Query psy1332
Match_columns 103
No_of_seqs 102 out of 276
Neff 6.1
Searched_HMMs 46136
Date Fri Aug 16 16:28:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1332.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1332hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2917|consensus 100.0 2.9E-31 6.4E-36 198.2 9.4 99 2-102 152-250 (250)
2 PRK13760 putative RNA-associat 99.9 2.8E-26 6E-31 172.8 9.2 87 2-91 144-231 (231)
3 TIGR00291 RNA_SBDS rRNA metabo 99.9 1.3E-25 2.7E-30 169.2 9.4 86 2-90 144-230 (231)
4 PF09377 SBDS_C: SBDS protein 99.9 1.1E-24 2.4E-29 150.7 7.8 77 2-80 47-125 (125)
5 PTZ00448 hypothetical protein; 99.8 7.6E-21 1.6E-25 150.6 8.1 85 2-96 152-239 (373)
6 COG1500 Predicted exosome subu 99.8 4.3E-20 9.4E-25 138.5 8.0 89 2-93 144-233 (234)
7 cd04097 mtEFG1_C mtEFG1_C: C-t 97.7 0.00035 7.6E-09 43.8 7.2 66 22-89 4-69 (78)
8 PF00679 EFG_C: Elongation fac 97.7 0.00051 1.1E-08 44.2 8.0 66 22-89 7-73 (89)
9 cd03710 BipA_TypA_C BipA_TypA_ 97.5 0.00071 1.5E-08 42.6 6.9 66 22-89 4-70 (79)
10 cd03713 EFG_mtEFG_C EFG_mtEFG_ 97.5 0.0006 1.3E-08 42.6 6.3 66 22-89 4-69 (78)
11 cd01514 Elongation_Factor_C El 97.4 0.00078 1.7E-08 42.1 6.3 66 22-89 4-70 (79)
12 cd04096 eEF2_snRNP_like_C eEF2 97.4 0.00064 1.4E-08 42.7 5.9 66 22-89 4-71 (80)
13 cd03711 Tet_C Tet_C: C-terminu 97.4 0.0012 2.6E-08 41.4 7.0 66 22-89 4-69 (78)
14 PF09186 DUF1949: Domain of un 97.4 0.0015 3.3E-08 37.8 6.7 55 29-84 2-56 (56)
15 cd04098 eEF2_C_snRNP eEF2_C_sn 97.3 0.00099 2.1E-08 42.2 6.0 66 22-89 4-71 (80)
16 cd03709 lepA_C lepA_C: This fa 97.3 0.0015 3.3E-08 41.3 6.9 66 22-89 4-71 (80)
17 smart00838 EFG_C Elongation fa 97.2 0.0016 3.5E-08 41.4 6.3 66 22-89 6-71 (85)
18 TIGR00257 IMPACT_YIGZ uncharac 96.1 0.085 1.8E-06 39.4 9.4 66 24-90 137-202 (204)
19 PRK11568 hypothetical protein; 96.1 0.082 1.8E-06 39.5 9.2 65 24-89 137-201 (204)
20 PRK05433 GTP-binding protein L 93.6 0.29 6.3E-06 41.6 7.0 65 22-88 407-472 (600)
21 PRK12740 elongation factor G; 92.7 0.33 7.1E-06 41.2 6.0 71 17-89 580-650 (668)
22 TIGR01393 lepA GTP-binding pro 92.7 0.56 1.2E-05 39.9 7.3 65 22-88 403-469 (595)
23 PRK12739 elongation factor G; 92.4 0.39 8.4E-06 41.2 6.1 69 19-89 600-668 (691)
24 PRK00007 elongation factor G; 91.7 0.52 1.1E-05 40.5 6.1 68 20-89 604-671 (693)
25 PRK07560 elongation factor EF- 91.7 0.37 8E-06 41.7 5.2 71 17-89 623-693 (731)
26 TIGR01394 TypA_BipA GTP-bindin 91.5 1.1 2.3E-05 38.2 7.7 66 22-89 397-463 (594)
27 PRK13351 elongation factor G; 91.1 0.77 1.7E-05 39.2 6.5 71 17-89 597-668 (687)
28 TIGR00484 EF-G translation elo 90.7 0.8 1.7E-05 39.3 6.2 67 21-89 602-668 (689)
29 PLN00116 translation elongatio 90.3 0.53 1.1E-05 41.5 4.9 69 19-89 727-797 (843)
30 PRK10218 GTP-binding protein; 89.7 1.6 3.5E-05 37.3 7.3 66 22-89 401-467 (607)
31 PF14257 DUF4349: Domain of un 89.3 1.7 3.7E-05 32.7 6.5 62 17-80 49-117 (262)
32 KOG0465|consensus 88.6 0.9 2E-05 39.5 4.9 66 21-88 635-700 (721)
33 COG1739 Uncharacterized conser 87.3 2.7 5.8E-05 31.3 6.3 65 23-89 137-201 (203)
34 PTZ00416 elongation factor 2; 86.5 1.3 2.9E-05 39.0 4.9 71 17-89 718-790 (836)
35 TIGR00490 aEF-2 translation el 85.9 1.5 3.3E-05 37.9 4.9 71 17-89 621-691 (720)
36 TIGR00119 acolac_sm acetolacta 74.9 18 0.0004 25.8 6.6 67 17-91 81-147 (157)
37 PRK11895 ilvH acetolactate syn 72.4 24 0.00052 25.3 6.7 67 17-91 82-148 (161)
38 COG0480 FusA Translation elong 72.1 8.6 0.00019 33.7 5.1 75 13-89 594-671 (697)
39 PTZ00204 hypothetical protein; 69.9 4.6 0.0001 27.3 2.4 38 45-88 50-88 (120)
40 PF09149 DUF1935: Domain of un 67.7 5.4 0.00012 26.7 2.4 41 21-69 44-84 (104)
41 CHL00100 ilvH acetohydroxyacid 60.9 48 0.001 24.1 6.5 67 17-91 82-148 (174)
42 PF06680 DUF1181: Protein of u 56.6 9.7 0.00021 25.7 2.1 38 45-88 50-88 (120)
43 TIGR02058 lin0512_fam conserve 52.9 20 0.00044 24.7 3.2 36 11-47 38-78 (116)
44 PRK13883 conjugal transfer pro 51.4 56 0.0012 23.4 5.4 45 4-50 37-81 (151)
45 COG0440 IlvH Acetolactate synt 45.9 1.1E+02 0.0025 22.1 6.6 68 16-91 83-150 (163)
46 KOG2943|consensus 45.5 47 0.001 26.1 4.5 34 16-49 204-237 (299)
47 PF09078 CheY-binding: CheY bi 43.8 78 0.0017 19.6 5.5 35 30-65 8-42 (65)
48 PF00542 Ribosomal_L12: Riboso 42.4 49 0.0011 20.3 3.5 44 5-50 14-66 (68)
49 PF07283 TrbH: Conjugal transf 41.8 68 0.0015 22.1 4.5 45 4-50 9-53 (121)
50 PRK13835 conjugal transfer pro 41.1 93 0.002 22.2 5.2 44 4-50 43-86 (145)
51 PF01267 F-actin_cap_A: F-acti 39.0 12 0.00026 28.9 0.5 17 6-22 242-258 (271)
52 PF14183 YwpF: YwpF-like prote 38.9 60 0.0013 22.9 3.9 33 49-81 30-62 (135)
53 PF09585 Lin0512_fam: Conserve 38.7 31 0.00067 23.6 2.4 24 10-33 37-60 (113)
54 COG1458 Predicted DNA-binding 38.3 22 0.00048 26.9 1.7 63 17-79 38-106 (221)
55 COG1458 Predicted DNA-binding 37.7 22 0.00047 27.0 1.6 20 59-78 45-64 (221)
56 KOG0467|consensus 36.9 64 0.0014 29.2 4.5 71 17-89 748-820 (887)
57 PF01037 AsnC_trans_reg: AsnC 32.8 1E+02 0.0022 17.7 6.2 49 30-80 5-56 (74)
58 KOG1145|consensus 32.0 62 0.0013 28.4 3.6 49 1-55 239-288 (683)
59 PF10369 ALS_ss_C: Small subun 29.9 1.4E+02 0.003 18.4 7.9 68 18-93 1-68 (75)
60 TIGR01573 cas2 CRISPR-associat 29.3 1.6E+02 0.0034 18.8 6.8 58 30-94 9-72 (95)
61 PRK12483 threonine dehydratase 28.3 1.7E+02 0.0037 24.7 5.6 63 15-79 379-463 (521)
62 PF14085 DUF4265: Domain of un 27.9 1.9E+02 0.0041 19.3 6.3 41 35-79 67-108 (117)
63 cd02978 KaiB_like KaiB-like fa 26.8 1.7E+02 0.0036 18.3 4.6 23 73-95 22-44 (72)
64 cd04904 ACT_AAAH ACT domain of 26.8 1.5E+02 0.0033 17.8 4.6 53 24-80 3-63 (74)
65 cd06406 PB1_P67 A PB1 domain i 26.6 1.8E+02 0.0039 18.6 4.4 35 60-94 12-47 (80)
66 cd01208 X11 X11 Phosphotyrosin 25.9 74 0.0016 23.0 2.6 30 1-31 29-59 (156)
67 PF11495 Regulator_TrmB: Archa 25.4 1.1E+02 0.0024 22.5 3.6 36 7-46 11-46 (233)
68 COG2262 HflX GTPases [General 25.1 87 0.0019 26.0 3.2 50 22-76 360-409 (411)
69 PF05951 Peptidase_M15_2: Bact 23.8 1.8E+02 0.0038 20.8 4.3 62 21-93 18-79 (152)
70 PF11890 DUF3410: Domain of un 23.8 48 0.001 20.9 1.3 28 6-35 47-74 (82)
71 PF06189 5-nucleotidase: 5'-nu 23.8 1.6E+02 0.0035 23.0 4.3 44 3-48 168-213 (264)
72 PRK11898 prephenate dehydratas 23.7 2.4E+02 0.0053 21.7 5.4 74 18-93 193-275 (283)
73 cd04446 DEP_DEPDC4 DEP (Dishev 23.3 73 0.0016 21.0 2.1 22 6-27 3-24 (95)
74 PF10440 WIYLD: Ubiquitin-bind 23.2 84 0.0018 19.4 2.2 16 64-79 45-60 (65)
75 COG4492 PheB ACT domain-contai 23.1 2.1E+02 0.0046 20.5 4.4 44 3-46 88-139 (150)
76 cd02861 E_set_proteins_like E 22.8 59 0.0013 19.9 1.5 15 56-70 35-49 (82)
77 PF08679 DsrD: Dissimilatory s 22.3 1.7E+02 0.0038 18.2 3.5 35 30-64 29-63 (67)
78 TIGR02654 circ_KaiB circadian 21.6 1.4E+02 0.003 19.5 3.1 22 74-95 25-46 (87)
79 PF14581 SseB_C: SseB protein 21.6 2.3E+02 0.005 18.1 5.9 72 21-94 5-90 (108)
80 PF01206 TusA: Sulfurtransfera 21.4 1.8E+02 0.004 16.9 5.8 29 35-63 40-68 (70)
81 PF12651 RHH_3: Ribbon-helix-h 21.4 89 0.0019 17.4 1.9 16 22-37 1-16 (44)
82 PF06816 NOD: NOTCH protein; 20.5 25 0.00055 21.1 -0.5 26 55-80 5-31 (57)
83 PF02108 FliH: Flagellar assem 20.3 1.1E+02 0.0024 19.7 2.5 24 16-43 64-87 (128)
No 1
>KOG2917|consensus
Probab=99.97 E-value=2.9e-31 Score=198.20 Aligned_cols=99 Identities=56% Similarity=0.828 Sum_probs=96.1
Q ss_pred ccHhHHHHhhhhhcCccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhc
Q psy1332 2 YYYSQVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTET 81 (103)
Q Consensus 2 ~QalevIk~Lk~~iPI~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~t 81 (103)
+||||||++|+++|||+||+|+|||+ +|.+..+.+.+++.++...+++|||++++|+++|+|+||+||+|+++++++|
T Consensus 152 ~QaleaIkkL~~~~pI~rarMrlRv~--v~~~~~~~l~ekl~~l~~~ve~e~~~~~~~~~~~lI~pg~fr~~d~lvr~et 229 (250)
T KOG2917|consen 152 QQALEAIKKLKEKMPIERARMRLRVS--VPVKEGKELKEKLKELIDSVESEDWDPDQLECVCLIDPGCFREIDELVRKET 229 (250)
T ss_pred HHHHHHHHHHHHhCchhhhceeEEEE--EeccchHHHHHHHHHHhhccccccCCCCceEEEEEEcCCchHHHHHHHhhhc
Confidence 69999999999999999999999999 9999999999999999999999999989999999999999999999999999
Q ss_pred CCceEEEEEEeeeeecCcccc
Q psy1332 82 RGQGTLELLNLKEVTEGEEVL 102 (103)
Q Consensus 82 kG~g~vevl~~~~~~eg~~~~ 102 (103)
||+|+++||+++++.+|++.+
T Consensus 230 k~kg~leiL~~~e~~e~e~~~ 250 (250)
T KOG2917|consen 230 KGKGRLEILDLKEVEEGEECF 250 (250)
T ss_pred cccceEEEEeecccccccccC
Confidence 999999999999999999764
No 2
>PRK13760 putative RNA-associated protein; Provisional
Probab=99.93 E-value=2.8e-26 Score=172.77 Aligned_cols=87 Identities=20% Similarity=0.328 Sum_probs=83.1
Q ss_pred ccHhHHHHhhhhhcCccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeee-CCeEEEEEEeCCCChHHHHHHHhhh
Q psy1332 2 YYYSQVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWS-GGGLLLICLIDPGKYREIDELVRTE 80 (103)
Q Consensus 2 ~QalevIk~Lk~~iPI~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~-~~~~~~v~~I~Pg~~r~i~~lv~~~ 80 (103)
+||+++||+|+++|||+||+|+++|+ +|.++++++++.|.+++. +++|+|. ||+|.++++||||+||+|+++++++
T Consensus 144 ~Qa~~vik~L~~~iPi~~~~~~~~v~--iP~~~~~~~~~~l~~~~~-i~~eew~~dgs~~~v~~Ip~G~~~~~~~~~~~~ 220 (231)
T PRK13760 144 EQVKDIVKALRPIIPIKFEKARIAVK--IPPEYAGKAYGELRKFGE-IKKEEWQSDGSWIAVLEIPAGLQNEFYDKLNKL 220 (231)
T ss_pred HHHHHHHHHHHHhCCcceeeEEEEEE--ECHHHHHHHHHHHHhhcc-cchhhccCCCcEEEEEEECCccHHHHHHHHHHh
Confidence 69999999999999999999999999 999999999999999884 8999995 7899999999999999999999999
Q ss_pred cCCceEEEEEE
Q psy1332 81 TRGQGTLELLN 91 (103)
Q Consensus 81 tkG~g~vevl~ 91 (103)
|||+|++++|.
T Consensus 221 tkG~~~~~vl~ 231 (231)
T PRK13760 221 TKGEAETKVLK 231 (231)
T ss_pred cCCcEEEEEcC
Confidence 99999999973
No 3
>TIGR00291 RNA_SBDS rRNA metabolism protein, SBDS family. This protein family, possibly universal in both archaea and eukaryotes, appears to be involved in (ribosomal) RNA metabolism. Mutations in the human ortholog are associated with Shwachman-Bodian-Diamond syndrome.
Probab=99.93 E-value=1.3e-25 Score=169.23 Aligned_cols=86 Identities=22% Similarity=0.402 Sum_probs=82.9
Q ss_pred ccHhHHHHhhhhhcCccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeee-CCeEEEEEEeCCCChHHHHHHHhhh
Q psy1332 2 YYYSQVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWS-GGGLLLICLIDPGKYREIDELVRTE 80 (103)
Q Consensus 2 ~QalevIk~Lk~~iPI~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~-~~~~~~v~~I~Pg~~r~i~~lv~~~ 80 (103)
+||+++||+|+++|||+||+|+++|+ +|.++++++++.|.+++. +++|+|. ||+|.++++||||+||+|+++++++
T Consensus 144 ~Qa~~vik~L~~iiPI~ra~m~i~v~--ip~~~~~~~~~~l~~~~~-i~~eew~~dgs~~~v~~I~pg~~~~~~~~l~~~ 220 (231)
T TIGR00291 144 EQVLEIVKALKQIIPIKFEKMKVAIK--IPPERAGEAIEAISNFGA-VTPEEWQEDGSWICVGEIPSGNYRDLMTLLDKK 220 (231)
T ss_pred HHHHHHHHHHhhhCCeeEeeEEEEEE--eCHHHHHHHHHHHHHhcc-cchhhccCCCcEEEEEEECCccHHHHHHHHHhh
Confidence 69999999999999999999999999 999999999999999997 8999995 7899999999999999999999999
Q ss_pred cCCceEEEEE
Q psy1332 81 TRGQGTLELL 90 (103)
Q Consensus 81 tkG~g~vevl 90 (103)
|+|++.+++|
T Consensus 221 tkG~~~~k~~ 230 (231)
T TIGR00291 221 TKGNVLTKVV 230 (231)
T ss_pred cCCeeEEEEe
Confidence 9999999986
No 4
>PF09377 SBDS_C: SBDS protein C-terminal domain; InterPro: IPR018978 This entry represents the C-terminal domain of proteins that are highly conserved in species ranging from archaea to vertebrates and plants []. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS, OMIM 260400) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. It is characterised by bone marrow failure and leukemia predisposition. Members of this family play a role in RNA metabolism [, ]. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes. Together with the EF-2-like GTPase RIA1 (EfI1), it triggers the GTP-dependent release of TIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for translation competence by allowing 80S ribosome assembly and facilitating TIF6 recycling to the nucleus, where it is required for 60S rRNA processing and nuclear export. This data links defective late 60S subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition []. A number of uncharacterised hydrophilic proteins of about 30 kDa share regions of similarity. These include, Mouse protein 22A3. Saccharomyces cerevisiae chromosome XII hypothetical protein YLR022c. Caenorhabditis elegans hypothetical protein W06E11.4. Methanocaldococcus jannaschii (Methanococcus jannaschii) hypothetical protein MJ0592. ; GO: 0042254 ribosome biogenesis; PDB: 2KDO_A 2L9N_A 2WBM_B 1P9Q_C 1T95_A.
Probab=99.91 E-value=1.1e-24 Score=150.70 Aligned_cols=77 Identities=45% Similarity=0.660 Sum_probs=70.7
Q ss_pred ccHhHHHHhhhh--hcCccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhh
Q psy1332 2 YYYSQVIPTLKQ--CMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRT 79 (103)
Q Consensus 2 ~QalevIk~Lk~--~iPI~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~ 79 (103)
+|||++||+|++ +|||+||+|+++|+ +|.++++++++.|.+++..+++++|++|+|+++|+||||+||+|++++++
T Consensus 47 ~QalevIk~L~~~~~ipI~ra~m~l~v~--ip~~~~~~~~~~l~~~~~~i~~~~~~~~~~~~~~~i~pg~~r~l~~~v~~ 124 (125)
T PF09377_consen 47 QQALEVIKKLKEKQIIPIKRAKMRLRVT--IPSKYAKKVKDKLLKLGAKIEEEEQNDGSWEMVFLIDPGLYRELDELVNK 124 (125)
T ss_dssp HHHHHHHHHHTT--TS--EEEEEEEEEE--EBCCCHHHHHHHHHHHSEEEEEEEETTSCEEEEEEEEGGGHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCceeeeeEEEEEE--eCHHHHHHHHHHHHHhhcEeeecccCCCeEEEEEEECCcchHHHHHHHcc
Confidence 599999999998 99999999999999 99999999999999999877666667999999999999999999999998
Q ss_pred h
Q psy1332 80 E 80 (103)
Q Consensus 80 ~ 80 (103)
|
T Consensus 125 e 125 (125)
T PF09377_consen 125 E 125 (125)
T ss_dssp H
T ss_pred C
Confidence 5
No 5
>PTZ00448 hypothetical protein; Provisional
Probab=99.84 E-value=7.6e-21 Score=150.64 Aligned_cols=85 Identities=27% Similarity=0.367 Sum_probs=77.2
Q ss_pred ccHhHHHHhhhhhcC--ccceeeEEEEEEeeCcchHHHHHHHHHhh-cccceeeeeeCCeEEEEEEeCCCChHHHHHHHh
Q psy1332 2 YYYSQVIPTLKQCMS--IERAQMRVRVEVSAGVKDVKKLKEKLVKC-ATSVENEEWSGGGLLLICLIDPGKYREIDELVR 78 (103)
Q Consensus 2 ~QalevIk~Lk~~iP--I~RA~Mrl~v~~~ip~~~~~~~~~~l~~~-~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~ 78 (103)
+||+++||+|+++|| |+||+|+|+|+ .|......++++|.++ ...++.++| ++.|+++|+||||+||.|+++
T Consensus 152 ~Qalevik~L~~iiPikiera~m~vki~--~~~~~~~~~~~~l~~~~~~~~~~e~~-~~~~~~~~~idP~~yR~~~~l-- 226 (373)
T PTZ00448 152 EQALKAFDILKKRIPDQIERAKMMLKLS--VDIVNKQNITKKLNEFNVFPISSEEK-HNTYSITFLCEPRYYREIDQL-- 226 (373)
T ss_pred HHHHHHHHHHHHhCCcceeEEEEEEEEe--cccccHHHHHHHHhhccccccccccc-CCceEEEEEECCccccchhcc--
Confidence 699999999999999 99999999998 8877788999999999 555788888 567999999999999999996
Q ss_pred hhcCCceEEEEEEeeeee
Q psy1332 79 TETRGQGTLELLNLKEVT 96 (103)
Q Consensus 79 ~~tkG~g~vevl~~~~~~ 96 (103)
.|+++||+++++.
T Consensus 227 -----~g~l~v~~~~v~~ 239 (373)
T PTZ00448 227 -----DCKLLLLDSNVKT 239 (373)
T ss_pred -----CceeEEEeeeccc
Confidence 7899999999998
No 6
>COG1500 Predicted exosome subunit [Translation, ribosomal structure and biogenesis]
Probab=99.82 E-value=4.3e-20 Score=138.53 Aligned_cols=89 Identities=24% Similarity=0.346 Sum_probs=84.3
Q ss_pred ccHhHHHHhhhhhcCccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeee-CCeEEEEEEeCCCChHHHHHHHhhh
Q psy1332 2 YYYSQVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWS-GGGLLLICLIDPGKYREIDELVRTE 80 (103)
Q Consensus 2 ~QalevIk~Lk~~iPI~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~-~~~~~~v~~I~Pg~~r~i~~lv~~~ 80 (103)
+||+++||+|++++||.+++++++|. +|+++++++++.+.+++. +..++|. ||+|.|+.+||||+|+++++++++.
T Consensus 144 ~Qv~evlK~l~~i~pIrfera~vaVk--ip~e~~~k~~~~l~k~g~-i~~eew~~dgsw~~~~~ipaG~q~e~~~~l~~~ 220 (234)
T COG1500 144 EQVQEVLKALRPIIPIRFERAKVAVK--IPVEYAGKAYGLLRKFGE-IKKEEWQEDGSWICVLEIPAGNQDEFYELLNEL 220 (234)
T ss_pred HHHHHHHHHHhhcCCceeeeeeEEEE--ecccccchHHHHHHHhhh-hhhhhcccCCceEEEEeeCcchHHHHHHHHHHh
Confidence 59999999999999999999999999 999999999999999995 9999994 9999999999999999999999999
Q ss_pred cCCceEEEEEEee
Q psy1332 81 TRGQGTLELLNLK 93 (103)
Q Consensus 81 tkG~g~vevl~~~ 93 (103)
++|.+.++++...
T Consensus 221 ~kG~~q~k~l~~~ 233 (234)
T COG1500 221 TKGEVQTKVLKVA 233 (234)
T ss_pred cCCcceeeeeeec
Confidence 9999998888653
No 7
>cd04097 mtEFG1_C mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals (desig
Probab=97.67 E-value=0.00035 Score=43.84 Aligned_cols=66 Identities=17% Similarity=0.173 Sum_probs=56.8
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
|++.|+ +|.++.+++...|.+-...+.+.+..++...+.+.+|-...-.+.+-+++.|+|+|....
T Consensus 4 ~~~~I~--~p~~~~g~v~~~l~~rrg~i~~~~~~~~~~~i~~~~P~~e~~g~~~~Lr~~T~G~~~~~~ 69 (78)
T cd04097 4 MKVEVT--APTEFQGNVIGLLNKRKGTIVDTDTGEDEFTLEAEVPLNDMFGYSTELRSMTQGKGEFSM 69 (78)
T ss_pred EEEEEE--ecHHHHHHHHHHHHHCCCEEeceEecCCeEEEEEEECHHHhhChHHHHHhhCCCcEEEEE
Confidence 567777 999999999999999888777665546778999999999988999999999999998753
No 8
>PF00679 EFG_C: Elongation factor G C-terminus; InterPro: IPR000640 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position [, ]. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. This entry represents the C-terminal domain found in EF2 (or EF-G) of both prokaryotes and eukaryotes (also known as eEF2), as well as in some tetracycline-resistance proteins. This domain adopts a ferredoxin-like fold consisting of an alpha/beta sandwich with anti-parallel beta-sheets. It resembles the topology of domain III found in these elongation factors, with which it forms the C-terminal block, but these two domains cannot be superimposed []. This domain is often found associated with (IPR000795 from INTERPRO), which contains the signatures for the N terminus of the proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 1WDT_A 2DY1_A 3CB4_F 3DEG_C 2EFG_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y ....
Probab=97.66 E-value=0.00051 Score=44.17 Aligned_cols=66 Identities=15% Similarity=0.172 Sum_probs=56.4
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeeee-CCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWS-GGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~-~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
|++.|. +|.++.++++..|.+..+.+.+.+-. ++...+.+.+|-..-..+..-+++.|+|+|....
T Consensus 7 ~~~~I~--~p~~~~g~v~~~l~~r~g~i~~~~~~~~~~~~i~~~iP~~~~~gf~~~Lr~~T~G~a~~~~ 73 (89)
T PF00679_consen 7 MSVEIS--VPEEYLGKVISDLSKRRGEILSMDPIGGDRVVIEAEIPVRELFGFRSELRSLTSGRASFSM 73 (89)
T ss_dssp EEEEEE--EEGGGHHHHHHHHHHTT-EEEEEEEESTTEEEEEEEEEGGGHTTHHHHHHHHTTTS-EEEE
T ss_pred EEEEEE--ECHHHHHHHHHHhcccccEEEechhhhhhheeEEEEEChhhhhhHHHHhhccCCCEEEEEE
Confidence 667777 99999999999999999888776665 7889999999999888999999999999998764
No 9
>cd03710 BipA_TypA_C BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secreti
Probab=97.50 E-value=0.00071 Score=42.63 Aligned_cols=66 Identities=21% Similarity=0.166 Sum_probs=56.2
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeC-CeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSG-GGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~-~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
|++.|+ +|.++.+++.+.|.+....+...+..+ +.+.+.+.+|-...-.+.+-+++.|+|.|....
T Consensus 4 ~~v~I~--~P~~~~g~V~~~l~~rrg~i~~~~~~~~~~~~i~~~~P~~~~~~~~~~Lrs~T~G~a~~~~ 70 (79)
T cd03710 4 EELTID--VPEEYSGAVIEKLGKRKGEMVDMEPDGNGRTRLEFKIPSRGLIGFRSEFLTDTRGTGIMNH 70 (79)
T ss_pred EEEEEE--eCchhhHHHHHHHHhCCCEEEccEECCCCEEEEEEEECHHHHcCcHHHHHhhCCCeEEEEE
Confidence 677788 999999999999999988777666544 678899999988888889999999999997653
No 10
>cd03713 EFG_mtEFG_C EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide
Probab=97.47 E-value=0.0006 Score=42.56 Aligned_cols=66 Identities=17% Similarity=0.205 Sum_probs=56.1
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
|++.|+ +|.++.++++..|.+-...+.+.+..++...+.+.+|-...-.+.+-+++.|+|.|....
T Consensus 4 ~~~~I~--~p~~~~g~v~~~l~~rrg~i~~~~~~~~~~~i~~~iP~~e~~~~~~~Lr~~T~G~a~~~~ 69 (78)
T cd03713 4 MKVEVT--VPEEYMGDVIGDLSSRRGQILGTESRGGWKVIKAEVPLAEMFGYSTDLRSLTQGRGSFTM 69 (78)
T ss_pred EEEEEE--cCHHHHHHHHHHHHHcCCceEceeccCCcEEEEEEcCHHHHhChHHHHHhhcCCeEEEEE
Confidence 677778 999999999999999887777655546788999999988888899999999999998643
No 11
>cd01514 Elongation_Factor_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p. This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain. EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the
Probab=97.42 E-value=0.00078 Score=42.05 Aligned_cols=66 Identities=15% Similarity=0.206 Sum_probs=56.6
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeC-CeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSG-GGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~-~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
|++.|+ +|.++.+++.+.|.+....+.+.+..+ +.+.+.+.+|-...-.+.+.++..|+|.|....
T Consensus 4 ~~~~I~--~p~~~~g~v~~~l~~rrg~v~~~~~~~~~~~~i~~~iP~~e~~g~~~~lr~~T~G~~~~~~ 70 (79)
T cd01514 4 MKVEIT--VPEEYLGAVIGDLSKRRGEILGMEPRGTGRVVIKAELPLAEMFGFATDLRSLTQGRASFSM 70 (79)
T ss_pred EEEEEE--cCHHHHHHHHHHHHhcCCeeEeeEecCCCeEEEEEECCHHHHcCcHHHhhhhcCCeEEEEE
Confidence 567777 999999999999999888777655545 789999999999999999999999999998754
No 12
>cd04096 eEF2_snRNP_like_C eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=97.41 E-value=0.00064 Score=42.69 Aligned_cols=66 Identities=20% Similarity=0.146 Sum_probs=55.3
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCe--EEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGG--LLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~--~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
|++.|+ +|.++.+++...|.+....+...+..+++ ..+.+.+|-...-.+.+.++..|+|.|....
T Consensus 4 ~~~~I~--~p~~~~g~V~~~l~~rrg~i~~~~~~~~~~~~~i~~~iP~~e~~~~~~~Lrs~T~G~~~~~~ 71 (80)
T cd04096 4 YLVEIQ--CPEDALGKVYSVLSKRRGHVLSEEPKEGTPLFEIKAYLPVIESFGFETDLRSATSGQAFPQL 71 (80)
T ss_pred EEEEEE--EcHHHhhHHHHhhhhCeeEEeEEeecCCCccEEEEEEEeHHHHhCcHHHHHhhCCCCcEEEE
Confidence 677788 99999999999999988877665553333 8899999998888899999999999998754
No 13
>cd03711 Tet_C Tet_C: C-terminus of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to the C terminal domains of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA.
Probab=97.40 E-value=0.0012 Score=41.36 Aligned_cols=66 Identities=20% Similarity=0.289 Sum_probs=56.1
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
|++.|+ +|.++.+++...|.+....+.+.+..++...+.+.+|-...-.+.+-+++.|+|.|....
T Consensus 4 ~~~~i~--~p~~~~g~v~~~l~~rrg~i~~~~~~~~~~~i~~~~P~~~~~g~~~~Lr~~T~G~~~~~~ 69 (78)
T cd03711 4 LRFELE--VPQDALGRAMSDLAKMGATFEDPQIKGDEVTLEGTIPVATSQDYQSELPSYTHGEGVLET 69 (78)
T ss_pred EEEEEE--cCHHHHHHHHHHHHHcCCEeeCcEecCCEEEEEEEECHHHHhhHHHHhHhhcCCeEEEEE
Confidence 677788 999999999999999888777655546789999999988888888889999999998643
No 14
>PF09186 DUF1949: Domain of unknown function (DUF1949); InterPro: IPR015269 Members of this entry are a set of functionally uncharacterised hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a beta-alpha-beta-beta-alpha-beta arrangement []. This entry contains the protein Impact, which is a translational regulator that ensures constant high levels of translation under amino acid starvation. It acts by interacting with Gcn1/Gcn1L1, thereby preventing activation of Gcn2 protein kinases (EIF2AK1 to 4) and subsequent down-regulation of protein synthesis. It is evolutionary conserved from eukaryotes to archaea []. ; PDB: 2CVE_A 1VI7_A.
Probab=97.36 E-value=0.0015 Score=37.84 Aligned_cols=55 Identities=15% Similarity=0.241 Sum_probs=48.0
Q ss_pred eeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCc
Q psy1332 29 SAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQ 84 (103)
Q Consensus 29 ~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~ 84 (103)
++|=...+.++..|.+++..+.+++++ +...+++.|||.....+...+.+.|.|+
T Consensus 2 ~~~Y~~~~~v~~~l~~~~~~i~~~~y~-~~V~~~v~v~~~~~~~f~~~l~~~t~G~ 56 (56)
T PF09186_consen 2 SCDYSQYGKVERLLEQNGIEIVDEDYT-DDVTLTVAVPEEEVEEFKAQLTDLTSGR 56 (56)
T ss_dssp EE-CCCHHHHHHHHHHTTTEEEEEEEC-TTEEEEEEEECCCHHHHHHHHHHHTTT-
T ss_pred EechhhHHHHHHHHHHCCCEEEcceec-ceEEEEEEECHHHHHHHHHHHHHHcCCC
Confidence 477778899999999999888899994 4599999999999999999999999985
No 15
>cd04098 eEF2_C_snRNP eEF2_C_snRNP: This family includes a C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to the C-terminal domain of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=97.32 E-value=0.00099 Score=42.24 Aligned_cols=66 Identities=17% Similarity=0.100 Sum_probs=56.6
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCe--EEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGG--LLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~--~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
|++.|+ +|.++.++++..|.+....|...+..++. ..+.+.+|-..--.+.+-++..|.|+|....
T Consensus 4 ~~~ei~--~p~~~~g~v~~~L~~rrg~i~~~~~~~~~~~~~i~a~vP~~e~~~~~~~Lrs~T~G~~~~~~ 71 (80)
T cd04098 4 YEVEIT--CPADAVSAVYEVLSRRRGHVIYDTPIPGTPLYEVKAFIPVIESFGFETDLRVHTQGQAFCQS 71 (80)
T ss_pred EEEEEE--ECHHHHhHHHHHHhhCCcEEeeeeccCCCCcEEEEEECCHHHHhChHHHHHhhCCCceEEEE
Confidence 778888 99999999999999998888776664555 7899999998888889999999999997643
No 16
>cd03709 lepA_C lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane. LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits significant homology to elongation factors (EFs) Tu and G. The function(s) of the proteins in this family are unknown. The N-terminal domain of LepA is homologous to a domain of similar size found in initiation factor 2 (IF2), and in EF-Tu and EF-G (factors required for translation in Escherichia coli). Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including S. cerevisiae GUF1) originated within the bacterial LepA family. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage.
Probab=97.32 E-value=0.0015 Score=41.30 Aligned_cols=66 Identities=8% Similarity=0.154 Sum_probs=54.8
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeee-eCCeEEEEEEeCCCCh-HHHHHHHhhhcCCceEEEE
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEW-SGGGLLLICLIDPGKY-REIDELVRTETRGQGTLEL 89 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~-~~~~~~~v~~I~Pg~~-r~i~~lv~~~tkG~g~vev 89 (103)
|++.|. +|.++.+.+.+.|.+....+..-+. .++...+.+.+|-... ..+..-+++.|+|.|....
T Consensus 4 ~~v~i~--vP~e~~G~V~~~l~~rrG~i~~~~~~~~~~~~i~~~~P~~~~~~g~~~~L~s~T~G~g~~~~ 71 (80)
T cd03709 4 VKATII--TPSEYLGAIMELCQERRGVQKDMEYLDANRVMLTYELPLAEIVYDFFDKLKSISKGYASLDY 71 (80)
T ss_pred EEEEEE--eCHHhhHHHHHHHHHhCCEEeccEecCCCeEEEEEECCHHHHhhhHHHHhHhhcCCEEEEEE
Confidence 677778 9999999999999998887765433 3457889999998887 7888889999999998754
No 17
>smart00838 EFG_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.
Probab=97.24 E-value=0.0016 Score=41.36 Aligned_cols=66 Identities=18% Similarity=0.225 Sum_probs=55.4
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
|++.|. +|.++.+.+++.|.+-...+.+.+..++.+.+.+.+|-...-.+.+-++..|+|+|....
T Consensus 6 ~~~~I~--~p~~~~g~v~~~l~~rrG~i~~~~~~~~~~~i~~~iP~~~~~~~~~~Lrs~T~G~~~~~~ 71 (85)
T smart00838 6 MKVEVT--VPEEYMGDVIGDLNSRRGKIEGMEQRGGAQVIKAKVPLSEMFGYATDLRSATQGRATWSM 71 (85)
T ss_pred EEEEEE--eCHHHHHHHHHHHHHcCCEEECeeccCCcEEEEEECCHHHHhchHHHHHHhcCCeEEEEE
Confidence 567778 999999999999999887776554445678999999998888889999999999998753
No 18
>TIGR00257 IMPACT_YIGZ uncharacterized protein, YigZ family. This uncharacterized protein family includes YigZ, which has been crystallized, from E. coli. YigZ is homologous to the protein product of the mouse IMPACT gene. Crystallography shows a two-domain stucture, and the C-terminal domain is suggested to bind nucleic acids. The function is unknown. Note that the ortholog from E. coli was shown fused to the pepQ gene in GenBank entry X54687. This caused occasional misidentification of this protein as pepQ; this family is found in a number of species that lack pepQ.
Probab=96.10 E-value=0.085 Score=39.36 Aligned_cols=66 Identities=14% Similarity=0.192 Sum_probs=54.5
Q ss_pred EEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEEE
Q psy1332 24 VRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLELL 90 (103)
Q Consensus 24 l~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vevl 90 (103)
..+++++|-+..+++...|..++..+.++++ ++...+.+.+|+.....+.+.+.+.+.|+..++..
T Consensus 137 ~~~~~~~~y~~~~~v~~~l~~~~~~i~~~~y-~~~V~~~~~v~~~~~~~~~~~l~~~t~g~~~~~~~ 202 (204)
T TIGR00257 137 EILSLHCDYKQLDALERELKKFQLEIIKSNF-SNNVVLVEISGTKENLAFSEQLTEISLGQLILKFN 202 (204)
T ss_pred EEEEEEechhHHHHHHHHHHHCCCEEEeeEe-cCCEEEEEEECHHHHHHHHHHHHHHhCCeEEEEec
Confidence 3333338888888999999999877888888 45699999999999999999999999998777654
No 19
>PRK11568 hypothetical protein; Provisional
Probab=96.08 E-value=0.082 Score=39.45 Aligned_cols=65 Identities=14% Similarity=0.125 Sum_probs=54.0
Q ss_pred EEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 24 VRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 24 l~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
..+++++|-+..+.++..|.+++..+.+++| ++...+.+.+++.....+.+.+.+.+.|+..++.
T Consensus 137 ~~~~i~~~y~~~~~v~~~l~~~~~~i~~~~y-~~~V~~~~~v~~~~~~~~~~~l~~~t~g~~~~~~ 201 (204)
T PRK11568 137 TEYTLQCEYAQLAGIEALLGQFDGKIVNSEY-QAFVTLRVALPAAKVAEFSAKLADFSRGSLQLLA 201 (204)
T ss_pred EEEEEEECcchHHHHHHHHHHCCCEEEccee-cCCEEEEEEECHHHHHHHHHHHHHHhCCeEEEEe
Confidence 3334338888899999999999877888888 5568999999999999999999999998777653
No 20
>PRK05433 GTP-binding protein LepA; Provisional
Probab=93.60 E-value=0.29 Score=41.60 Aligned_cols=65 Identities=12% Similarity=0.147 Sum_probs=53.7
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCCh-HHHHHHHhhhcCCceEEE
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKY-REIDELVRTETRGQGTLE 88 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~-r~i~~lv~~~tkG~g~ve 88 (103)
|++.|. +|.++.+.+++.+.+.-..+..-+..++...+.+.+|-.-. .++.+-+++.|+|.|++.
T Consensus 407 ~~~~i~--~P~~~~G~vm~~~~~rRG~~~~~~~~~~~~~i~~~~Pl~e~~~~~~~~Lks~T~G~gs~~ 472 (600)
T PRK05433 407 VKATII--VPQEYVGAVMELCQEKRGVQKDMEYLGNRVELTYELPLAEIVFDFFDRLKSVSRGYASLD 472 (600)
T ss_pred EEEEEE--ecHHHHHHHHHHHHHcCCEEeCcEecCCeEEEEEEechHHhhhhHHHHhHhhcCCEEEEE
Confidence 667777 99999999999999887766655554566889999998877 888899999999999765
No 21
>PRK12740 elongation factor G; Reviewed
Probab=92.69 E-value=0.33 Score=41.24 Aligned_cols=71 Identities=18% Similarity=0.209 Sum_probs=57.5
Q ss_pred ccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 17 IERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 17 I~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
+--.-|++.|+ +|.++.++++..|.+-...+.+++-.++...+.+.+|-..--.+.+-+++.|+|.|....
T Consensus 580 LlEPi~~~eI~--~p~~~~g~v~~~l~~rrg~i~~~~~~~~~~~i~a~~P~~e~~g~~~~Lr~~T~G~a~~~~ 650 (668)
T PRK12740 580 LLEPIMKVEVS--VPEEFVGDVIGDLSSRRGRILGMESRGGGDVVRAEVPLAEMFGYATDLRSLTQGRGSFSM 650 (668)
T ss_pred eecceEEEEEE--echhhhhhHHHHHHhCCCeEeccccCCCCEEEEEEcCHHHhhchHHHHHHhcCCeEEEEE
Confidence 33445788888 999999999999999888776655434458999999988888888888999999998754
No 22
>TIGR01393 lepA GTP-binding protein LepA. LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function is unknown.
Probab=92.68 E-value=0.56 Score=39.87 Aligned_cols=65 Identities=9% Similarity=0.123 Sum_probs=53.5
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeee-eCCeEEEEEEeCCCCh-HHHHHHHhhhcCCceEEE
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEW-SGGGLLLICLIDPGKY-REIDELVRTETRGQGTLE 88 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~-~~~~~~~v~~I~Pg~~-r~i~~lv~~~tkG~g~ve 88 (103)
|++.|. +|.++.+.+++.+...-..+..-+. +++...+.+.+|-.-. .++.+-+++.|+|.|+..
T Consensus 403 ~~~~i~--~P~~~~G~vm~~~~~rRG~~~~~~~~~~~~~~i~~~~Plae~~~~~~~~Lks~T~G~gs~~ 469 (595)
T TIGR01393 403 VKATII--TPTEYLGPIMTLCQEKRGVQTNMEYLDPNRVELIYEMPLAEIVYDFFDKLKSISRGYASFD 469 (595)
T ss_pred EEEEEE--ccHHHHHHHHHHHHHcCCEEeCcEEcCCCeEEEEEEeccchhhhchhHHhhhhcCCEEEEE
Confidence 677777 9999999999999988776665555 3356889999998885 888899999999999765
No 23
>PRK12739 elongation factor G; Reviewed
Probab=92.44 E-value=0.39 Score=41.24 Aligned_cols=69 Identities=16% Similarity=0.236 Sum_probs=57.9
Q ss_pred ceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 19 RAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 19 RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
-.-|++.|+ +|.++.+.++..|.+-...+.+++-.++...+.+.+|-..--.+.+-++..|+|.|....
T Consensus 600 EPi~~~eI~--~p~~~~g~v~~~L~~RRg~i~~~~~~~~~~~i~a~vP~~e~~g~~~~Lr~~T~G~a~~~~ 668 (691)
T PRK12739 600 EPIMKVEVV--TPEEYMGDVIGDLNRRRGQIQGMEARGGAQIVKAFVPLSEMFGYATDLRSATQGRATFSM 668 (691)
T ss_pred cceEEEEEE--EchHhhhhHHHHHHhcCCeEECccccCCcEEEEEEeCHHHhhccHHHHHhhccCceEEEE
Confidence 345788888 999999999999999888777665545667899999998888888888999999998754
No 24
>PRK00007 elongation factor G; Reviewed
Probab=91.68 E-value=0.52 Score=40.52 Aligned_cols=68 Identities=18% Similarity=0.179 Sum_probs=56.0
Q ss_pred eeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 20 AQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 20 A~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
--|++.|+ +|.++.+.++..|.+--..+...+-.++...+.+.+|-.---.+..-++..|+|.|....
T Consensus 604 Pi~~~eI~--~p~~~~g~v~~~L~~RRg~i~~~~~~~~~~~i~a~vP~~e~~g~~~~Lrs~T~G~a~~~~ 671 (693)
T PRK00007 604 PIMKVEVV--TPEEYMGDVIGDLNSRRGQIEGMEDRGGAKVIRAEVPLSEMFGYATDLRSMTQGRATYSM 671 (693)
T ss_pred CcEEEEEE--echhhhhhHHHHHHhCCCeEecccccCCcEEEEEEcCHHHhhccHHHHHhhcCCceEEEE
Confidence 34788888 999999999999999887776544335678899999988888888888999999998754
No 25
>PRK07560 elongation factor EF-2; Reviewed
Probab=91.68 E-value=0.37 Score=41.67 Aligned_cols=71 Identities=8% Similarity=0.075 Sum_probs=57.1
Q ss_pred ccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 17 IERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 17 I~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
+----|++.|+ +|.++.+.++.-|..-...|...+..++...+.+.+|-...-.+..-++..|+|+|....
T Consensus 623 LlEPi~~veI~--~p~~~~g~v~~~L~~rrg~i~~~~~~~~~~~I~a~vP~~e~~gy~~~Lrs~T~G~~~~~~ 693 (731)
T PRK07560 623 LLEPIQKVDIN--VPQDYMGAVTREIQGRRGKILDMEQEGDMAIIEAEAPVAEMFGFAGEIRSATEGRALWST 693 (731)
T ss_pred EeecEEEEEEE--ecHHHhhHHHHHHHhcCCeeeeeecCCCcEEEEEEEehHHhcCCchHHHhhCcCCceEEE
Confidence 33445788888 999999999999999887776554434567899999988777888888999999998754
No 26
>TIGR01394 TypA_BipA GTP-binding protein TypA/BipA. This bacterial (and Arabidopsis) protein, termed TypA or BipA, a GTP-binding protein, is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown.
Probab=91.48 E-value=1.1 Score=38.24 Aligned_cols=66 Identities=21% Similarity=0.171 Sum_probs=52.8
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeee-eCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEW-SGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~-~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
|++.|. +|.++.+.+.+.|..--..+..-+- .+|...+.+.+|-.-.-.+..-+++.|+|.|....
T Consensus 397 ~~~~i~--vp~e~~G~v~~~l~~RrG~~~~~~~~~~~~~~i~~~vP~~~l~~y~~~l~s~T~G~g~~~~ 463 (594)
T TIGR01394 397 EELTID--VPEEHVGAVIEKLGKRKGEMVDMEPSGNGRTRLEFKIPSRGLIGFRTEFLTDTRGTGIMNH 463 (594)
T ss_pred EEEEEE--echHHHHHHHHHHHHhCCEEeccEECCCCEEEEEEEeChHHhhhHHHHHHhhcCCeEEEEE
Confidence 567777 9999999999999998877665444 24566799999987777777888899999998754
No 27
>PRK13351 elongation factor G; Reviewed
Probab=91.15 E-value=0.77 Score=39.25 Aligned_cols=71 Identities=15% Similarity=0.230 Sum_probs=56.6
Q ss_pred ccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeee-CCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 17 IERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWS-GGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 17 I~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~-~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
+--.-|++.|. +|.++.+.++..|.+-...+.+.+-. ++.+.+.+.+|--.--.+.+-+++.|+|.|....
T Consensus 597 LlEPi~~~eI~--~p~~~~g~v~~~l~~rrg~i~~~~~~~~~~~~i~a~vP~~e~~~~~~~Lrs~T~G~a~~~~ 668 (687)
T PRK13351 597 LLEPIMELEIT--VPTEHVGDVLGDLSQRRGRIEGTEPRGDGEVLVKAEAPLAELFGYATRLRSMTKGRGSFTM 668 (687)
T ss_pred eecceEEEEEE--echHhhhhHHHHHHhCCcEEeceecCCCcEEEEEEEECHHHhhChHHHHHhhcCCceEEEE
Confidence 33445788888 99999999999999988777665543 3444489999988888888889999999998754
No 28
>TIGR00484 EF-G translation elongation factor EF-G. After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G.
Probab=90.68 E-value=0.8 Score=39.30 Aligned_cols=67 Identities=19% Similarity=0.168 Sum_probs=55.4
Q ss_pred eeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 21 QMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 21 ~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
=|++.|. +|.++.+.++..|.+-...+...+-.++...+.+.+|--.--.+..-+++.|+|.|....
T Consensus 602 i~~~eI~--~p~~~~g~v~~~L~~rrg~i~~~~~~~~~~~I~a~vP~~e~~g~~~~Lrs~T~G~~~~~~ 668 (689)
T TIGR00484 602 IMKVEVE--VPEEYMGDVMGDLSSRRGIIEGMEARGNVQKIKAEVPLSEMFGYATDLRSFTQGRGTYSM 668 (689)
T ss_pred cEEEEEE--ecHHHhHhHHHHHHhcCCeEecccccCCcEEEEEEeCHHHHhChHHHHHHhcCCceEEEE
Confidence 4677888 999999999999999888776544335678899999988888888888999999998754
No 29
>PLN00116 translation elongation factor EF-2 subunit; Provisional
Probab=90.28 E-value=0.53 Score=41.48 Aligned_cols=69 Identities=14% Similarity=0.048 Sum_probs=56.2
Q ss_pred ceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCe--EEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 19 RAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGG--LLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 19 RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~--~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
---|++.|+ +|.++.+.++.-|.+-...|..++-.++. +.+.+.+|-.---.+.+-++..|+|+|....
T Consensus 727 EPi~~veI~--~p~~~~G~V~~dL~~RRG~i~~~~~~~~t~~~~I~A~vPl~e~~gy~~~LRs~T~G~g~~~~ 797 (843)
T PLN00116 727 EPVYLVEIQ--APEQALGGIYSVLNQKRGHVFEEMQRPGTPLYNIKAYLPVIESFGFSGTLRAATSGQAFPQC 797 (843)
T ss_pred eceeEEEEE--ccHHHHhHHHHHHHhcCCccceeeecCCCceEEEEEEeeHHHHcCCCHHHHhhCCCCCeEEE
Confidence 344788888 99999999999999988887766553443 7899999988777788888999999998654
No 30
>PRK10218 GTP-binding protein; Provisional
Probab=89.74 E-value=1.6 Score=37.31 Aligned_cols=66 Identities=17% Similarity=0.097 Sum_probs=53.2
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeee-eCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEW-SGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~-~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
|++.|. +|.++.+.+.+.|..--..+..-+- .+|...+.+.||..-.-.+..-+.+.|+|.|....
T Consensus 401 ~~v~i~--vP~e~~G~V~~~l~~RrG~~~~m~~~~~~~~~l~~~vP~~~l~~y~~~l~s~T~G~g~~~~ 467 (607)
T PRK10218 401 ENVTLD--VEEQHQGSVMQALGERKGDLKNMNPDGKGRVRLDYVIPSRGLIGFRSEFMTMTSGTGLLYS 467 (607)
T ss_pred EEEEEE--echhhHHHHHHHHHhcCCEEeccEECCCCEEEEEEEcCHHHHhhHHHHhhhhCCCeEEEEE
Confidence 567777 9999999999999998877665444 24567899999987777888888899999998754
No 31
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=89.33 E-value=1.7 Score=32.72 Aligned_cols=62 Identities=18% Similarity=0.183 Sum_probs=44.0
Q ss_pred ccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeee-------CCeEEEEEEeCCCChHHHHHHHhhh
Q psy1332 17 IERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWS-------GGGLLLICLIDPGKYREIDELVRTE 80 (103)
Q Consensus 17 I~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~-------~~~~~~v~~I~Pg~~r~i~~lv~~~ 80 (103)
|..+.|++.+. =+.+..+++.+.+.+++..+.+++.+ .....+++.|||..|..+.+.+.+.
T Consensus 49 i~~~~l~lev~--d~~~a~~~i~~~~~~~gG~i~~~~~~~~~~~~~~~~~~ltiRVP~~~~~~~l~~l~~~ 117 (262)
T PF14257_consen 49 IKTADLSLEVK--DVEKAVKKIENLVESYGGYIESSSSSSSGGSDDERSASLTIRVPADKFDSFLDELSEL 117 (262)
T ss_pred EEEEEEEEEEC--CHHHHHHHHHHHHHHcCCEEEEEeeecccCCCCcceEEEEEEECHHHHHHHHHHHhcc
Confidence 66777777766 44555666777777777666654442 4667899999999999988887643
No 32
>KOG0465|consensus
Probab=88.60 E-value=0.9 Score=39.47 Aligned_cols=66 Identities=15% Similarity=0.087 Sum_probs=53.2
Q ss_pred eeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEE
Q psy1332 21 QMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLE 88 (103)
Q Consensus 21 ~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~ve 88 (103)
=|.|.++ .|.++.+.+..-|.+-.+.|...|-+++...+.+.+|=..-=.-.+-+++.|+|+|+.-
T Consensus 635 IM~Vevt--~P~EfqG~Vi~~L~kR~a~I~~~d~~~~~~ti~A~VPL~~mfgYss~LRslTqGkgeft 700 (721)
T KOG0465|consen 635 IMNVEVT--TPEEFQGTVIGDLNKRKAQITGIDSSEDYKTIKAEVPLNEMFGYSSELRSLTQGKGEFT 700 (721)
T ss_pred ceeeEEe--cchhhhhhhhhhhhhcccEEecccCCCceEEEEecccHHHHhhhhhhhhhhhcCcceEE
Confidence 3899999 99999999999999887766666556778888999986655555667788999999763
No 33
>COG1739 Uncharacterized conserved protein [Function unknown]
Probab=87.31 E-value=2.7 Score=31.30 Aligned_cols=65 Identities=18% Similarity=0.253 Sum_probs=54.2
Q ss_pred EEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 23 RVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 23 rl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
.+.+. ++=+..+.+...+..+...++.++|++++..+.+.++...+..+..++...+.|+.+++-
T Consensus 137 ~~~~~--~~y~~l~~l~~~l~~~~~~i~~~~~~~~~v~~~v~~~~~~~~~~~~~~~~~~~g~~~~~~ 201 (203)
T COG1739 137 ANHVG--CAYRILGLLERLLKQNDDDVEEARYSGGSVLLTVRFRHIVIEAVSRLLKGNHIGPDRFKH 201 (203)
T ss_pred heeec--cchhhhHHHHHHHHhccceEEEeeecCCeEEEEEEechhhHHHHHHHHhhccCCceEEec
Confidence 34444 666677788888888866788999988889999999999999999999999999887763
No 34
>PTZ00416 elongation factor 2; Provisional
Probab=86.54 E-value=1.3 Score=39.03 Aligned_cols=71 Identities=15% Similarity=0.090 Sum_probs=55.8
Q ss_pred ccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCe--EEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 17 IERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGG--LLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 17 I~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~--~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
+--.=|++.|+ +|.++.+.++.-|.+-...+..++-.+|. ..+.+.+|-----.+.+-++..|+|+|....
T Consensus 718 LlEPi~~veI~--~p~~~lg~V~~dL~~RRG~i~~~~~~~~t~~~~I~a~vP~~e~~gy~~~LRs~T~G~g~~~~ 790 (836)
T PTZ00416 718 LLEPMFLVDIT--APEDAMGGIYSVLNRRRGVVIGEEQRPGTPLSNIKAYLPVAESFGFTAALRAATSGQAFPQC 790 (836)
T ss_pred EEeeeEEEEEE--EcHHHHhHHHHHHHhcCCCccCcccCCCCCcEEEEEEEehHHhcCCCHHHHhhCcCCceEEE
Confidence 33445788888 99999999999999988777765544444 6899999987777777778888999998754
No 35
>TIGR00490 aEF-2 translation elongation factor aEF-2. This model represents archaeal elongation factor 2, a protein more similar to eukaryotic EF-2 than to bacterial EF-G, both in sequence similarity and in sharing with eukaryotes the property of having a diphthamide (modified His) residue at a conserved position. The diphthamide can be ADP-ribosylated by diphtheria toxin in the presence of NAD.
Probab=85.87 E-value=1.5 Score=37.92 Aligned_cols=71 Identities=8% Similarity=0.050 Sum_probs=55.6
Q ss_pred ccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 17 IERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 17 I~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
+--.-|++.|+ +|.++.+.++.-|.+-...|...+-.++...+.+.+|-.---.+.+-+++.|+|+|....
T Consensus 621 LlEPi~~~ei~--~p~~~~g~v~~~L~~RRg~i~~~~~~~~~~~I~A~vP~~e~fgy~~~Lrs~T~G~a~~~~ 691 (720)
T TIGR00490 621 LLEPYQKVFIN--VPQDMMGAATREIQNRRGQILEMKQEGDMVTIIAKAPVAEMFGFAGAIRGATSGRCLWST 691 (720)
T ss_pred EecceEEEEEE--ccHHHHhHHHHHHhhCCceeeeeccCCCcEEEEEEEehHHhcCCcHHHHhhCCCCceEEE
Confidence 33445888898 999999999999999887776544334567889999987777777778889999998654
No 36
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=74.87 E-value=18 Score=25.81 Aligned_cols=67 Identities=18% Similarity=0.143 Sum_probs=45.0
Q ss_pred ccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEEEE
Q psy1332 17 IERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLELLN 91 (103)
Q Consensus 17 I~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vevl~ 91 (103)
+.|.-|-++|. .+.+....+.+....|.+++. |++.+++.+.+. |.-..++.|+.-. +.-|-+|+..
T Consensus 81 v~rEl~LiKv~--~~~~~r~~i~~i~~~f~a~iv--dv~~~~~~ie~t---G~~~ki~~~~~~l-~~~gi~e~~R 147 (157)
T TIGR00119 81 VERELCLVKVS--APGEGRDEIIRLTNIFRGRIV--DVSPDSYTVEVT---GDSDKIDAFLELL-RPFGIKEVAR 147 (157)
T ss_pred eeeEEEEEEEE--CCccCHHHHHHHHHHhCCEEE--EecCCEEEEEEc---CCHHHHHHHHHHh-hhcCCEEEEc
Confidence 89999999999 988888888888888887654 344555665555 4445555554433 3345555543
No 37
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=72.35 E-value=24 Score=25.33 Aligned_cols=67 Identities=18% Similarity=0.212 Sum_probs=44.8
Q ss_pred ccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEEEE
Q psy1332 17 IERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLELLN 91 (103)
Q Consensus 17 I~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vevl~ 91 (103)
+.|.-|-++|. .+......+.+....|.+++. |++.+++.+.+. |.-..++.|++-. +.-|-+|+..
T Consensus 82 v~rEl~LiKv~--~~~~~r~~i~~i~~~f~a~iv--dv~~~~~~iE~t---G~~~ki~~~~~~l-~~~gi~e~~R 148 (161)
T PRK11895 82 VERELALVKVR--ASGENRAEILRLADIFRAKIV--DVTPESLTIEVT---GDSDKIDAFIDLL-RPYGIKEIVR 148 (161)
T ss_pred hheEEEEEEEE--CCcccHHHHHHHHHHhCCEEE--EecCCEEEEEEe---CCHHHHHHHHHHh-hhcCCEEEEc
Confidence 88999999999 888777888888888887654 334555665555 4555555555443 4445555543
No 38
>COG0480 FusA Translation elongation factors (GTPases) [Translation, ribosomal structure and biogenesis]
Probab=72.09 E-value=8.6 Score=33.66 Aligned_cols=75 Identities=12% Similarity=0.143 Sum_probs=56.9
Q ss_pred hhcC-ccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeee--CCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 13 QCMS-IERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWS--GGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 13 ~~iP-I~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~--~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
+.-| +=--=|++.|+ +|.++.+.++.-|.+-...|...+.. .+-..+.+.+|=.-.=.+..-++..|+|+|....
T Consensus 594 ~a~P~lLEPi~~veI~--~P~d~~G~V~~~l~~rRG~I~~~~~~~~~~~~~i~A~vPl~Emfgya~dLRs~T~Gra~~~m 671 (697)
T COG0480 594 KAKPVLLEPIMKVEIT--TPEEYMGDVIGDLNSRRGQILGMEQRPGGGLDVIKAEVPLAEMFGYATDLRSATQGRASFSM 671 (697)
T ss_pred hCCceEecceEEEEEE--cchhhhchhHHhhhhcceEEeceeeccCCceEEEEEEechHHhccchhhhHhhcCCceeEEE
Confidence 4455 44556899999 99999999999999877667654443 2446888899977666667777899999998754
No 39
>PTZ00204 hypothetical protein; Provisional
Probab=69.94 E-value=4.6 Score=27.30 Aligned_cols=38 Identities=18% Similarity=0.559 Sum_probs=28.4
Q ss_pred hcccceeeeee-CCeEEEEEEeCCCChHHHHHHHhhhcCCceEEE
Q psy1332 45 CATSVENEEWS-GGGLLLICLIDPGKYREIDELVRTETRGQGTLE 88 (103)
Q Consensus 45 ~~~~ie~e~~~-~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~ve 88 (103)
|.+.-++|||+ ++++.++|-++ ++++..++-.|++.+-
T Consensus 50 w~arg~sedwdysn~fvvvc~v~------lenia~nereg~chlt 88 (120)
T PTZ00204 50 WVARGESEDWDYSNSFVVVCAVL------LENIAANEREGKCHLT 88 (120)
T ss_pred hhhcCCcccccccCceEEEEeeh------hhhhccccccceEEEE
Confidence 55566899996 78898888775 5667777777877653
No 40
>PF09149 DUF1935: Domain of unknown function (DUF1935); InterPro: IPR015232 This entry represents a conserved region found in various bacterial and eukaryotic hypothetical proteins, as well as in the cysteine protease calpain. Its function has not, as yet, been defined. ; PDB: 1R75_A 2FE0_A.
Probab=67.70 E-value=5.4 Score=26.68 Aligned_cols=41 Identities=17% Similarity=0.204 Sum_probs=25.0
Q ss_pred eeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCC
Q psy1332 21 QMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGK 69 (103)
Q Consensus 21 ~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~ 69 (103)
.|.|+++ +++. +.++.++.+....+-.+|++.+.+.|.|+-
T Consensus 44 ~m~V~v~--F~~~------S~v~~lg~t~~~~~~~~g~~~~~v~V~P~e 84 (104)
T PF09149_consen 44 EMHVTVT--FGPD------SSVKPLGNTTVEREEEDGETVAEVVVYPLE 84 (104)
T ss_dssp EEEEEEE--EETT-------EEEE-TT-EEEEE-TTSEEEEEEEE-TT-
T ss_pred EEEEEEE--ECCC------CcEEECCCcEEEEecCCCcEEEEEEECCcc
Confidence 6888888 8764 234666654333233489999999999974
No 41
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=60.94 E-value=48 Score=24.11 Aligned_cols=67 Identities=18% Similarity=0.220 Sum_probs=45.4
Q ss_pred ccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEEEE
Q psy1332 17 IERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLELLN 91 (103)
Q Consensus 17 I~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vevl~ 91 (103)
|.|.-|-++|. .|+.....+.+....|.++|. |++.+++.+.+. |.-..++.++.-. +.-|-+|+..
T Consensus 82 v~rEl~LiKv~--~~~~~r~ei~~~~~~f~a~iv--dv~~~~~~ie~t---G~~~ki~a~~~~l-~~~gi~e~~R 148 (174)
T CHL00100 82 VERELMLIKIN--VNSQTRPEILEIAQIFRAKVV--DLSEESLILEVT---GDPGKIVAIEQLL-EKFGIIEIAR 148 (174)
T ss_pred eeeEEEEEEEe--cCCcCHHHHHHHHHHhCCEEE--EecCCEEEEEEc---CCHHHHHHHHHHh-hhcCCEEEEc
Confidence 99999999999 988888888888888887654 344455555544 5555555555433 3345556544
No 42
>PF06680 DUF1181: Protein of unknown function (DUF1181); InterPro: IPR009566 This family consists of several hypothetical proteins of around 120 residues in length which are found specifically in Trypanosoma brucei. The function of this family is unknown.
Probab=56.58 E-value=9.7 Score=25.66 Aligned_cols=38 Identities=18% Similarity=0.559 Sum_probs=27.6
Q ss_pred hcccceeeeee-CCeEEEEEEeCCCChHHHHHHHhhhcCCceEEE
Q psy1332 45 CATSVENEEWS-GGGLLLICLIDPGKYREIDELVRTETRGQGTLE 88 (103)
Q Consensus 45 ~~~~ie~e~~~-~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~ve 88 (103)
|.+.-++|||+ ++++.++|-+. ++++..++-.|++.+-
T Consensus 50 wvargesedwdysnsfvvvc~vl------lenia~neregkchl~ 88 (120)
T PF06680_consen 50 WVARGESEDWDYSNSFVVVCAVL------LENIAANEREGKCHLT 88 (120)
T ss_pred eeecCCccccCccCceEEEEehh------hhhhccccccceEEEE
Confidence 45556899996 78888888764 5667777777877653
No 43
>TIGR02058 lin0512_fam conserved hypothetical protein. This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N-terminus.
Probab=52.91 E-value=20 Score=24.68 Aligned_cols=36 Identities=17% Similarity=0.279 Sum_probs=24.7
Q ss_pred hhhhcCccc-eeeEEEEEEeeCcc----hHHHHHHHHHhhcc
Q psy1332 11 LKQCMSIER-AQMRVRVEVSAGVK----DVKKLKEKLVKCAT 47 (103)
Q Consensus 11 Lk~~iPI~R-A~Mrl~v~~~ip~~----~~~~~~~~l~~~~~ 47 (103)
|.+.+|+.. ..|++.+++.+|.. +...+ ....+++.
T Consensus 38 ~~~~~~~~~~~~M~v~V~igVp~p~e~vD~e~v-~~~~PyG~ 78 (116)
T TIGR02058 38 IWESLPDSSLNEMIVEVKLAVPYDLDQLDEDKV-KAIIPYGT 78 (116)
T ss_pred HHHhcCCCChhheEEEEEEECCCchHhcCHHHH-HHhCCCCe
Confidence 567889987 99999999888844 12223 44556664
No 44
>PRK13883 conjugal transfer protein TrbH; Provisional
Probab=51.44 E-value=56 Score=23.40 Aligned_cols=45 Identities=7% Similarity=0.005 Sum_probs=37.0
Q ss_pred HhHHHHhhhhhcCccceeeEEEEEEeeCcchHHHHHHHHHhhcccce
Q psy1332 4 YSQVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVE 50 (103)
Q Consensus 4 alevIk~Lk~~iPI~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie 50 (103)
|-|++++|.+.+|=.+....|+-. .|..++..+-+.|+.+|-.|.
T Consensus 37 A~D~v~qL~~~ypPA~Tt~~l~q~--~~D~Fg~aL~~aLR~~GYaV~ 81 (151)
T PRK13883 37 ATDAVQQLATLYPPAQTRFELQQP--TPDAFGQALVKALRDKGYALL 81 (151)
T ss_pred HHHHHHHHHHhCCCcceEEEEecC--CCcHHHHHHHHHHHHcCeEEE
Confidence 568999999999987777777666 777888899999999997654
No 45
>COG0440 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]
Probab=45.90 E-value=1.1e+02 Score=22.14 Aligned_cols=68 Identities=21% Similarity=0.173 Sum_probs=48.2
Q ss_pred CccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEEEE
Q psy1332 16 SIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLELLN 91 (103)
Q Consensus 16 PI~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vevl~ 91 (103)
+++|.-|.+++. .++...+.+.....-|.+++. |-+..++.+.+.=+|+....+.+++. +-|-.|+..
T Consensus 83 ~veRel~LiKv~--~~~~~R~ei~~~~~ifr~~vv--Dvs~~~~~~eltG~~~ki~afi~~l~----~~gi~e~~r 150 (163)
T COG0440 83 HVERELALIKVS--AEGSERGEIARITEIFRASVV--DVSPESLTIELTGDEEKIEAFIRLLR----PYGIIEIAR 150 (163)
T ss_pred hhheeeEEEEEe--cCccchHHHHHHHHHhCceEE--ecCcceEEEEEeCChHHHHHHHHHhc----ccceeEEEe
Confidence 499999999999 888776667666666665443 33456777877778888877777754 445666544
No 46
>KOG2943|consensus
Probab=45.47 E-value=47 Score=26.10 Aligned_cols=34 Identities=24% Similarity=0.336 Sum_probs=25.3
Q ss_pred CccceeeEEEEEEeeCcchHHHHHHHHHhhcccc
Q psy1332 16 SIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSV 49 (103)
Q Consensus 16 PI~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~i 49 (103)
||.||+--=|+.+++|.++..++.+.++..+.+|
T Consensus 204 ~id~~kg~griafaip~d~~~~l~e~iK~~n~~i 237 (299)
T KOG2943|consen 204 VIDRAKGFGRIAFAIPTDDLPKLQEAIKSANGTI 237 (299)
T ss_pred cccccccceeEEEeccccccccHHHHHHHhcccc
Confidence 5777765555555599999999999999886543
No 47
>PF09078 CheY-binding: CheY binding; InterPro: IPR015162 The CheY binding domain is found in the response regulator histidine kinase CheA. It adopts a secondary structure consisting of an open-face beta/alpha sandwich, with four antiparallel beta-strands and two alpha-helices. It binds to a corresponding domain on CheY, with subsequent phosphorylation of the CheY Asp57 residue, and activation of CheY, which then affects flagellar rotation []. ; PDB: 1FWP_A 1EAY_C 1A0O_D 1FFG_B 1FFS_B 1FFW_D.
Probab=43.78 E-value=78 Score=19.59 Aligned_cols=35 Identities=31% Similarity=0.255 Sum_probs=23.2
Q ss_pred eCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEe
Q psy1332 30 AGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLI 65 (103)
Q Consensus 30 ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I 65 (103)
++.++...+.+.|..+|. +....-.++++.+...-
T Consensus 8 l~~kd~~lL~eELgnLG~-v~~~~~~~~~l~~~L~T 42 (65)
T PF09078_consen 8 LKEKDVDLLLEELGNLGT-VSDQEKGGDSLEVWLET 42 (65)
T ss_dssp --TTHHHHHHHHHHHHS---EEEEEESSEEEEEE-S
T ss_pred CCHHHHHHHHHHHhcCcc-EEEEecCCCeEEEEECC
Confidence 456788899999999995 66555557777776643
No 48
>PF00542 Ribosomal_L12: Ribosomal protein L7/L12 C-terminal domain; InterPro: IPR013823 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the C-terminal domain of the large subunit ribosomal proteins, known as the L7/L12 family. L7/L12 is present in each 50S subunit in four copies organised as two dimers. The L8 protein complex consisting of two dimers of L7/L12 and L10 in Escherichia coli ribosomes is assembled on the conserved region of 23 S rRNA termed the GTPase-associated domain []. The L7/L12 dimer probably interacts with EF-Tu. L7 and L12 only differ in a single post translational modification of the addition of an acetyl group to the N terminus of L7.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1DD4_B 1DD3_A 1RQU_B 2GYA_5 2GYC_5 1RQS_A 1RQV_A 1CTF_A 2XUX_L.
Probab=42.39 E-value=49 Score=20.32 Aligned_cols=44 Identities=16% Similarity=0.314 Sum_probs=29.3
Q ss_pred hHHHHhhhhhcC---------ccceeeEEEEEEeeCcchHHHHHHHHHhhcccce
Q psy1332 5 SQVIPTLKQCMS---------IERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVE 50 (103)
Q Consensus 5 levIk~Lk~~iP---------I~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie 50 (103)
.++||.+|..-. ++.++-.|.=. +|...+..++.+|...|++++
T Consensus 14 i~vIK~vR~~tgl~L~eAK~~vd~~p~~ik~~--v~keeAe~ik~~Le~aGa~v~ 66 (68)
T PF00542_consen 14 IKVIKEVREITGLGLKEAKKLVDSLPKVIKEG--VSKEEAEEIKKKLEAAGAKVE 66 (68)
T ss_dssp HHHHHHHHHHC---HHHHHHHHCTTTEEEEEE--E-HHHHHHHHHHHHCCT-EEE
T ss_pred HHHHHHHHHHhCCcHHHHHHHHHhCCHHHHcC--CCHHHHHHHHHHHHHcCCEEE
Confidence 356666654322 45556667777 888999999999999887654
No 49
>PF07283 TrbH: Conjugal transfer protein TrbH; InterPro: IPR010837 This entry represents TrbH, a bacterial conjugal transfer protein approximately 150 residues long. TrbH contains a putative membrane lipoprotein lipid attachment site [].
Probab=41.81 E-value=68 Score=22.08 Aligned_cols=45 Identities=9% Similarity=0.054 Sum_probs=38.2
Q ss_pred HhHHHHhhhhhcCccceeeEEEEEEeeCcchHHHHHHHHHhhcccce
Q psy1332 4 YSQVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVE 50 (103)
Q Consensus 4 alevIk~Lk~~iPI~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie 50 (103)
|-|++++|.+.+|=.+....|.=+ .|..++..+-+.|+.+|-.|.
T Consensus 9 A~D~v~qL~~~ypPA~Tt~~L~q~--~~d~Fg~aL~~~LR~~GYaV~ 53 (121)
T PF07283_consen 9 AGDMVSQLAEQYPPAKTTFELKQK--DPDPFGQALENALRAKGYAVI 53 (121)
T ss_pred HHHHHHHHHHhcCCCccEEEEEcC--CCChHHHHHHHHHHhcCcEEE
Confidence 568999999999988888888656 788888999999999997653
No 50
>PRK13835 conjugal transfer protein TrbH; Provisional
Probab=41.06 E-value=93 Score=22.20 Aligned_cols=44 Identities=9% Similarity=0.123 Sum_probs=34.7
Q ss_pred HhHHHHhhhhhcCccceeeEEEEEEeeCcchHHHHHHHHHhhcccce
Q psy1332 4 YSQVIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVE 50 (103)
Q Consensus 4 alevIk~Lk~~iPI~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie 50 (103)
|-|.+++|.+.+|=......|+-. . ..++..+-..|+.||-.+.
T Consensus 43 A~D~vsqLae~~pPa~tt~~l~q~--~-d~Fg~aL~~aLr~~GYaVv 86 (145)
T PRK13835 43 AGDMVSRLAEQIGPGTTTIKLKKD--T-SPFGQALEAALKGWGYAVV 86 (145)
T ss_pred HHHHHHHHHHhcCCCceEEEEeec--C-cHHHHHHHHHHHhcCeEEe
Confidence 568899999999977766666666 4 5677788899999998765
No 51
>PF01267 F-actin_cap_A: F-actin capping protein alpha subunit; InterPro: IPR002189 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. The actin filament system, a prominent part of the cytoskeleton in eukaryotic cells, is both a static structure and a dynamic network that can undergo rearrangements: it is thought to be involved in processes such as cell movement and phagocytosis [], as well as muscle contraction. The F-actin capping protein binds in a calcium-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits at these ends. Unlike gelsolin and severin this protein does not sever actin filaments. The F-actin capping protein is a heterodimer composed of two unrelated subunits: alpha and beta (see IPR001698 from INTERPRO). Neither of the subunits shows sequence similarity to other filament-capping proteins []. The alpha subunit is a protein of about 268 to 286 amino acid residues whose sequence is well conserved in eukaryotic species [].; GO: 0003779 actin binding, 0030036 actin cytoskeleton organization, 0008290 F-actin capping protein complex; PDB: 1MQ1_D 1MWN_X 2KBM_Y 2KZ7_A 3AAE_C 3AA6_A 3LK4_G 1IZN_A 3AA7_A 3AAA_A ....
Probab=38.98 E-value=12 Score=28.89 Aligned_cols=17 Identities=12% Similarity=0.477 Sum_probs=12.5
Q ss_pred HHHHhhhhhcCccceee
Q psy1332 6 QVIPTLKQCMSIERAQM 22 (103)
Q Consensus 6 evIk~Lk~~iPI~RA~M 22 (103)
+.+|.||..+||.|.+|
T Consensus 242 ~tFK~LRR~LPVTRsKi 258 (271)
T PF01267_consen 242 KTFKALRRQLPVTRSKI 258 (271)
T ss_dssp THHHHHS-SS-TTTSS-
T ss_pred HHHHHhhhhCCCCCCcc
Confidence 47899999999999987
No 52
>PF14183 YwpF: YwpF-like protein
Probab=38.94 E-value=60 Score=22.89 Aligned_cols=33 Identities=27% Similarity=0.302 Sum_probs=26.6
Q ss_pred ceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhc
Q psy1332 49 VENEEWSGGGLLLICLIDPGKYREIDELVRTET 81 (103)
Q Consensus 49 ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~t 81 (103)
|.+.+.+++.|-+.+.++..+|.-+.++.++.+
T Consensus 30 IINkEd~~~~WllEa~i~~~~~~~f~~~~~~~~ 62 (135)
T PF14183_consen 30 IINKEDSENTWLLEAVISKEYYEFFEEYQQSQT 62 (135)
T ss_pred EEeeeCCCCcEEEEEEEchhhHHHHHHHHhCCc
Confidence 345444589999999999999999999987764
No 53
>PF09585 Lin0512_fam: Conserved hypothetical protein (Lin0512_fam); InterPro: IPR011719 This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N terminus.
Probab=38.68 E-value=31 Score=23.64 Aligned_cols=24 Identities=17% Similarity=0.308 Sum_probs=19.8
Q ss_pred hhhhhcCccceeeEEEEEEeeCcc
Q psy1332 10 TLKQCMSIERAQMRVRVEVSAGVK 33 (103)
Q Consensus 10 ~Lk~~iPI~RA~Mrl~v~~~ip~~ 33 (103)
-|.+.+|..+..|+|.++|-+|..
T Consensus 37 ~l~~~~~~~~~~M~v~V~igVp~p 60 (113)
T PF09585_consen 37 GLFEILGLDLDDMKVEVKIGVPRP 60 (113)
T ss_pred HHHHHcCCChHHEEEEEEEeCCCc
Confidence 456778999999999999777754
No 54
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=38.31 E-value=22 Score=26.93 Aligned_cols=63 Identities=16% Similarity=0.171 Sum_probs=40.4
Q ss_pred ccceeeEEEEEEeeCcchHHHHHHHHHhhccc----ceeeee--eCCeEEEEEEeCCCChHHHHHHHhh
Q psy1332 17 IERAQMRVRVEVSAGVKDVKKLKEKLVKCATS----VENEEW--SGGGLLLICLIDPGKYREIDELVRT 79 (103)
Q Consensus 17 I~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~----ie~e~~--~~~~~~~v~~I~Pg~~r~i~~lv~~ 79 (103)
|.||+|++.++.-+|+.-...+++.+...+-. ..-+-| .-..-...+.||+-.|.+..+-++.
T Consensus 38 ia~ar~~~~iscyiPPsVY~El~~fm~r~gc~~e~~~ki~twivkKtPnryevkiPa~ifyeyV~diR~ 106 (221)
T COG1458 38 IARARLKLGISCYIPPSVYRELMGFMERNGCPEEVIAKIETWIVKKTPNRYEVKIPAAIFYEYVEDIRE 106 (221)
T ss_pred HHHhhhhcCeEEEeChHHHHHHHHHHHhCCCcHHHHHhhheeeEecCCCceeecCcHHHHHHHHHHHHH
Confidence 77887666666558988888888888755421 123456 1223345667888888887665554
No 55
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=37.65 E-value=22 Score=26.96 Aligned_cols=20 Identities=35% Similarity=0.680 Sum_probs=17.9
Q ss_pred EEEEEEeCCCChHHHHHHHh
Q psy1332 59 LLLICLIDPGKYREIDELVR 78 (103)
Q Consensus 59 ~~~v~~I~Pg~~r~i~~lv~ 78 (103)
+-+.|-|||+.|+++..++.
T Consensus 45 ~~iscyiPPsVY~El~~fm~ 64 (221)
T COG1458 45 LGISCYIPPSVYRELMGFME 64 (221)
T ss_pred cCeEEEeChHHHHHHHHHHH
Confidence 45899999999999999975
No 56
>KOG0467|consensus
Probab=36.88 E-value=64 Score=29.19 Aligned_cols=71 Identities=21% Similarity=0.207 Sum_probs=56.8
Q ss_pred ccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeee--eCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEE
Q psy1332 17 IERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEW--SGGGLLLICLIDPGKYREIDELVRTETRGQGTLEL 89 (103)
Q Consensus 17 I~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~--~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vev 89 (103)
|.-|.-.-.|+ +.++..+++|.-|.+--.+|.+||. +.|-+.+++++|---+=.+-+-+++-|.|-+.-++
T Consensus 748 l~~aMYsC~I~--t~~e~LGkvYAVlskR~gkVLsEem~EgT~~F~V~aliPVvESFgFadeiRK~TSG~A~pQL 820 (887)
T KOG0467|consen 748 IMAAMYSCDIQ--TASEVLGKVYAVLSKRHGKVLSEEMKEGTGFFIVTALIPVVESFGFADEIRKGTSGAASPQL 820 (887)
T ss_pred Hhhhheeeeee--ehHHHhhhHHhhhhhhcchhhhhhhhCCCCcEEEEEEeeeeccccHHHHHhhccccccchhh
Confidence 55555555666 8999999999999998888988877 46889999999987666676667889999886554
No 57
>PF01037 AsnC_trans_reg: AsnC family; InterPro: IPR019887 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One such family is the AsnC/Lrp subfamily []. The Lrp family of transcriptional regulators appears to be widely distributed among bacteria and archaea, as an important regulatory system of the amino acid metabolism and related processes []. Members of the Lrp family are small DNA-binding proteins with molecular masses of around 15 kDa. Target promoters often contain a number of binding sites that typically lack obvious inverted repeat elements, and to which binding is usually co-operative. LrpA from Pyrococcus furiosus is the first Lrp-like protein to date of which a three-dimensional structure has been solved. In the crystal structure LrpA forms an octamer consisting of four dimers. The structure revealed that the N-terminal part of the protein consists of a helix-turn-helix (HTH) domain, a fold generally involved in DNA binding. The C terminus of Lrp-like proteins has a beta-fold, where the two alpha-helices are located at one side of the four-stranded antiparallel beta-sheet. LrpA forms a homodimer mainly through interactions between the beta-strands of this C-terminal domain, and an octamer through further interactions between the second alpha-helix and fourth beta-strand of the motif. Hence, the C-terminal domain of Lrp-like proteins appears to be involved in ligand-response and activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2DJW_F 2GQQ_A 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2CG4_B 2DBB_B 1I1G_A ....
Probab=32.76 E-value=1e+02 Score=17.73 Aligned_cols=49 Identities=20% Similarity=0.296 Sum_probs=35.2
Q ss_pred eCcch--HHHHHHHHHhhcccceeeee-eCCeEEEEEEeCCCChHHHHHHHhhh
Q psy1332 30 AGVKD--VKKLKEKLVKCATSVENEEW-SGGGLLLICLIDPGKYREIDELVRTE 80 (103)
Q Consensus 30 ip~~~--~~~~~~~l~~~~~~ie~e~~-~~~~~~~v~~I~Pg~~r~i~~lv~~~ 80 (103)
+.+.. ...+.+.|.++-. +. +=| -.|.+.+.+.+-.....++++++.+.
T Consensus 5 ~~~~~~~~~~~~~~l~~~p~-V~-~~~~vtG~~d~~~~v~~~d~~~l~~~i~~~ 56 (74)
T PF01037_consen 5 VEPGHDAYDEFAEALAEIPE-VV-ECYSVTGEYDLILKVRARDMEELEEFIREK 56 (74)
T ss_dssp ESTTGTHHHHHHHHHHTSTT-EE-EEEEESSSSSEEEEEEESSHHHHHHHHHHT
T ss_pred EcCCCchHHHHHHHHHcCCC-EE-EEEEEeCCCCEEEEEEECCHHHHHHHHHHH
Confidence 66555 6777777777664 33 223 37788888888889999999997773
No 58
>KOG1145|consensus
Probab=32.04 E-value=62 Score=28.36 Aligned_cols=49 Identities=18% Similarity=0.148 Sum_probs=35.0
Q ss_pred CccHhHHHHhhhh-hcCccceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeee
Q psy1332 1 MYYYSQVIPTLKQ-CMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWS 55 (103)
Q Consensus 1 ~~QalevIk~Lk~-~iPI~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~ 55 (103)
|.|-+|+|+.-|. --||--|==++- =|...-.+++..|...+ +.-|+|+
T Consensus 239 mpQT~EaIkhAk~A~VpiVvAinKiD----kp~a~pekv~~eL~~~g--i~~E~~G 288 (683)
T KOG1145|consen 239 MPQTLEAIKHAKSANVPIVVAINKID----KPGANPEKVKRELLSQG--IVVEDLG 288 (683)
T ss_pred cHhHHHHHHHHHhcCCCEEEEEeccC----CCCCCHHHHHHHHHHcC--ccHHHcC
Confidence 7899999999874 466543332222 26666779999999988 6778894
No 59
>PF10369 ALS_ss_C: Small subunit of acetolactate synthase; InterPro: IPR019455 This entry represents the C-terminal domain of the small subunit of acetolactate synthase (the N-terminal domain being an ACT domain). Acetolactate synthase is a tetrameric enzyme, composed of two large and two small subunits, which catalyses the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides []. ; PDB: 2F1F_B 2FGC_A 2PC6_A.
Probab=29.86 E-value=1.4e+02 Score=18.37 Aligned_cols=68 Identities=16% Similarity=0.213 Sum_probs=44.3
Q ss_pred cceeeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEEEEee
Q psy1332 18 ERAQMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLELLNLK 93 (103)
Q Consensus 18 ~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vevl~~~ 93 (103)
+|.-|-++|. .+......+.+....|.+.+. |++.+++.+.+. |.-..++.++...-+ -|-+|+...-
T Consensus 1 erEl~LiKV~--~~~~~r~ei~~l~~~f~a~iv--d~~~~~~iie~t---G~~~kid~fi~~l~~-~gi~Ei~RtG 68 (75)
T PF10369_consen 1 ERELALIKVK--ATPENRSEILQLAEIFRARIV--DVSPDSIIIELT---GTPEKIDAFIKLLKP-FGILEIARTG 68 (75)
T ss_dssp EEEEEEEEEE---SCHHHHHHHHHHHHTT-EEE--EEETTEEEEEEE---E-HHHHHHHHHHSTG-GGEEEEEEEE
T ss_pred CeEEEEEEEE--CCccCHHHHHHHHHHhCCEEE--EECCCEEEEEEc---CCHHHHHHHHHHhhh-cCCEEEEccc
Confidence 4778889999 877788888888888887554 456676666665 455566666655433 5677766543
No 60
>TIGR01573 cas2 CRISPR-associated endoribonuclease Cas2. This model describes most members of the family of Cas2, one of the first four protein families found to mark prokaryotic genomes that contain multiple CRISPR elements. It is an endoribonuclease, capable of cleaving single-stranded RNA. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. The cas genes are found near the repeats. A distinct branch of the Cas2 family shows a very low level of sequence identity and is modeled by TIGR01873 instead.
Probab=29.32 E-value=1.6e+02 Score=18.83 Aligned_cols=58 Identities=17% Similarity=0.322 Sum_probs=42.5
Q ss_pred eCcc----hHHHHHHHHHhhc-ccceeeeeeCCeEEEEEEeCCCChH-HHHHHHhhhcCCceEEEEEEeee
Q psy1332 30 AGVK----DVKKLKEKLVKCA-TSVENEEWSGGGLLLICLIDPGKYR-EIDELVRTETRGQGTLELLNLKE 94 (103)
Q Consensus 30 ip~~----~~~~~~~~l~~~~-~~ie~e~~~~~~~~~v~~I~Pg~~r-~i~~lv~~~tkG~g~vevl~~~~ 94 (103)
+|.+ ...++...|..+| .-+... ...|.+++..+. .+...+.+.....++|-++.+..
T Consensus 9 I~~~~~~k~r~kv~k~L~~~G~~rvQ~S-------Vf~~~~~~~~~~~~l~~~l~~~i~~~dsv~i~~l~~ 72 (95)
T TIGR01573 9 IPTDGERKRRRKLRKLLEKYGLQRVQYS-------VFEGILEPNQLARKLIERLKRIIPDEGDIRIYPLTE 72 (95)
T ss_pred CCCCchHHHHHHHHHHHHHcchhheecc-------EEEEEcCHHHHHHHHHHHHHHhCCCCCeEEEEEeCh
Confidence 5544 5567777777777 422221 367789999999 79999998888888888887765
No 61
>PRK12483 threonine dehydratase; Reviewed
Probab=28.31 E-value=1.7e+02 Score=24.72 Aligned_cols=63 Identities=17% Similarity=0.145 Sum_probs=41.1
Q ss_pred cCccceeeEEEEEEeeCc-chH-HHHHHHHHhhccccee---eee---------------eCCeEEEEEEeC--CCChHH
Q psy1332 15 MSIERAQMRVRVEVSAGV-KDV-KKLKEKLVKCATSVEN---EEW---------------SGGGLLLICLID--PGKYRE 72 (103)
Q Consensus 15 iPI~RA~Mrl~v~~~ip~-~~~-~~~~~~l~~~~~~ie~---e~~---------------~~~~~~~v~~I~--Pg~~r~ 72 (103)
.+...++..+.|. ++. ++. ..+.+.|.+.+-.+.. .++ ...+-.+-+.|| ||.|+.
T Consensus 379 ~~~~~~~v~v~ie--~~~~~~~~~~i~~~l~~~g~~~~dlsdne~~k~h~r~~~g~~~~~~~~E~~~~v~iPE~pGa~~~ 456 (521)
T PRK12483 379 ADAREAHLFVGVQ--THPRHDPRAQLLASLRAQGFPVLDLTDDELAKLHIRHMVGGRAPLAHDERLFRFEFPERPGALMK 456 (521)
T ss_pred cCCCeeEEEEEEE--eCChhhhHHHHHHHHHHCCCCeEECCCCHHHHHHHHhccCCCCCCCCceEEEEEEcCCCCcHHHH
Confidence 4556677777776 764 455 7888999887754321 111 012335677885 999999
Q ss_pred HHHHHhh
Q psy1332 73 IDELVRT 79 (103)
Q Consensus 73 i~~lv~~ 79 (103)
|-+.+..
T Consensus 457 f~~~l~~ 463 (521)
T PRK12483 457 FLSRLGP 463 (521)
T ss_pred HHHHhCC
Confidence 9998876
No 62
>PF14085 DUF4265: Domain of unknown function (DUF4265)
Probab=27.91 E-value=1.9e+02 Score=19.27 Aligned_cols=41 Identities=17% Similarity=0.343 Sum_probs=30.7
Q ss_pred HHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCC-ChHHHHHHHhh
Q psy1332 35 VKKLKEKLVKCATSVENEEWSGGGLLLICLIDPG-KYREIDELVRT 79 (103)
Q Consensus 35 ~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg-~~r~i~~lv~~ 79 (103)
...+.+.|..++-..+.. +. --+.+.|||. .|..+..+++.
T Consensus 67 ~~~v~~~l~~lG~~~E~~---~~-~~lav~VP~~~~~~~i~~~L~~ 108 (117)
T PF14085_consen 67 IEAVREELEALGCTVEGF---SE-RMLAVDVPPSVDFDAIKDYLDR 108 (117)
T ss_pred HHHHHHHHHHcCCeEEcc---CC-CEEEEEECCCCCHHHHHHHHHh
Confidence 578899999988654432 22 4577789988 89999998876
No 63
>cd02978 KaiB_like KaiB-like family; composed of the circadian clock proteins, KaiB and the N-terminal KaiB-like sensory domain of SasA. KaiB is an essential protein in maintaining circadian rhythm. It was originally discovered from the cyanobacterium Synechococcus as part of the circadian clock gene cluster, kaiABC. KaiB attenuates KaiA-enhanced KaiC autokinase activity by interacting with KaiA-KaiC complexes in a circadian fashion. KaiB is membrane-associated as well as cytosolic. The amount of membrane-associated protein peaks in the evening (at circadian time (CT) 12-16) while the cytosolic form peaks later (at CT 20). The rhythmic localization of KaiB may function in regulating the formation of Kai complexes. SasA is a sensory histidine kinase which associates with KaiC. Although it is not an essential oscillator component, it is important in enhancing kaiABC expression and is important in metabolic growth control under day/night cycle conditions. SasA contains an N-terminal sensor
Probab=26.85 E-value=1.7e+02 Score=18.34 Aligned_cols=23 Identities=13% Similarity=0.286 Sum_probs=15.9
Q ss_pred HHHHHhhhcCCceEEEEEEeeee
Q psy1332 73 IDELVRTETRGQGTLELLNLKEV 95 (103)
Q Consensus 73 i~~lv~~~tkG~g~vevl~~~~~ 95 (103)
+..+..+...|..++||+|+..+
T Consensus 22 l~~i~e~~l~~~~~LeVIDv~~~ 44 (72)
T cd02978 22 LKRILEELLGGPYELEVIDVLKQ 44 (72)
T ss_pred HHHHHHHhcCCcEEEEEEEcccC
Confidence 34455556678888888887765
No 64
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=26.78 E-value=1.5e+02 Score=17.77 Aligned_cols=53 Identities=13% Similarity=0.104 Sum_probs=26.2
Q ss_pred EEEEEeeCcchHHHHHHHHHhhcc------cceeeeeeCCeEEEE--EEeCCCChHHHHHHHhhh
Q psy1332 24 VRVEVSAGVKDVKKLKEKLVKCAT------SVENEEWSGGGLLLI--CLIDPGKYREIDELVRTE 80 (103)
Q Consensus 24 l~v~~~ip~~~~~~~~~~l~~~~~------~ie~e~~~~~~~~~v--~~I~Pg~~r~i~~lv~~~ 80 (103)
+.++ +|. ..+.+++.|..+.. .|++--..++.|... +.|+- ....+...+...
T Consensus 3 l~f~--l~~-~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~~~~y~Ffvd~~~-~~~~~~~~l~~L 63 (74)
T cd04904 3 LIFS--LKE-EVGALARALKLFEEFGVNLTHIESRPSRRNGSEYEFFVDCEV-DRGDLDQLISSL 63 (74)
T ss_pred EEEE--eCC-CCcHHHHHHHHHHHCCCcEEEEECCCCCCCCceEEEEEEEEc-ChHHHHHHHHHH
Confidence 4455 654 45667777666644 244432233444444 44443 444555555443
No 65
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=26.63 E-value=1.8e+02 Score=18.65 Aligned_cols=35 Identities=11% Similarity=0.135 Sum_probs=21.8
Q ss_pred EEEEEeCCC-ChHHHHHHHhhhcCCceEEEEEEeee
Q psy1332 60 LLICLIDPG-KYREIDELVRTETRGQGTLELLNLKE 94 (103)
Q Consensus 60 ~~v~~I~Pg-~~r~i~~lv~~~tkG~g~vevl~~~~ 94 (103)
.+.+.++|| .|.++.++|.+..+=.++-=.|+-+.
T Consensus 12 tIaIrvp~~~~y~~L~~ki~~kLkl~~e~i~LsYkd 47 (80)
T cd06406 12 TVAIQVARGLSYATLLQKISSKLELPAEHITLSYKS 47 (80)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHhCCCchhcEEEecc
Confidence 566677777 48888888877766544333344433
No 66
>cd01208 X11 X11 Phosphotyrosine-binding (PTB) domain. X11 Phosphotyrosine-binding (PTB) domain. The neuronal protein X11 has a PTB domain followed by two PDZ domains. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether. X11 binds to the cytoplasmic domain of the beta-amyloid precursor protein (beta-APP) and does not require the substrate to be tyrosine-phosphorylated for binding.
Probab=25.91 E-value=74 Score=22.99 Aligned_cols=30 Identities=13% Similarity=0.159 Sum_probs=19.2
Q ss_pred CccHhHHHHhhhhhcC-ccceeeEEEEEEeeC
Q psy1332 1 MYYYSQVIPTLKQCMS-IERAQMRVRVEVSAG 31 (103)
Q Consensus 1 ~~QalevIk~Lk~~iP-I~RA~Mrl~v~~~ip 31 (103)
|.||.|+|..+|+- | =..+.+.|.++||+-
T Consensus 29 ~~~a~Eai~rik~~-eG~~~~~t~V~L~IS~~ 59 (156)
T cd01208 29 MXQAQEAVSRIKAP-EGESQPSTEVDLFISTE 59 (156)
T ss_pred HHHHHHHHHHHhcc-ccCCCCCcEEEEEEEeC
Confidence 78999999999843 2 123345666664443
No 67
>PF11495 Regulator_TrmB: Archaeal transcriptional regulator TrmB; InterPro: IPR021586 TrmB is an alpha-glucoside sensing transcriptional regulator. The protein is the transcriptional repressor for gene cluster encoding trehalose/maltose ABC transporter in T.litoralis and P.furiosus []. TrmB has lost its DNA binding domain but retained its sugar recognition site. A nonreducing glucosyl residue is shared by all substrates bound to TrmB which suggests that its a common recognition motif []. ; PDB: 3QPH_A 2F5T_X.
Probab=25.44 E-value=1.1e+02 Score=22.48 Aligned_cols=36 Identities=14% Similarity=0.350 Sum_probs=24.8
Q ss_pred HHHhhhhhcCccceeeEEEEEEeeCcchHHHHHHHHHhhc
Q psy1332 7 VIPTLKQCMSIERAQMRVRVEVSAGVKDVKKLKEKLVKCA 46 (103)
Q Consensus 7 vIk~Lk~~iPI~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~ 46 (103)
+++++++. |++|+-.|-+. +|.+....+++.|.+-.
T Consensus 11 I~~~i~el--I~~Ae~eI~is--~~~~~l~~l~~~L~~a~ 46 (233)
T PF11495_consen 11 ILERIREL--IENAESEIYIS--IPPEFLEELRDELEEAV 46 (233)
T ss_dssp HHHHHHHH--HHC-SSEEEEE--E-GGGHHHHHHHHHHHH
T ss_pred HHHHHHHH--HHHhheEEEEE--cCHHHHHHHHHHHHHHH
Confidence 44555555 78888888888 88888888877776644
No 68
>COG2262 HflX GTPases [General function prediction only]
Probab=25.05 E-value=87 Score=26.02 Aligned_cols=50 Identities=16% Similarity=0.115 Sum_probs=34.4
Q ss_pred eEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHH
Q psy1332 22 MRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDEL 76 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~l 76 (103)
-...+. +|....+ ....+...+. +.+.+|+++ ..+.+.++|..++.+.++
T Consensus 360 ~~~~l~--lp~~~~~-~~~~l~~~~~-v~~~~~~e~-~~i~~~~~~~~~~~~~~~ 409 (411)
T COG2262 360 TEVTLE--LPYTDAG-RLSWLHDNGI-VLEEEYGED-VRIKAEAPERLAKRLQEF 409 (411)
T ss_pred cceEEE--cCccccc-HHHHHHhcce-eeecccCCc-eEEEEEECHHHHHhhhhh
Confidence 334455 7776666 4466666663 667777555 889999999888887665
No 69
>PF05951 Peptidase_M15_2: Bacterial protein of unknown function (DUF882); InterPro: IPR010275 This family consists of proteins related to metallopeptidases belong to MEROPS peptidase family M15A. They are classed as non-peptidase homologues (M15A.UNA) and include A3D3U2 from SWISSPROT, where the metal ligands (marked by *) are conserved but the catalytic Asn has been replaced by Asp (+): 70 80 90 100 110 120 A3D3U2: QSKVLNDFNHLLRDHRQNVAAPMDKRLFDLLYSLKTTLNVDDEIHVISGYRSPKTNAMLA : .:. .:. : :.: ::.:: . :: . B1W1A6: PELNTCNSTWAGGKVAAGTARANALSSMWKLEALRHALG-DRSIRVTSGFRSASCNAAV- 20 30 40 50 60 70 * 130 * 140 150 160 170 * + A3D3U2: SNSGGVAKKSYHMRGMAMDIAIPSVKLKTLREAALSLKLGGV---GYYPNSGFVHVDCGP :: :..: :: : :.:.. .: :: . : . :. :: .. :::. :: B1W1A6: ---GG-ASNSRHMYGDAVDLGASPHSLCTLAKQARYHGFRGILGPGYVGHNDHVHVNQGP 80 90 100 110 120 B1W1A6 from SWISSPROT belongs to IPR013230 from INTERPRO, whcih contains peptidases belonging to the M15A family. The function of the proteins in this entry are not known.
Probab=23.85 E-value=1.8e+02 Score=20.85 Aligned_cols=62 Identities=11% Similarity=0.073 Sum_probs=40.9
Q ss_pred eeEEEEEEeeCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEEeCCCChHHHHHHHhhhcCCceEEEEEEee
Q psy1332 21 QMRVRVEVSAGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICLIDPGKYREIDELVRTETRGQGTLELLNLK 93 (103)
Q Consensus 21 ~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~I~Pg~~r~i~~lv~~~tkG~g~vevl~~~ 93 (103)
+..+..- ....+....+..|.-+.. ||..| -+..|||.+|.-|..+= ..+..+..++|++=-
T Consensus 18 ~~~~~y~--~~g~y~~~al~~l~~~lR-----D~r~~---~~~~iDp~L~d~L~~~~-~~~g~~~~i~iiSGY 79 (152)
T PF05951_consen 18 RLDIVYW--ADGRYDPEALAQLNHLLR-----DHRTN---EVHPIDPRLLDLLYELQ-QRLGSRNPIQIISGY 79 (152)
T ss_pred EEEEEEe--cCCEECHHHHHHHHHHHc-----CCCCC---CceecCHHHHHHHHHHH-HHhCCCCcEEEEeec
Confidence 3444444 455666667777666664 56433 35789999999998874 455666678888743
No 70
>PF11890 DUF3410: Domain of unknown function (DUF3410); InterPro: IPR024531 This entry represents the dimerisation domain found at the C-terminal of erythronate-4-phosphate dehydrogenases [].; GO: 0046983 protein dimerization activity; PDB: 2O4C_B 3OET_D.
Probab=23.84 E-value=48 Score=20.95 Aligned_cols=28 Identities=18% Similarity=0.172 Sum_probs=15.9
Q ss_pred HHHHhhhhhcCccceeeEEEEEEeeCcchH
Q psy1332 6 QVIPTLKQCMSIERAQMRVRVEVSAGVKDV 35 (103)
Q Consensus 6 evIk~Lk~~iPI~RA~Mrl~v~~~ip~~~~ 35 (103)
.....|++++|+.|.==-++|. ++....
T Consensus 47 ~~FD~LRk~Yp~RRE~s~~~v~--~~~~~~ 74 (82)
T PF11890_consen 47 KGFDYLRKNYPIRREFSALQVE--LDGSSA 74 (82)
T ss_dssp CHHHHHHHT------GGGSEEE--ETTHHH
T ss_pred cHHHHHHhcCchhccchheeee--cCChhH
Confidence 4567889999999988888887 666544
No 71
>PF06189 5-nucleotidase: 5'-nucleotidase; InterPro: IPR010394 This family consists of both eukaryotic and prokaryotic 5'-nucleotidase sequences (3.1.3.5 from EC).; GO: 0000166 nucleotide binding, 0000287 magnesium ion binding, 0008253 5'-nucleotidase activity, 0009117 nucleotide metabolic process, 0005737 cytoplasm
Probab=23.79 E-value=1.6e+02 Score=23.02 Aligned_cols=44 Identities=9% Similarity=0.169 Sum_probs=33.9
Q ss_pred cHhHHHHhhhhhcCccceeeEEEEEEeeC--cchHHHHHHHHHhhccc
Q psy1332 3 YYSQVIPTLKQCMSIERAQMRVRVEVSAG--VKDVKKLKEKLVKCATS 48 (103)
Q Consensus 3 QalevIk~Lk~~iPI~RA~Mrl~v~~~ip--~~~~~~~~~~l~~~~~~ 48 (103)
.-|..|-+|++.+|-..++.|+.+. .. +....++...|+.|+-.
T Consensus 168 ~fl~~L~~lQ~~~~~~~~piRtalV--TAR~apah~RvI~TLr~Wgv~ 213 (264)
T PF06189_consen 168 DFLKKLSKLQKKFPPENSPIRTALV--TARSAPAHERVIRTLRSWGVR 213 (264)
T ss_pred HHHHHHHHHHHhcCCCCCceEEEEE--EcCCCchhHHHHHHHHHcCCc
Confidence 4577888899999999999998885 32 12236888999999964
No 72
>PRK11898 prephenate dehydratase; Provisional
Probab=23.68 E-value=2.4e+02 Score=21.66 Aligned_cols=74 Identities=9% Similarity=-0.049 Sum_probs=38.2
Q ss_pred cceeeEEEEEEeeCcchHHHHHHHHHhhcc------cceeeeeeCCeEEEE--EEeCCCChH-HHHHHHhhhcCCceEEE
Q psy1332 18 ERAQMRVRVEVSAGVKDVKKLKEKLVKCAT------SVENEEWSGGGLLLI--CLIDPGKYR-EIDELVRTETRGQGTLE 88 (103)
Q Consensus 18 ~RA~Mrl~v~~~ip~~~~~~~~~~l~~~~~------~ie~e~~~~~~~~~v--~~I~Pg~~r-~i~~lv~~~tkG~g~ve 88 (103)
...+.-+-++ ++.+..+.+.+.|..|.. +|++.-+.+..|... +.++..... .+...+....+-...++
T Consensus 193 ~~~ktslif~--l~~~~pGsL~~~L~~F~~~~INLt~IeSRP~~~~~~~y~F~vd~eg~~~~~~~~~al~~L~~~~~~~k 270 (283)
T PRK11898 193 GGDKTSLVLT--LPNNLPGALYKALSEFAWRGINLTRIESRPTKTGLGTYFFFIDVEGHIDDVLVAEALKELEALGEDVK 270 (283)
T ss_pred CCCeEEEEEE--eCCCCccHHHHHHHHHHHCCCCeeeEecccCCCCCccEEEEEEEEccCCCHHHHHHHHHHHHhcCcEE
Confidence 3445667777 776546777777777644 355543334444444 444433321 34444433322233677
Q ss_pred EEEee
Q psy1332 89 LLNLK 93 (103)
Q Consensus 89 vl~~~ 93 (103)
+|..-
T Consensus 271 ~LGsY 275 (283)
T PRK11898 271 VLGSY 275 (283)
T ss_pred EEEee
Confidence 77654
No 73
>cd04446 DEP_DEPDC4 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.
Probab=23.31 E-value=73 Score=21.03 Aligned_cols=22 Identities=9% Similarity=0.301 Sum_probs=20.3
Q ss_pred HHHHhhhhhcCccceeeEEEEE
Q psy1332 6 QVIPTLKQCMSIERAQMRVRVE 27 (103)
Q Consensus 6 evIk~Lk~~iPI~RA~Mrl~v~ 27 (103)
++|+.|+..+||++-+.++++-
T Consensus 3 ~ii~~~r~~v~ikdRr~~lk~y 24 (95)
T cd04446 3 SIIDALQTQVEVKKRRHNLKSY 24 (95)
T ss_pred HHHHHHHhcCcccceeeeceec
Confidence 5799999999999999999986
No 74
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=23.17 E-value=84 Score=19.45 Aligned_cols=16 Identities=25% Similarity=0.532 Sum_probs=12.2
Q ss_pred EeCCCChHHHHHHHhh
Q psy1332 64 LIDPGKYREIDELVRT 79 (103)
Q Consensus 64 ~I~Pg~~r~i~~lv~~ 79 (103)
+|+-++||.+.+.+-+
T Consensus 45 lIEed~Y~~L~dai~e 60 (65)
T PF10440_consen 45 LIEEDNYRVLADAIFE 60 (65)
T ss_pred hhhcccHHHHHHHHHH
Confidence 4888999988776543
No 75
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=23.15 E-value=2.1e+02 Score=20.48 Aligned_cols=44 Identities=32% Similarity=0.395 Sum_probs=26.6
Q ss_pred cHhHHHHhh-------hhhcCcc-ceeeEEEEEEeeCcchHHHHHHHHHhhc
Q psy1332 3 YYSQVIPTL-------KQCMSIE-RAQMRVRVEVSAGVKDVKKLKEKLVKCA 46 (103)
Q Consensus 3 QalevIk~L-------k~~iPI~-RA~Mrl~v~~~ip~~~~~~~~~~l~~~~ 46 (103)
++|++|-+. -|.||+. ||...+.+..|--.....++.++|+++-
T Consensus 88 ~vLd~iA~~~~nvLTI~Q~ipl~g~Anvtlsi~~ssm~~~V~~ii~kl~k~e 139 (150)
T COG4492 88 DVLDVIAREEINVLTIHQTIPLQGRANVTLSIDTSSMEKDVDKIIEKLRKVE 139 (150)
T ss_pred HHHHHHHHhCCcEEEEecccccCceeeEEEEEEchhhhhhHHHHHHHHhccc
Confidence 567777665 2668864 7888888872222233445666666554
No 76
>cd02861 E_set_proteins_like E or "early" set-like proteins. These alpha amylase-like sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies are associated with different types of catalytic domains at either the N-terminal or C-terminal end. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase.
Probab=22.82 E-value=59 Score=19.90 Aligned_cols=15 Identities=27% Similarity=0.645 Sum_probs=13.3
Q ss_pred CCeEEEEEEeCCCCh
Q psy1332 56 GGGLLLICLIDPGKY 70 (103)
Q Consensus 56 ~~~~~~v~~I~Pg~~ 70 (103)
+|.|++++.++||.|
T Consensus 35 ~G~w~~~~~l~~G~y 49 (82)
T cd02861 35 DGLWVVTVELRPGRY 49 (82)
T ss_pred CCcEEEEEeCCCCcE
Confidence 689999999999984
No 77
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=22.28 E-value=1.7e+02 Score=18.23 Aligned_cols=35 Identities=17% Similarity=0.199 Sum_probs=23.1
Q ss_pred eCcchHHHHHHHHHhhcccceeeeeeCCeEEEEEE
Q psy1332 30 AGVKDVKKLKEKLVKCATSVENEEWSGGGLLLICL 64 (103)
Q Consensus 30 ip~~~~~~~~~~l~~~~~~ie~e~~~~~~~~~v~~ 64 (103)
+|......++..+..+...-.-+-|++|+-.+-.+
T Consensus 29 ~pd~k~R~vKKi~~~LV~Eg~l~yWSSGSTTmYgl 63 (67)
T PF08679_consen 29 FPDAKPREVKKIVNELVNEGKLEYWSSGSTTMYGL 63 (67)
T ss_dssp -TTS-HHHHHHHHHHHHHTTSEEEEEETTEEEEEE
T ss_pred CCCcCHHHHHHHHHHHHhhCeEEEEcCCCcEEecC
Confidence 46555566777777777654568898888777654
No 78
>TIGR02654 circ_KaiB circadian clock protein KaiB. Members of this protein family are the circadian clock protein KaiB of Cyanobacteria, encoded in the circadian clock gene cluster kaiABC. KaiB has homologs of unknown function in some Archaea and Proteobacteria, and has paralogs of unknown function in some Cyanobacteria. KaiB forms homodimers, homotetramers, and multimeric complexes with KaiA and/or KaiC.
Probab=21.57 E-value=1.4e+02 Score=19.46 Aligned_cols=22 Identities=18% Similarity=0.368 Sum_probs=14.0
Q ss_pred HHHHhhhcCCceEEEEEEeeee
Q psy1332 74 DELVRTETRGQGTLELLNLKEV 95 (103)
Q Consensus 74 ~~lv~~~tkG~g~vevl~~~~~ 95 (103)
..+..+...|..++||+++..+
T Consensus 25 ~~i~e~~l~g~y~LeVIDv~~q 46 (87)
T TIGR02654 25 KNILETEFQGVYALKVIDVLKN 46 (87)
T ss_pred HHHHHHhcCCceEEEEEEcccC
Confidence 3344556677777777776654
No 79
>PF14581 SseB_C: SseB protein C-terminal domain
Probab=21.56 E-value=2.3e+02 Score=18.08 Aligned_cols=72 Identities=13% Similarity=0.066 Sum_probs=44.6
Q ss_pred eeEEEEEEeeCcchHHHHHHHHHhhcccce---------eee-eeCCeEEEEEEeCCCChHHHHHHHhhh----cCCceE
Q psy1332 21 QMRVRVEVSAGVKDVKKLKEKLVKCATSVE---------NEE-WSGGGLLLICLIDPGKYREIDELVRTE----TRGQGT 86 (103)
Q Consensus 21 ~Mrl~v~~~ip~~~~~~~~~~l~~~~~~ie---------~e~-~~~~~~~~v~~I~Pg~~r~i~~lv~~~----tkG~g~ 86 (103)
.++|++. -|.++...+.+.|.++..+-. ..+ ..+-+|-+++.++....+.+..-+.+. ..+.-.
T Consensus 5 g~~v~l~--~P~~~p~~l~~aL~~~~~~~~~V~~Ayl~~~~~~~~~~~~li~vd~~~~~~~~~~~~i~~~~~~~~~~~~~ 82 (108)
T PF14581_consen 5 GEKVLLG--EPEEEPTDLLAALSEYFKQHKNVRAAYLALMQDEDEQPSLLIGVDFDGEDIEEIFQEIGRAARPYLPDGWP 82 (108)
T ss_pred CCEEEec--CCccCHHHHHHHHHHHHhhCccHHHhHHHHhhccCCCceEEEEEeccChhHHHHHHHHHHHhhhcCCCCce
Confidence 4677888 999998888999888876311 111 125667777777664444444444443 344456
Q ss_pred EEEEEeee
Q psy1332 87 LELLNLKE 94 (103)
Q Consensus 87 vevl~~~~ 94 (103)
+.++.+..
T Consensus 83 vd~~~~~~ 90 (108)
T PF14581_consen 83 VDFVLLDD 90 (108)
T ss_pred EEEEEccC
Confidence 77776664
No 80
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=21.45 E-value=1.8e+02 Score=16.89 Aligned_cols=29 Identities=17% Similarity=0.160 Sum_probs=16.3
Q ss_pred HHHHHHHHHhhcccceeeeeeCCeEEEEE
Q psy1332 35 VKKLKEKLVKCATSVENEEWSGGGLLLIC 63 (103)
Q Consensus 35 ~~~~~~~l~~~~~~ie~e~~~~~~~~~v~ 63 (103)
...+...+...+..+...+..++.|.+.+
T Consensus 40 ~~di~~~~~~~g~~~~~~~~~~~~~~i~I 68 (70)
T PF01206_consen 40 VEDIPRWCEENGYEVVEVEEEGGEYRILI 68 (70)
T ss_dssp HHHHHHHHHHHTEEEEEEEESSSSEEEEE
T ss_pred HHHHHHHHHHCCCEEEEEEEeCCEEEEEE
Confidence 35666666666665433322466676654
No 81
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=21.35 E-value=89 Score=17.39 Aligned_cols=16 Identities=25% Similarity=0.117 Sum_probs=8.8
Q ss_pred eEEEEEEeeCcchHHH
Q psy1332 22 MRVRVEVSAGVKDVKK 37 (103)
Q Consensus 22 Mrl~v~~~ip~~~~~~ 37 (103)
||.++++++|.+...+
T Consensus 1 ~r~r~t~~l~~el~~~ 16 (44)
T PF12651_consen 1 NRKRFTFSLDKELYEK 16 (44)
T ss_pred CceEEEEecCHHHHHH
Confidence 4556665577544333
No 82
>PF06816 NOD: NOTCH protein; InterPro: IPR010660 NOTCH signalling plays a fundamental role during a great number of developmental processes in multicellular animals []. NOD (NOTCH protein domain) represents a region present in many NOTCH proteins and NOTCH homologues in multiple species such as 0, NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. Role of NOD domain remains to be elucidated.; GO: 0030154 cell differentiation, 0016021 integral to membrane; PDB: 2OO4_A 3ETO_A 3I08_A 3L95_X.
Probab=20.52 E-value=25 Score=21.08 Aligned_cols=26 Identities=27% Similarity=0.672 Sum_probs=18.5
Q ss_pred eCCeEEEEEEeCCCChHHHH-HHHhhh
Q psy1332 55 SGGGLLLICLIDPGKYREID-ELVRTE 80 (103)
Q Consensus 55 ~~~~~~~v~~I~Pg~~r~i~-~lv~~~ 80 (103)
..|.+.++++++|-.|+.-. .++++.
T Consensus 5 a~G~lvivvl~~P~~f~~~~~~FLr~L 31 (57)
T PF06816_consen 5 AEGTLVIVVLMDPEEFRNNSVQFLREL 31 (57)
T ss_dssp -BSEEEEEESS-HHHHHHTHHHHHHHH
T ss_pred cceeEEEEEEeCHHHHHHHHHHHHHHH
Confidence 37899999999999987643 555554
No 83
>PF02108 FliH: Flagellar assembly protein FliH; InterPro: IPR018035 This entry represents a region found in the flagellar assembly protein FliH, as well as in type III secretion system protein HrpE. Many flagellar proteins are exported by a flagellum-specific export pathway. Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export []. The sequence of fliH has been deduced and shown to encode a protein of molecular mass of 25,782 Da. Bacterial HrpE proteins are belived to function on the type III secretion system, specifically the secretion of HrpZ (harpinPss) [].
Probab=20.34 E-value=1.1e+02 Score=19.70 Aligned_cols=24 Identities=25% Similarity=0.383 Sum_probs=13.2
Q ss_pred CccceeeEEEEEEeeCcchHHHHHHHHH
Q psy1332 16 SIERAQMRVRVEVSAGVKDVKKLKEKLV 43 (103)
Q Consensus 16 PI~RA~Mrl~v~~~ip~~~~~~~~~~l~ 43 (103)
|-.+.+++|++. +++...+.+.+.
T Consensus 64 ~~~~~~v~I~v~----p~d~~~l~~~~~ 87 (128)
T PF02108_consen 64 PRDEEKVTIRVH----PDDYEALEELLE 87 (128)
T ss_pred hccCCCeEEEEC----HHHHHHHHHHHH
Confidence 555555555554 455565655555
Done!