIVVF 14 (109)
Q Consensus 2 ~~~~~~~GDIIvf 14 (109)
|...+++||+|.|
T Consensus 45 rg~Kl~~GD~V~~ 57 (65)
T PF13275_consen 45 RGKKLRPGDVVEI 57 (65)
T ss_dssp SS----SSEEEEE
T ss_pred cCCcCCCCCEEEE
Confidence 3467899999999
No 65
>cd03470 Rieske_cytochrome_bc1 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including uni- and multi-cellular eukaryotes, plants (in their mitochondria) and bacteria. The cytochrome bc(1) and b6f complexes are central components of the respiratory and photosynthetic electron transport chains, respectively, which carry out similar core electron and proton transfer steps. The bc(1) and b6f complexes share a common core structure of three catalytic subunits: cyt b, the Rieske ISP, and either a cyt c1 in the bc(1) complex or cyt f in the b6f complex, which are arranged in an integral membrane-bound dimeric complex. While the core of the b6f complex is similar to that of the bc(1) complex, the domain arrangement outside the core and the complement of prosthetic groups are strikingly different.
Probab=28.43 E-value=48 Score=22.84 Aligned_cols=23 Identities=22% Similarity=0.465 Sum_probs=20.7
Q ss_pred CCCCcCcEEEEeeCCccccEEEE
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHR 26 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHR 26 (109)
+++++|...++.-.|..++|.||
T Consensus 7 ~~l~~G~~~~v~w~Gkpv~I~~r 29 (126)
T cd03470 7 SKIEEGQLITVEWRGKPVFIRRR 29 (126)
T ss_pred hhCCCCCEEEEEECCeEEEEEEC
Confidence 67899999999988988888888
No 66
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=27.91 E-value=47 Score=22.98 Aligned_cols=15 Identities=27% Similarity=0.164 Sum_probs=11.5
Q ss_pred CCCCcCcEEEEeeCC
Q 033895 4 DPIRAGEIVVFNVDG 18 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g 18 (109)
++.++||+|+|+..+
T Consensus 72 ~~p~~GDiv~f~~~~ 86 (129)
T TIGR02594 72 SKPAYGCIAVKRRGG 86 (129)
T ss_pred CCCCccEEEEEECCC
Confidence 356899999997543
No 67
>cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma.
Probab=27.85 E-value=71 Score=21.86 Aligned_cols=38 Identities=26% Similarity=0.308 Sum_probs=26.3
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEecCCCCeeEEEEeC
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHERQDTGEVEVLTKG 45 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~~~~g~~~~iTKG 45 (109)
..|++||.|+.-.... ||+-||.+..... +....+.|+
T Consensus 25 GtL~~GD~Iv~g~~~G--pi~tkVRaLl~~~--~~~E~r~~~ 62 (110)
T cd03703 25 GTLREGDTIVVCGLNG--PIVTKVRALLKPQ--PLKELRVKS 62 (110)
T ss_pred CeEecCCEEEEccCCC--CceEEEeEecCCC--Cchhhcccc
Confidence 5689999999954332 8899999988763 433444553
No 68
>PF07313 DUF1460: Protein of unknown function (DUF1460); InterPro: IPR010846 This family consists of several hypothetical bacterial proteins of around 260 residues in length. The function of this family is unknown.; PDB: 2P1G_B 2IM9_A.
Probab=26.98 E-value=2e+02 Score=21.89 Aligned_cols=30 Identities=20% Similarity=0.381 Sum_probs=22.5
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEec
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHER 33 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~ 33 (109)
+.++.||||.+..+-.+.=++|==+.+...
T Consensus 152 ~~i~~GDiI~i~t~~~GLDvsH~Giav~~~ 181 (216)
T PF07313_consen 152 SQIKNGDIIAIVTNIKGLDVSHVGIAVWKN 181 (216)
T ss_dssp TTS-TT-EEEEEEECTTECEEEEEEEEEET
T ss_pred hcCCCCCEEEEEeCCCCCceeeEEEEEEEC
Confidence 568999999997765667799988888776
No 69
>PRK10838 spr outer membrane lipoprotein; Provisional
Probab=26.56 E-value=47 Score=24.71 Aligned_cols=15 Identities=33% Similarity=0.835 Sum_probs=12.4
Q ss_pred CCCCCCcCcEEEEee
Q 033895 2 SKDPIRAGEIVVFNV 16 (109)
Q Consensus 2 ~~~~~~~GDIIvf~~ 16 (109)
+.+++++||+|.|+.
T Consensus 125 ~~~~lqpGDLVfF~~ 139 (190)
T PRK10838 125 SRSKLRTGDLVLFRA 139 (190)
T ss_pred ccCCCCCCcEEEECC
Confidence 347899999999974
No 70
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=26.44 E-value=1.2e+02 Score=19.37 Aligned_cols=24 Identities=13% Similarity=0.285 Sum_probs=13.9
Q ss_pred CCCcCcEEEE--eeCCccccEEEEEE
Q 033895 5 PIRAGEIVVF--NVDGREIPIVHRVI 28 (109)
Q Consensus 5 ~~~~GDIIvf--~~~g~~~~itHRVi 28 (109)
.++.||||-- +++..+..++=|++
T Consensus 48 g~k~GdVvkI~R~S~taG~~v~YR~V 73 (74)
T PF01191_consen 48 GAKPGDVVKIIRKSETAGEYVTYRLV 73 (74)
T ss_dssp T--TTSEEEEEEEETTTSEEEEEEEE
T ss_pred CCCCCCEEEEEecCCCCCCcEEEEEe
Confidence 4678999854 34444456777765
No 71
>PF05708 DUF830: Orthopoxvirus protein of unknown function (DUF830); PDB: 2IF6_B 3KW0_C.
Probab=26.39 E-value=47 Score=22.77 Aligned_cols=29 Identities=17% Similarity=0.347 Sum_probs=14.5
Q ss_pred CCCcCcEEEEeeCCc---------cccEEEEEEEEEec
Q 033895 5 PIRAGEIVVFNVDGR---------EIPIVHRVIKVHER 33 (109)
Q Consensus 5 ~~~~GDIIvf~~~g~---------~~~itHRVi~v~~~ 33 (109)
.+++||||.++..+. .....|=-+-+...
T Consensus 1 ~l~~GDIil~~~~~~~s~~i~~~t~~~~~HvgI~~~~~ 38 (158)
T PF05708_consen 1 KLQTGDIILTRGKSSLSKAIRPVTSSPYSHVGIVIGDE 38 (158)
T ss_dssp ---TT-EEEEEE-SCCHHHHHHHHTSS--EEEEEEEET
T ss_pred CCCCeeEEEEECCchHHHHHHHHhCCCCCEEEEEEecC
Confidence 478999999986531 13567766666654
No 72
>PF04970 LRAT: Lecithin retinol acyltransferase; InterPro: IPR007053 This entry represents a conserved sequence region found in proteins from viruses, bacteria and eukaryotes. It contains a well-conserved NCEHF motif, though its function in these proteins is unknown.; PDB: 2KYT_A 4DOT_A 4FA0_A.
Probab=26.10 E-value=70 Score=21.38 Aligned_cols=24 Identities=17% Similarity=0.156 Sum_probs=16.0
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEE
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVH 31 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~ 31 (109)
..+++||+|.++.. ...|=-|-+-
T Consensus 5 ~~~~~GD~I~~~r~----~y~H~gIYvG 28 (125)
T PF04970_consen 5 KRLKPGDHIEVPRG----LYEHWGIYVG 28 (125)
T ss_dssp -S--TT-EEEEEET----TEEEEEEEEE
T ss_pred cCCCCCCEEEEecC----CccEEEEEec
Confidence 57899999999875 6888777764
No 73
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=26.07 E-value=2e+02 Score=19.13 Aligned_cols=30 Identities=20% Similarity=0.382 Sum_probs=23.9
Q ss_pred CCCcCcEEEEeeCCc-cccEEEEEEEEEecC
Q 033895 5 PIRAGEIVVFNVDGR-EIPIVHRVIKVHERQ 34 (109)
Q Consensus 5 ~~~~GDIIvf~~~g~-~~~itHRVi~v~~~~ 34 (109)
.+++||-|.+..++. ..+.+=||.++..+.
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~ 33 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDE 33 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEEEECC
Confidence 468999999987654 568899999988764
No 74
>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.
Probab=26.07 E-value=1.7e+02 Score=18.00 Aligned_cols=24 Identities=13% Similarity=0.289 Sum_probs=15.1
Q ss_pred CCcCcEEEEeeCCccccEEEEEEEEE
Q 033895 6 IRAGEIVVFNVDGREIPIVHRVIKVH 31 (109)
Q Consensus 6 ~~~GDIIvf~~~g~~~~itHRVi~v~ 31 (109)
.++||.+.|..++. ...=||.+|.
T Consensus 53 ~~~Gd~v~~~~~~g--~~~~~I~~I~ 76 (77)
T PF01272_consen 53 KKVGDEVEVELPGG--ERKYEILEIE 76 (77)
T ss_dssp -BTT-EEEEEETTB--EEEEEEEEEE
T ss_pred CCCCCEEEEEeCCc--eEEEEEEEEE
Confidence 47899999998765 3444555553
No 75
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=25.45 E-value=2e+02 Score=18.64 Aligned_cols=29 Identities=14% Similarity=0.204 Sum_probs=19.2
Q ss_pred CCCCCcCcEEEEee--CCccccEEEEEEEEEe
Q 033895 3 KDPIRAGEIVVFNV--DGREIPIVHRVIKVHE 32 (109)
Q Consensus 3 ~~~~~~GDIIvf~~--~g~~~~itHRVi~v~~ 32 (109)
..+.++||+|.... |=+ ...-|+++++.+
T Consensus 51 ~n~~k~GD~V~I~e~rPlS-K~K~~~v~~i~~ 81 (84)
T PRK05610 51 NNEAKIGDVVRIMETRPLS-KTKRWRLVEIVE 81 (84)
T ss_pred CCCCCCCCEEEEEEcccCC-CCEEEEEEEEEe
Confidence 35689999999974 211 246677777654
No 76
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.23 E-value=49 Score=22.76 Aligned_cols=25 Identities=28% Similarity=0.481 Sum_probs=16.0
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEe
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHE 32 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~ 32 (109)
..+++||.|.|.- . -+--+|+++..
T Consensus 32 r~ik~GD~IiF~~--~--~l~v~V~~vr~ 56 (111)
T COG4043 32 RQIKPGDKIIFNG--D--KLKVEVIDVRV 56 (111)
T ss_pred cCCCCCCEEEEcC--C--eeEEEEEEEee
Confidence 4689999999963 2 23335555543
No 77
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=25.18 E-value=1.7e+02 Score=19.24 Aligned_cols=13 Identities=31% Similarity=0.552 Sum_probs=10.2
Q ss_pred CCCCcCcEEEEee
Q 033895 4 DPIRAGEIVVFNV 16 (109)
Q Consensus 4 ~~~~~GDIIvf~~ 16 (109)
-++++||-|.|..
T Consensus 52 ~~Vk~GD~Vl~~~ 64 (91)
T PRK14533 52 FDIKVGDKVIFSK 64 (91)
T ss_pred ccccCCCEEEEcc
Confidence 4688999999864
No 78
>cd05829 Sortase_E Sortase E (SrtE) is a membrane transpeptidase found in gram-positive bacteria that cleaves surface proteins at a cell sorting motif and catalyzes a transpeptidation reaction in which the surface protein substrate is covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. The function of Sortase E is unknown. In two different sortase families, the N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring, or it contains a signal peptide only and the C-terminus serves as a membrane anchor. Most gram-positive bacteria contain more than one sortase and it is thought that the different sortases anchor different surface protein classes. The sortase domain is a modified beta-barrel flanked by two (SrtA) or three (SrtB) short alpha-helices.
Probab=25.17 E-value=1.5e+02 Score=20.55 Aligned_cols=25 Identities=32% Similarity=0.484 Sum_probs=17.0
Q ss_pred CCCCcCcEEEEee-CCccccEEEEEEEE
Q 033895 4 DPIRAGEIVVFNV-DGREIPIVHRVIKV 30 (109)
Q Consensus 4 ~~~~~GDIIvf~~-~g~~~~itHRVi~v 30 (109)
.++++||.|.... .++ ..+=||.++
T Consensus 71 ~~l~~GD~I~v~~~~g~--~~~Y~V~~~ 96 (144)
T cd05829 71 GDLRKGDKVEVTRADGQ--TATFRVDRV 96 (144)
T ss_pred hcCCCCCEEEEEECCCC--EEEEEEeEE
Confidence 5789999999987 343 345555444
No 79
>PF02559 CarD_CdnL_TRCF: CarD-like/TRCF domain; InterPro: IPR003711 The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. A single gene, carD, is required for the activation of both light- and starvation-inducible genes []. The predicted protein contains four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3MLQ_H 2EYQ_A.
Probab=25.06 E-value=90 Score=19.97 Aligned_cols=24 Identities=29% Similarity=0.423 Sum_probs=14.9
Q ss_pred CCCcCcEEEEeeCCccccEEEEEEEEEec
Q 033895 5 PIRAGEIVVFNVDGREIPIVHRVIKVHER 33 (109)
Q Consensus 5 ~~~~GDIIvf~~~g~~~~itHRVi~v~~~ 33 (109)
.+++||.|+|...| +.|+.++.+.
T Consensus 1 mf~~GD~VVh~~~G-----v~~i~~i~~~ 24 (98)
T PF02559_consen 1 MFKIGDYVVHPNHG-----VGRIEGIEEI 24 (98)
T ss_dssp T--TTSEEEETTTE-----EEEEEEEEEE
T ss_pred CCCCCCEEEECCCc-----eEEEEEEEEE
Confidence 36899999996544 4556666554
No 80
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=24.95 E-value=48 Score=22.33 Aligned_cols=14 Identities=21% Similarity=0.439 Sum_probs=11.6
Q ss_pred CCCCCcCcEEEEee
Q 033895 3 KDPIRAGEIVVFNV 16 (109)
Q Consensus 3 ~~~~~~GDIIvf~~ 16 (109)
|-++++||.|.|..
T Consensus 56 ~~~VkvGD~Vlf~k 69 (96)
T COG0234 56 PLDVKVGDRVLFGK 69 (96)
T ss_pred ccccccCCEEEECc
Confidence 45799999999964
No 81
>PF12436 USP7_ICP0_bdg: ICP0-binding domain of Ubiquitin-specific protease 7; InterPro: IPR024729 This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found in proteins of the peptidase C19 family, which contains contains ubiquitinyl hydrolases like ubiquitin-specific protease 7 (USP7). USP7 regulates the turnover of p53 [].; PDB: 2KVR_A 2YLM_A.
Probab=24.45 E-value=51 Score=25.17 Aligned_cols=14 Identities=21% Similarity=0.596 Sum_probs=9.9
Q ss_pred CCCCcCcEEEEeeC
Q 033895 4 DPIRAGEIVVFNVD 17 (109)
Q Consensus 4 ~~~~~GDIIvf~~~ 17 (109)
.++.-||||+|+..
T Consensus 139 ~el~~GdIi~fQ~~ 152 (249)
T PF12436_consen 139 AELQDGDIICFQRA 152 (249)
T ss_dssp TT--TTEEEEEEE-
T ss_pred cccCCCCEEEEEec
Confidence 68899999999863
No 82
>PF02839 CBM_5_12: Carbohydrate binding domain; InterPro: IPR003610 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This entry represents CBM5 from CAZY and CBM12 from CAZY. These modules have a core structure consisting of a 3-stranded meander beta-sheet, which contain six aromatic groups that may be important for binding. CBM5/12 is found in proteins such as chitinase A1, chitinase B [], and endoglucanase Z []. The overall topology of the CBM is structurally similar to the C-terminal chitin-binding domains (ChBD) of chitinase A1 and chitinase B, however the binding mechanism for the ChBD may be different from that of the CBM [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process, 0005576 extracellular region; PDB: 1ED7_A 1W1V_A 1E15_B 1UR8_A 1E6Z_B 1E6P_A 1W1T_A 1W1P_B 1UR9_A 1E6R_A ....
Probab=24.18 E-value=34 Score=18.48 Aligned_cols=12 Identities=33% Similarity=0.564 Sum_probs=6.8
Q ss_pred CCCCcCcEEEEe
Q 033895 4 DPIRAGEIVVFN 15 (109)
Q Consensus 4 ~~~~~GDIIvf~ 15 (109)
..++.||+|+|+
T Consensus 8 ~~Y~~Gd~V~~~ 19 (41)
T PF02839_consen 8 TTYNAGDRVSYN 19 (41)
T ss_dssp CEE-TT-EEEET
T ss_pred CEEcCCCEEEEC
Confidence 345678888884
No 83
>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=23.13 E-value=1.6e+02 Score=20.51 Aligned_cols=31 Identities=19% Similarity=0.277 Sum_probs=24.2
Q ss_pred CCCCcCcEEEEeeC-CccccEEEEEEEEEecC
Q 033895 4 DPIRAGEIVVFNVD-GREIPIVHRVIKVHERQ 34 (109)
Q Consensus 4 ~~~~~GDIIvf~~~-g~~~~itHRVi~v~~~~ 34 (109)
+.+++||-|..+.+ ....+.+.||....++.
T Consensus 2 ~~i~vGD~V~v~~~~~~~p~~I~rV~~mfe~~ 33 (124)
T cd04760 2 EELEAGDCVSVKPDDPTKPLYIARVTYMWKDS 33 (124)
T ss_pred CEEecCCEEEEecCCCCCCcEEEEEhhheecC
Confidence 45789999998865 44468999999888764
No 84
>PF13793 Pribosyltran_N: N-terminal domain of ribose phosphate pyrophosphokinase; PDB: 2JI4_A 1DKU_B 1IBS_B 1DKR_B 3MBI_C 3LRT_B 3LPN_B 3NAG_B 2H07_B 2H06_B ....
Probab=22.60 E-value=41 Score=22.81 Aligned_cols=15 Identities=20% Similarity=0.423 Sum_probs=10.8
Q ss_pred ceEEEEcccccEEEE
Q 033895 70 GRAVGFLPYVGWVTI 84 (109)
Q Consensus 70 G~v~~~IP~lG~v~~ 84 (109)
-++.+++||+||--.
T Consensus 80 ~~i~~ViPYl~YaRQ 94 (116)
T PF13793_consen 80 KRITLVIPYLPYARQ 94 (116)
T ss_dssp SEEEEEESS-TTTTS
T ss_pred cEEEEeccchhhhhh
Confidence 477789999998644
No 85
>PF13759 2OG-FeII_Oxy_5: Putative 2OG-Fe(II) oxygenase; PDB: 3BVC_B 2RG4_A.
Probab=22.35 E-value=1.2e+02 Score=19.33 Aligned_cols=24 Identities=21% Similarity=0.266 Sum_probs=13.6
Q ss_pred CCCcCcEEEEeeCCccccEEEEEEEEEec
Q 033895 5 PIRAGEIVVFNVDGREIPIVHRVIKVHER 33 (109)
Q Consensus 5 ~~~~GDIIvf~~~g~~~~itHRVi~v~~~ 33 (109)
+.+.||+++|.. .+-|+|.....+
T Consensus 69 ~p~~G~lvlFPs-----~l~H~v~p~~~~ 92 (101)
T PF13759_consen 69 EPEEGDLVLFPS-----WLWHGVPPNNSD 92 (101)
T ss_dssp ---TTEEEEEET-----TSEEEE----SS
T ss_pred CCCCCEEEEeCC-----CCEEeccCcCCC
Confidence 457899999953 688998776644
No 86
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=22.30 E-value=59 Score=21.50 Aligned_cols=12 Identities=33% Similarity=0.714 Sum_probs=8.0
Q ss_pred CCCCcCcEEEEe
Q 033895 4 DPIRAGEIVVFN 15 (109)
Q Consensus 4 ~~~~~GDIIvf~ 15 (109)
...++|||++|+
T Consensus 61 ~~P~~Gdivv~~ 72 (124)
T PF05257_consen 61 STPQPGDIVVWD 72 (124)
T ss_dssp S---TTEEEEEE
T ss_pred cccccceEEEec
Confidence 567899999995
No 87
>PF02298 Cu_bind_like: Plastocyanin-like domain; InterPro: IPR003245 Blue (type 1) copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm [, ]. The most well known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus []; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings []; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) [], a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans []; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved. This domain is found in a variety of plant cyanins and pollern allergen. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Amb a 3.; GO: 0005507 copper ion binding, 0009055 electron carrier activity; PDB: 1JER_A 1WS7_A 1WS8_D 1F56_B 1X9R_B 1X9U_A 2CBP_A.
Probab=22.14 E-value=99 Score=19.69 Aligned_cols=26 Identities=35% Similarity=0.640 Sum_probs=16.6
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEec
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHER 33 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~ 33 (109)
...++||.++|+-+.. .|=|+++.+.
T Consensus 17 ~~F~vGD~LvF~y~~~----~h~V~~V~~~ 42 (85)
T PF02298_consen 17 KTFRVGDTLVFNYDSG----QHSVVEVSKA 42 (85)
T ss_dssp S-BETTEEEEEE--TT----TB-EEEESHH
T ss_pred CcEeCCCEEEEEecCC----CCeEEecChh
Confidence 4678999999975533 2778888754
No 88
>PLN03148 Blue copper-like protein; Provisional
Probab=21.85 E-value=1.1e+02 Score=22.43 Aligned_cols=26 Identities=15% Similarity=0.368 Sum_probs=18.7
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEEEEec
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIKVHER 33 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~v~~~ 33 (109)
...++||.++|+-+.. .|-|.+++++
T Consensus 44 k~F~VGD~LvF~Y~~~----~hnV~~V~~~ 69 (167)
T PLN03148 44 QTFYVGDLISFRYQKT----QYNVFEVNQT 69 (167)
T ss_pred CCCccCCEEEEEecCC----CceEEEEChH
Confidence 5678999999986432 2777777654
No 89
>PF08909 DUF1854: Domain of unknown function (DUF1854); InterPro: IPR015005 These protein is functionally uncharacterised. It is found at the C terminus of a number of ATP transporter proteins suggesting it may be involved in ligand binding.
Probab=21.65 E-value=1.6e+02 Score=20.79 Aligned_cols=27 Identities=26% Similarity=0.541 Sum_probs=19.5
Q ss_pred ccEEEEEEEEEecC---------CCCeeEEEEeCCC
Q 033895 21 IPIVHRVIKVHERQ---------DTGEVEVLTKGDN 47 (109)
Q Consensus 21 ~~itHRVi~v~~~~---------~~g~~~~iTKGD~ 47 (109)
.|.+.||.+|...+ +.|.+.|.+||..
T Consensus 58 ~P~I~rI~~Vs~~~~p~~W~VeTdrG~t~f~l~g~e 93 (133)
T PF08909_consen 58 MPEILRIVSVSSFGTPSTWDVETDRGPTRFVLKGEE 93 (133)
T ss_pred ceEEEEEEEEecccCCcEEEEEecCCcEEEEEcCcc
Confidence 47888888877653 1478889999853
No 90
>PF06605 Prophage_tail: Prophage endopeptidase tail; InterPro: IPR010572 This entry is represented by the Bacteriophage 53, Orf003. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 3GS9_A.
Probab=21.17 E-value=1.7e+02 Score=22.67 Aligned_cols=30 Identities=17% Similarity=0.297 Sum_probs=21.1
Q ss_pred CCCCCcCcEEEEeeCCccccEEEEEEEEEe
Q 033895 3 KDPIRAGEIVVFNVDGREIPIVHRVIKVHE 32 (109)
Q Consensus 3 ~~~~~~GDIIvf~~~g~~~~itHRVi~v~~ 32 (109)
.+++..||.|....+.-++-+.-||++...
T Consensus 261 ~~~~~lGD~V~v~~~~~gi~~~~RIv~~~~ 290 (327)
T PF06605_consen 261 LEKVNLGDTVTVIDEDLGIDVKARIVKITY 290 (327)
T ss_dssp -----TT-EEEEEETTTTEEEEEEEEEEEE
T ss_pred cCCCCCCCEEEEEECCCCEEEEEEEEEEEE
Confidence 367899999999877666789999999998
No 91
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=21.16 E-value=2.4e+02 Score=19.16 Aligned_cols=25 Identities=20% Similarity=0.481 Sum_probs=13.9
Q ss_pred CCCcCcEEEEeeCCccccEEEEEEEEEe
Q 033895 5 PIRAGEIVVFNVDGREIPIVHRVIKVHE 32 (109)
Q Consensus 5 ~~~~GDIIvf~~~g~~~~itHRVi~v~~ 32 (109)
.+++||-+.|+..+... ..|+++-+
T Consensus 39 ~mk~GD~vifY~s~~~~---~~ivai~~ 63 (143)
T PF01878_consen 39 RMKPGDKVIFYHSGCKE---RGIVAIGE 63 (143)
T ss_dssp C--TT-EEEEEETSSSS----EEEEEEE
T ss_pred cCCCCCEEEEEEcCCCC---CEEEEEEE
Confidence 68999999999877222 44444443
No 92
>cd03688 eIF2_gamma_II eIF2_gamma_II: this subfamily represents the domain II of the gamma subunit of eukaryotic translation initiation factor 2 (eIF2-gamma) found in Eukaryota and Archaea. eIF2 is a G protein that delivers the methionyl initiator tRNA to the small ribosomal subunit and releases it upon GTP hydrolysis after the recognition of the initiation codon. eIF2 is composed three subunits, alpha, beta and gamma. Subunit gamma shows strongest conservation, and it confers both tRNA binding and GTP/GDP binding.
Probab=20.95 E-value=2.9e+02 Score=19.04 Aligned_cols=63 Identities=17% Similarity=0.317 Sum_probs=42.3
Q ss_pred CCCCcCcEEEEeeC------C--ccccEEEEEEEEEecCCCCeeEEEEeCCCCCC---CChhhhccCccccccceEeceE
Q 033895 4 DPIRAGEIVVFNVD------G--REIPIVHRVIKVHERQDTGEVEVLTKGDNNYG---DDRLLYAQGQLWLKRQHIMGRA 72 (109)
Q Consensus 4 ~~~~~GDIIvf~~~------g--~~~~itHRVi~v~~~~~~g~~~~iTKGD~N~~---~D~~~y~~~~~~V~~~~v~G~v 72 (109)
..+++||-|--.+- + .-.++.-+|+++.... ....+.+=||+=-. =||.+ -+++..+|.|
T Consensus 38 G~lkvgdeIEIrpg~~~~~~~~~~~~pi~T~I~sl~~~~--~~l~~a~pGgliGvgT~Ldpsl-------tk~D~l~GqV 108 (113)
T cd03688 38 GVLKVGDEIEIRPGIVVKDEGKIKCRPIFTKIVSLKAEN--NDLQEAVPGGLIGVGTKLDPTL-------TKADRLVGQV 108 (113)
T ss_pred EEEeCCCEEEEeeceeeecCCCeeEEEEEEEEEEEEecC--ccccEEeCCCeEEEccccCccc-------cccceeeEEE
Confidence 35678888866421 1 1146888999998773 45567777887555 78876 3457788888
Q ss_pred EEE
Q 033895 73 VGF 75 (109)
Q Consensus 73 ~~~ 75 (109)
+..
T Consensus 109 ~g~ 111 (113)
T cd03688 109 VGE 111 (113)
T ss_pred eec
Confidence 754
No 93
>PF03120 DNA_ligase_OB: NAD-dependent DNA ligase OB-fold domain; InterPro: IPR004150 DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This family is a small domain found after the adenylation domain DNA_ligase_N in NAD+-dependent ligases (IPR001679 from INTERPRO). OB-fold domains generally are involved in nucleic acid binding.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 2OWO_A 1TAE_A 3UQ8_A 1DGS_A 1V9P_B 3SGI_A.
Probab=20.95 E-value=1.2e+02 Score=19.66 Aligned_cols=26 Identities=35% Similarity=0.502 Sum_probs=15.4
Q ss_pred CCCCcCcEEEEeeCCccccEEEEEEE
Q 033895 4 DPIRAGEIVVFNVDGREIPIVHRVIK 29 (109)
Q Consensus 4 ~~~~~GDIIvf~~~g~~~~itHRVi~ 29 (109)
-++.+||.|.....|+-+|-+.+++.
T Consensus 48 ~~i~~Gd~V~V~raGdVIP~I~~vv~ 73 (82)
T PF03120_consen 48 LDIRIGDTVLVTRAGDVIPKIVGVVK 73 (82)
T ss_dssp TT-BBT-EEEEEEETTTEEEEEEE-G
T ss_pred cCCCCCCEEEEEECCCccceEeEeeh
Confidence 47889999988777774444444443
No 94
>PRK05467 Fe(II)-dependent oxygenase superfamily protein; Provisional
Probab=20.85 E-value=1.2e+02 Score=23.23 Aligned_cols=22 Identities=32% Similarity=0.626 Sum_probs=14.3
Q ss_pred CCcCcEEEEeeCCccccEEEEEEEEEe
Q 033895 6 IRAGEIVVFNVDGREIPIVHRVIKVHE 32 (109)
Q Consensus 6 ~~~GDIIvf~~~g~~~~itHRVi~v~~ 32 (109)
.+.||+|+|.. -..|+|..|+.
T Consensus 145 p~aG~~vlfps-----~~lH~v~pVt~ 166 (226)
T PRK05467 145 LPAGDLVLYPS-----TSLHRVTPVTR 166 (226)
T ss_pred cCCCeEEEECC-----CCceeeeeccC
Confidence 35777777753 25587777764
No 95
>PF02038 ATP1G1_PLM_MAT8: ATP1G1/PLM/MAT8 family; InterPro: IPR000272 The FXYD protein family contains at least seven members in mammals []. Two other family members that are not obvious orthologs of any identified mammalian FXYD protein exist in zebrafish. All these proteins share a signature sequence of six conserved amino acids comprising the FXYD motif in the NH2-terminus, and two glycines and one serine residue in the transmembrane domain. FXYD proteins are widely distributed in mammalian tissues with prominent expression in tissues that perform fluid and solute transport or that are electrically excitable. Initial functional characterisation suggested that FXYD proteins act as channels or as modulators of ion channels however studies have revealed that most FXYD proteins have another specific function and act as tissue-specific regulatory subunits of the Na,K-ATPase. Each of these auxiliary subunits produces a distinct functional effect on the transport characteristics of the Na,K-ATPase that is adjusted to the specific functional demands of the tissue in which the FXYD protein is expressed. FXYD proteins appear to preferentially associate with Na,K-ATPase alpha1-beta isozymes, and affect their function in a way that render them operationally complementary or supplementary to coexisting isozymes.; GO: 0005216 ion channel activity, 0006811 ion transport, 0016020 membrane; PDB: 2JO1_A 2JP3_A 2ZXE_G 3A3Y_G 3N23_E 3B8E_H 3KDP_G 3N2F_E.
Probab=20.47 E-value=1.2e+02 Score=18.11 Aligned_cols=16 Identities=31% Similarity=0.270 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHhhhcC
Q 033895 93 KYILIGALGLLVITSK 108 (109)
Q Consensus 93 ~~~i~~~l~~~~l~~~ 108 (109)
..+++.++|+++++++
T Consensus 21 ~A~vlfi~Gi~iils~ 36 (50)
T PF02038_consen 21 FAGVLFILGILIILSG 36 (50)
T ss_dssp HHHHHHHHHHHHHCTT
T ss_pred HHHHHHHHHHHHHHcC
Confidence 3456667777777753
No 96
>TIGR02480 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica.
Probab=20.34 E-value=1.1e+02 Score=19.03 Aligned_cols=13 Identities=8% Similarity=0.279 Sum_probs=10.7
Q ss_pred CCCcCcEEEEeeC
Q 033895 5 PIRAGEIVVFNVD 17 (109)
Q Consensus 5 ~~~~GDIIvf~~~ 17 (109)
++++||++.+..+
T Consensus 28 ~L~~Gdvi~L~~~ 40 (77)
T TIGR02480 28 KLGEGSVIELDKL 40 (77)
T ss_pred cCCCCCEEEcCCC
Confidence 6889999999743
No 97
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=20.21 E-value=1.3e+02 Score=19.22 Aligned_cols=22 Identities=27% Similarity=0.356 Sum_probs=13.7
Q ss_pred CCcCcEEEEeeC-C--ccccEEEEE
Q 033895 6 IRAGEIVVFNVD-G--REIPIVHRV 27 (109)
Q Consensus 6 ~~~GDIIvf~~~-g--~~~~itHRV 27 (109)
+.+||+|..... . +..-|++|-
T Consensus 47 I~~GD~V~Ve~~~~d~~kg~I~~Ry 71 (75)
T COG0361 47 ILPGDVVLVELSPYDLTKGRIVYRY 71 (75)
T ss_pred eCCCCEEEEEecccccccccEEEEe
Confidence 568999998753 1 123466663
Done!