Query psy6083
Match_columns 74
No_of_seqs 140 out of 1048
Neff 8.5
Searched_HMMs 46136
Date Fri Aug 16 17:12:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6083.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6083hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0100|consensus 99.9 1.9E-25 4.2E-30 149.9 5.9 74 1-74 93-167 (663)
2 KOG0103|consensus 99.8 6.4E-19 1.4E-23 123.0 4.0 73 1-73 58-131 (727)
3 KOG0102|consensus 99.7 3E-18 6.6E-23 117.6 5.4 70 1-74 85-155 (640)
4 PTZ00009 heat shock 70 kDa pro 99.7 2.5E-17 5.4E-22 115.9 7.3 74 1-74 61-135 (653)
5 KOG0101|consensus 99.7 1.5E-17 3.3E-22 115.8 2.6 74 1-74 64-138 (620)
6 PTZ00400 DnaK-type molecular c 99.7 2.3E-16 5E-21 111.2 6.6 70 1-74 99-169 (663)
7 PTZ00186 heat shock 70 kDa pre 99.6 1.1E-15 2.3E-20 107.9 6.0 71 1-74 84-155 (657)
8 PF00012 HSP70: Hsp70 protein; 99.6 6.8E-15 1.5E-19 101.8 7.3 73 1-73 56-129 (602)
9 PRK13410 molecular chaperone D 99.5 1.2E-14 2.7E-19 102.7 6.2 70 1-74 60-130 (668)
10 PRK13411 molecular chaperone D 99.5 1.5E-14 3.3E-19 101.9 6.0 68 1-74 60-128 (653)
11 PRK00290 dnaK molecular chaper 99.5 4.4E-14 9.5E-19 99.1 6.0 68 1-74 60-128 (627)
12 PLN03184 chloroplast Hsp70; Pr 99.5 5.4E-14 1.2E-18 99.5 6.0 70 1-74 97-167 (673)
13 TIGR02350 prok_dnaK chaperone 99.4 1.5E-13 3.3E-18 95.8 5.8 68 1-74 58-125 (595)
14 TIGR01991 HscA Fe-S protein as 99.4 3.3E-13 7.1E-18 94.5 5.3 67 1-74 57-124 (599)
15 CHL00094 dnaK heat shock prote 99.4 5.1E-13 1.1E-17 93.8 5.9 69 1-73 60-129 (621)
16 PRK05183 hscA chaperone protei 99.4 8.9E-13 1.9E-17 92.6 5.3 68 1-74 76-144 (616)
17 KOG0104|consensus 99.1 1.9E-10 4.2E-15 82.0 5.2 71 1-74 80-153 (902)
18 PRK01433 hscA chaperone protei 98.8 3.2E-09 6.8E-14 74.7 3.9 65 6-74 71-136 (595)
19 COG0443 DnaK Molecular chapero 98.7 1.5E-08 3.3E-13 71.2 4.4 51 1-74 64-115 (579)
20 PRK11678 putative chaperone; P 96.6 0.0025 5.4E-08 44.1 3.1 20 55-74 125-144 (450)
21 PF03484 B5: tRNA synthetase B 86.2 0.97 2.1E-05 23.4 2.5 57 7-64 8-65 (70)
22 cd02426 Pol_gamma_b_Cterm C-te 82.8 2.4 5.2E-05 24.6 3.3 43 25-67 79-126 (128)
23 PF12971 NAGLU_N: Alpha-N-acet 72.2 9.7 0.00021 20.5 3.6 54 10-72 9-67 (86)
24 PRK04081 hypothetical protein; 71.1 13 0.00028 23.6 4.3 38 32-69 61-101 (207)
25 cd00460 RNAP_RPB11_RPB3 RPB11 69.9 15 0.00033 19.7 4.2 33 38-73 53-85 (86)
26 COG1097 RRP4 RNA-binding prote 68.3 12 0.00026 24.4 3.8 36 8-45 155-191 (239)
27 smart00874 B5 tRNA synthetase 67.2 6.8 0.00015 19.9 2.2 30 7-36 8-37 (71)
28 PF10788 DUF2603: Protein of u 65.5 22 0.00048 21.2 4.3 34 38-71 39-72 (137)
29 cd00862 ProRS_anticodon_zinc P 64.1 32 0.0007 21.3 5.4 44 25-68 63-111 (202)
30 PF08127 Propeptide_C1: Peptid 59.7 4.2 9.2E-05 19.1 0.5 16 4-19 24-39 (41)
31 KOG1004|consensus 56.0 19 0.00041 23.2 3.1 35 10-46 158-193 (230)
32 PRK04163 exosome complex RNA-b 52.0 53 0.0012 21.0 4.8 35 9-45 155-190 (235)
33 PF02593 dTMP_synthase: Thymid 49.8 24 0.00051 22.6 2.9 60 4-71 156-215 (217)
34 PRK14894 glycyl-tRNA synthetas 45.4 55 0.0012 23.9 4.3 51 13-67 475-537 (539)
35 PF14847 Ras_bdg_2: Ras-bindin 41.4 49 0.0011 18.7 3.0 28 36-67 7-34 (105)
36 TIGR00746 arcC carbamate kinas 41.1 59 0.0013 21.8 3.8 33 7-39 122-154 (310)
37 PF03646 FlaG: FlaG protein; 40.9 63 0.0014 17.7 4.6 40 30-70 57-99 (107)
38 PF12937 F-box-like: F-box-lik 40.8 7.9 0.00017 18.0 -0.2 13 55-67 4-16 (47)
39 KOG1434|consensus 39.9 40 0.00086 22.7 2.8 44 31-74 211-255 (335)
40 COG4545 Glutaredoxin-related p 39.7 34 0.00073 18.6 2.1 21 6-26 37-57 (85)
41 PRK08661 prolyl-tRNA synthetas 39.4 1.1E+02 0.0024 21.6 5.1 46 25-70 340-390 (477)
42 COG3721 HugX Putative heme iro 38.8 31 0.00067 21.2 2.0 28 35-62 139-167 (176)
43 PF04986 Y2_Tnp: Putative tran 37.6 82 0.0018 19.2 3.9 35 33-67 123-162 (183)
44 PRK13669 hypothetical protein; 37.0 32 0.00069 18.5 1.7 16 54-69 59-74 (78)
45 PF01193 RNA_pol_L: RNA polyme 36.9 39 0.00084 17.0 2.0 31 38-71 35-65 (66)
46 PF01614 IclR: Bacterial trans 36.4 51 0.0011 18.3 2.7 20 54-73 106-125 (129)
47 PF03129 HGTP_anticodon: Antic 35.6 53 0.0012 17.1 2.6 39 26-64 49-92 (94)
48 PF01913 FTR: Formylmethanofur 34.9 1E+02 0.0022 18.6 3.8 30 37-70 66-95 (144)
49 TIGR00408 proS_fam_I prolyl-tR 34.3 1.6E+02 0.0036 20.8 5.3 45 26-70 335-384 (472)
50 PRK15322 invasion protein OrgB 34.1 1.3E+02 0.0028 19.3 4.3 41 28-69 134-176 (210)
51 PRK08868 flagellar protein Fla 33.9 1.1E+02 0.0024 18.4 4.1 41 28-69 89-132 (144)
52 PF02058 Guanylin: Guanylin pr 33.4 47 0.001 18.4 2.0 13 60-72 61-73 (89)
53 COG4844 Uncharacterized protei 33.4 37 0.00079 18.0 1.6 16 55-70 60-75 (78)
54 cd07028 RNAP_RPB3_like RPB3 su 33.1 1.1E+02 0.0024 19.3 4.0 39 32-73 170-208 (212)
55 smart00256 FBOX A Receptor for 32.8 21 0.00045 15.4 0.5 12 56-67 2-13 (41)
56 PF00427 PBS_linker_poly: Phyc 30.8 24 0.00052 20.8 0.7 14 8-21 76-89 (131)
57 PF08673 RsbU_N: Phosphoserine 30.8 59 0.0013 17.3 2.2 21 52-72 33-53 (77)
58 PF12993 DUF3877: Domain of un 30.5 52 0.0011 20.4 2.1 54 7-62 32-86 (175)
59 TIGR00472 pheT_bact phenylalan 29.7 59 0.0013 24.5 2.7 34 6-39 411-444 (798)
60 PRK07738 flagellar protein Fla 29.5 1.2E+02 0.0026 17.5 3.9 41 29-70 65-108 (117)
61 PF10178 DUF2372: Uncharacteri 29.2 19 0.00041 19.8 0.0 25 4-30 27-51 (90)
62 PF10726 DUF2518: Protein of f 28.4 1.2E+02 0.0026 18.3 3.3 29 31-62 71-99 (145)
63 PF13280 WYL: WYL domain 28.3 80 0.0017 18.0 2.7 21 51-71 152-172 (172)
64 PF07498 Rho_N: Rho terminatio 28.1 31 0.00067 16.0 0.7 15 59-73 2-16 (43)
65 KOG3493|consensus 28.1 25 0.00053 18.5 0.4 17 2-18 19-35 (73)
66 PF00646 F-box: F-box domain; 28.0 24 0.00052 16.1 0.3 13 56-68 7-19 (48)
67 PF11955 PORR: Plant organelle 28.0 68 0.0015 21.8 2.6 56 4-61 120-178 (335)
68 TIGR00471 pheT_arch phenylalan 28.0 79 0.0017 22.8 3.0 30 7-36 284-313 (551)
69 PRK05339 PEP synthetase regula 27.5 22 0.00047 23.5 0.1 28 37-70 238-265 (269)
70 PF13656 RNA_pol_L_2: RNA poly 27.4 1E+02 0.0023 16.1 3.5 38 32-72 33-71 (77)
71 PF05965 FYRC: F/Y rich C-term 27.1 1.1E+02 0.0023 16.1 4.1 32 39-70 2-37 (86)
72 PRK09616 pheT phenylalanyl-tRN 26.8 82 0.0018 22.7 2.9 30 7-36 281-310 (552)
73 PRK01146 DNA-directed RNA poly 26.7 1.1E+02 0.0025 16.4 3.5 33 38-73 50-82 (85)
74 PF07293 DUF1450: Protein of u 26.7 54 0.0012 17.6 1.6 16 55-70 60-75 (78)
75 PF08171 Mad3_BUB1_II: Mad3/BU 26.7 24 0.00053 18.5 0.2 17 47-63 37-53 (68)
76 TIGR00409 proS_fam_II prolyl-t 26.0 70 0.0015 23.2 2.4 39 26-64 523-566 (568)
77 PF02575 YbaB_DNA_bd: YbaB/Ebf 25.8 1.2E+02 0.0025 16.1 5.6 48 23-70 14-71 (93)
78 TIGR02431 pcaR_pcaU beta-ketoa 25.2 1.4E+02 0.003 18.8 3.5 36 37-72 207-242 (248)
79 PF04407 DUF531: Protein of un 24.9 37 0.00081 20.9 0.8 19 47-65 100-118 (173)
80 PF14756 Pdase_C33_assoc: Pept 24.8 46 0.00099 19.5 1.1 21 51-71 92-112 (147)
81 PF05047 L51_S25_CI-B8: Mitoch 23.5 99 0.0021 14.5 4.4 37 21-57 10-48 (52)
82 cd01786 STE50_RA Ubiquitin-lik 23.4 1.5E+02 0.0033 16.6 3.5 28 43-70 60-87 (98)
83 PLN02975 complex I subunit 23.3 52 0.0011 18.5 1.1 19 8-26 77-95 (97)
84 PRK14537 50S ribosomal protein 22.9 73 0.0016 20.7 1.8 18 57-74 189-206 (230)
85 COG0072 PheT Phenylalanyl-tRNA 22.6 82 0.0018 23.3 2.3 31 6-36 270-300 (650)
86 PRK00629 pheT phenylalanyl-tRN 22.4 1E+02 0.0023 23.2 2.8 30 7-36 407-436 (791)
87 COG3172 NadR Predicted ATPase/ 22.3 2.1E+02 0.0046 18.0 3.7 39 3-43 88-128 (187)
88 PF02831 gpW: gpW; InterPro: 22.3 1.3E+02 0.0029 15.6 4.9 31 38-69 19-49 (68)
89 PRK14645 hypothetical protein; 22.2 89 0.0019 18.8 2.1 55 3-62 90-145 (154)
90 TIGR02529 EutJ ethanolamine ut 22.0 72 0.0016 20.2 1.7 21 53-73 35-55 (239)
91 PF14053 DUF4248: Domain of un 22.0 78 0.0017 16.4 1.6 17 50-67 50-66 (69)
92 KOG1584|consensus 21.9 12 0.00027 25.0 -1.8 24 2-25 201-224 (297)
93 COG4302 EutC Ethanolamine ammo 21.9 69 0.0015 21.3 1.6 20 9-28 134-153 (294)
94 PF09545 RE_AccI: AccI restric 21.9 2E+02 0.0043 19.8 3.7 26 37-62 333-358 (366)
95 PF11918 DUF3436: Domain of un 21.9 46 0.00099 16.8 0.6 16 53-68 37-52 (55)
96 PF01202 SKI: Shikimate kinase 21.6 67 0.0015 18.7 1.5 15 54-68 144-158 (158)
97 cd06927 RNAP_L L subunit of Ar 21.0 1.5E+02 0.0033 15.8 3.8 33 38-73 48-80 (83)
98 PF07671 DUF1601: Protein of u 20.7 1.1E+02 0.0024 14.0 2.0 22 53-74 7-28 (37)
99 PF12321 DUF3634: Protein of u 20.6 1.8E+02 0.004 16.6 3.6 14 61-74 44-57 (108)
100 PLN02496 probable phosphopanto 20.6 1.1E+02 0.0024 19.4 2.4 52 18-71 146-201 (209)
101 cd08031 LARP_4_5_like La RNA-b 20.6 69 0.0015 16.9 1.2 29 3-31 34-62 (75)
102 PF10407 Cytokin_check_N: Cdc1 20.3 55 0.0012 17.3 0.8 22 2-31 10-31 (73)
103 smart00662 RPOLD RNA polymeras 20.2 2.4E+02 0.0051 17.8 3.8 32 39-73 192-223 (224)
104 PLN02720 complex II 20.1 71 0.0015 19.0 1.3 25 7-31 24-53 (140)
No 1
>KOG0100|consensus
Probab=99.92 E-value=1.9e-25 Score=149.88 Aligned_cols=74 Identities=64% Similarity=0.930 Sum_probs=70.8
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEeCCCcceEEEEEC-CeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVNDCSKPKIQVEFK-GERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~~~g~~~~~v~~~-~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
+||.|||++.||||||.|+|+.||.+.++|||++++.+|++.++|... |+.+.|+||||+||||.+||++||+|
T Consensus 93 ~NPenTiFD~KRLIGr~~~d~~vq~Dik~~Pfkvv~k~~kp~i~v~v~~g~~K~FtPeEiSaMiL~KMKe~AEay 167 (663)
T KOG0100|consen 93 SNPENTIFDAKRLIGRKFNDKSVQKDIKFLPFKVVNKDGKPYIQVKVGGGETKVFTPEEISAMILTKMKETAEAY 167 (663)
T ss_pred cCcccceechHHHhCcccCChhhhhhhhcCceEEEcCCCCccEEEEccCCcccccCHHHHHHHHHHHHHHHHHHH
Confidence 599999999999999999999999999999999999999999999986 56899999999999999999999987
No 2
>KOG0103|consensus
Probab=99.75 E-value=6.4e-19 Score=123.01 Aligned_cols=73 Identities=48% Similarity=0.730 Sum_probs=70.3
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhc
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALY 73 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~ 73 (74)
+|++||+.++|||+||.|+||.+|.+.+++|+.++. .||.+++.+.|.|+.+.|||+||.||+|.+||++|++
T Consensus 58 ~n~kntv~~~KRl~Gr~f~dP~~q~~~~~~~~~vv~~~dg~vgi~v~ylge~~~ft~~Qv~Am~l~klk~~ae~ 131 (727)
T KOG0103|consen 58 TNVKNTVSNFKRLIGRKFSDPEVQREIKSLPRSVVQLKDGDVGIKVEYLGEKHPFTPEQVLAMLLTKLKATAEK 131 (727)
T ss_pred ecccccchhhhhhhccccCChHhhhcccccchheeecCCCCcceeehcccCCCCCChHHHHHHHHHHHHHHHHH
Confidence 589999999999999999999999999999999988 8999999999999999999999999999999999975
No 3
>KOG0102|consensus
Probab=99.74 E-value=3e-18 Score=117.60 Aligned_cols=70 Identities=44% Similarity=0.777 Sum_probs=66.0
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
.||.|||+..||||||+|+||++|.+.+.+||+++. .||+.|++. ..+.|+|.|+.+++|.+||+.|++|
T Consensus 85 ~n~~ntffatKrligRrf~d~evq~~~k~vpyKiVk~~ngdaw~e~----~G~~~spsqig~~vl~kmk~tae~y 155 (640)
T KOG0102|consen 85 TNPENTFFATKRLIGRRFDDPEVQKDIKQVPYKIVKASNGDAWVEA----RGKQYSPSQIGAFVLMKMKETAEAY 155 (640)
T ss_pred cCCCceEEEehhhhhhhccCHHHHHHHHhCCcceEEccCCcEEEEe----CCeEecHHHHHHHHHHHHHHHHHHH
Confidence 489999999999999999999999999999999998 899999988 3678999999999999999999986
No 4
>PTZ00009 heat shock 70 kDa protein; Provisional
Probab=99.71 E-value=2.5e-17 Score=115.86 Aligned_cols=74 Identities=68% Similarity=1.029 Sum_probs=68.3
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
+||+||++++|||||+.++|+.++...+.|||+++. .+|.+.+.+.+.++.+.|+|+||+|++|++||+.|+.|
T Consensus 61 ~~p~~ti~~~KrliG~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~peel~a~iL~~lk~~ae~~ 135 (653)
T PTZ00009 61 RNPENTVFDAKRLIGRKFDDSVVQSDMKHWPFKVTTGGDDKPMIEVTYQGEKKTFHPEEISSMVLQKMKEIAEAY 135 (653)
T ss_pred hCcccEEhhhHHHhCCCCCchhHhhhhhcCceEEEEcCCCceEEEEEeCCceEEECHHHHHHHHHHHHHHHHHHH
Confidence 489999999999999999999999999999999887 78888999988877789999999999999999999864
No 5
>KOG0101|consensus
Probab=99.68 E-value=1.5e-17 Score=115.82 Aligned_cols=74 Identities=70% Similarity=1.067 Sum_probs=69.8
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
+||.||++++||||||.++||.++.++++|||++.. .++.+.+.+.++++.+.|+|+++++++|.+||+.|++|
T Consensus 64 ~np~ntv~~~krliGr~f~d~~v~~~~k~~pf~V~~~~~~~~~i~~~~~~~~~~f~peeiss~~L~klke~Ae~~ 138 (620)
T KOG0101|consen 64 RNPDNTVFDAKRLIGRFFDDPEVQSDMKLWPFKVISDQGGKPKIQVTYKGETKSFNPEEISSMVLTKLKETAEAY 138 (620)
T ss_pred cCCcceeeehhhhcCccccchhhHhHhhcCCcccccccCCcceEEecccccceeeeeeeeeehhccccHHHHHHH
Confidence 589999999999999999999999999999999986 56789999999998999999999999999999999976
No 6
>PTZ00400 DnaK-type molecular chaperone; Provisional
Probab=99.66 E-value=2.3e-16 Score=111.21 Aligned_cols=70 Identities=40% Similarity=0.683 Sum_probs=62.9
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
+||.||++++|||||++++|+.++...+.+||+++. ++|.+.+.+. .+.|+|+||+|++|++||+.|+.|
T Consensus 99 ~~p~~ti~~~KrliG~~~~d~~~~~~~~~~p~~~~~~~~~~~~~~~~----~~~~speel~a~iL~~lk~~ae~~ 169 (663)
T PTZ00400 99 TNPENTVFATKRLIGRRYDEDATKKEQKILPYKIVRASNGDAWIEAQ----GKKYSPSQIGAFVLEKMKETAESY 169 (663)
T ss_pred hCCcceehhhhhhcCCCcCcHHHHhhhccCCeEEEecCCCceEEEEC----CEEECHHHHHHHHHHHHHHHHHHH
Confidence 489999999999999999999999999999999987 7788887763 468999999999999999999864
No 7
>PTZ00186 heat shock 70 kDa precursor protein; Provisional
Probab=99.61 E-value=1.1e-15 Score=107.89 Aligned_cols=71 Identities=41% Similarity=0.684 Sum_probs=62.4
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
+||.||++++||+||++++|+.++...+.|||+++. .+|.+.+... ..+.|+|+||+|++|++||+.|++|
T Consensus 84 ~~p~~ti~~~KRliG~~~~d~~v~~~~~~~p~~vv~~~~~~~~i~~~---~~~~~speeisa~iL~~Lk~~Ae~~ 155 (657)
T PTZ00186 84 TNPQSTFYAVKRLIGRRFEDEHIQKDIKNVPYKIVRAGNGDAWVQDG---NGKQYSPSQIGAFVLEKMKETAENF 155 (657)
T ss_pred hCchhHHHHHHHHhccccccHHHHHhhccCcEEEEEcCCCceEEEeC---CCeEEcHHHHHHHHHHHHHHHHHHH
Confidence 489999999999999999999999999999999987 6777666542 3578999999999999999999864
No 8
>PF00012 HSP70: Hsp70 protein; InterPro: IPR013126 Heat shock proteins, Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region []. Hsp70 proteins have an average molecular weight of 70 kDa [, , ]. In most species,there are many proteins that belong to the hsp70 family. Some of these are only expressed under stress conditions (strictly inducible), while some are present in cells under normal growth conditions and are not heat-inducible (constitutive or cognate) [, ]. Hsp70 proteins can be found in different cellular compartments(nuclear, cytosolic, mitochondrial, endoplasmic reticulum, for example).; PDB: 2P32_D 3D2F_A 2QXL_A 3D2E_C 3C7N_A 3FE1_C 4ANI_C 2V7Y_A 2KHO_A 3DPQ_B ....
Probab=99.58 E-value=6.8e-15 Score=101.79 Aligned_cols=73 Identities=48% Similarity=0.850 Sum_probs=68.1
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhc
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALY 73 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~ 73 (74)
++|++|++++|||||+.++++.++.+.+.+||+++. ++|.+.+++.+.|..+.|+|+||++++|++|++.|+.
T Consensus 56 ~~~~~~~~~~k~liG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~a~~ 129 (602)
T PF00012_consen 56 RNPKNTIYNLKRLIGRKFDDPDVQKEKKKFPYKVVEDPDGKVYFEVDYDGKSKTYSPEELSAMILKYLKEMAEK 129 (602)
T ss_dssp TSGGGEEESGGGTTTSBTTSHHHHHHHTTSSSEEEEETTTEEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHH
T ss_pred cccccccccccccccccccccccchhhhcccccccccccccccccccccccceeeeeecccccchhhhcccchh
Confidence 479999999999999999999999999999999987 6899999999888788999999999999999999875
No 9
>PRK13410 molecular chaperone DnaK; Provisional
Probab=99.54 E-value=1.2e-14 Score=102.69 Aligned_cols=70 Identities=34% Similarity=0.677 Sum_probs=59.7
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
+||+||++++|||||++++| ++.+.+++||++.. ++|.+.+.+.. ..+.|+|+||+|++|++|++.|+.|
T Consensus 60 ~~p~~ti~~~KRliG~~~~~--~~~~~~~~~~~v~~~~~g~~~i~~~~--~~~~~speel~a~iL~~lk~~ae~~ 130 (668)
T PRK13410 60 LNPQNTFYNLKRFIGRRYDE--LDPESKRVPYTIRRNEQGNVRIKCPR--LEREFAPEELSAMILRKLADDASRY 130 (668)
T ss_pred hCccceehHHhhhhCCCchh--hHHhhccCCeEEEECCCCcEEEEEec--CCeEEcHHHHHHHHHHHHHHHHHHH
Confidence 48999999999999999977 56677889999987 67887777643 3578999999999999999999764
No 10
>PRK13411 molecular chaperone DnaK; Provisional
Probab=99.53 E-value=1.5e-14 Score=101.93 Aligned_cols=68 Identities=35% Similarity=0.653 Sum_probs=57.9
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
+||.||++++|||||++++|+. .+.+++||+++. .+|.+.+.+. .+.|+|+||+|++|++||+.|+.+
T Consensus 60 ~~p~~ti~~~KrliG~~~~d~~--~~~~~~~~~~v~~~~~~~~~~i~----~~~~~peei~a~iL~~lk~~ae~~ 128 (653)
T PRK13411 60 TNAENTVYSIKRFIGRRWDDTE--EERSRVPYTCVKGRDDTVNVQIR----GRNYTPQEISAMILQKLKQDAEAY 128 (653)
T ss_pred hCcccchHHHHHHhCCCccchh--HHhhcCCceEEecCCCceEEEEC----CEEECHHHHHHHHHHHHHHHHHHH
Confidence 4899999999999999999964 456889999887 6777777762 468999999999999999999864
No 11
>PRK00290 dnaK molecular chaperone DnaK; Provisional
Probab=99.50 E-value=4.4e-14 Score=99.10 Aligned_cols=68 Identities=40% Similarity=0.732 Sum_probs=58.9
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
+||.||++++|||||+. ++.++...+++||+++. .+|...+.+ . .+.|+|+||+|++|++|++.|+.+
T Consensus 60 ~~p~~~i~~~Kr~iG~~--~~~~~~~~~~~p~~~~~~~~~~~~~~~--~--~~~~~peel~a~iL~~lk~~ae~~ 128 (627)
T PRK00290 60 TNPENTIFSIKRLMGRR--DEEVQKDIKLVPYKIVKADNGDAWVEI--D--GKKYTPQEISAMILQKLKKDAEDY 128 (627)
T ss_pred hCchhhHHHHHHHhCCC--chHHHHHhhcCCeEEEEcCCCceEEEE--C--CEEEcHHHHHHHHHHHHHHHHHHH
Confidence 48999999999999998 67788888999999987 677777765 2 468999999999999999999763
No 12
>PLN03184 chloroplast Hsp70; Provisional
Probab=99.49 E-value=5.4e-14 Score=99.49 Aligned_cols=70 Identities=37% Similarity=0.573 Sum_probs=59.7
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
+||.||++++|||||++++| ++...+.+||+++. ++|.+.+.+... .+.|+|+||+|++|++|++.|+.+
T Consensus 97 ~~p~~ti~~~KrliG~~~~d--~~~~~~~~~~~v~~~~~~~v~~~~~~~--~~~~speei~a~iL~~lk~~ae~~ 167 (673)
T PLN03184 97 VNPENTFFSVKRFIGRKMSE--VDEESKQVSYRVVRDENGNVKLDCPAI--GKQFAAEEISAQVLRKLVDDASKF 167 (673)
T ss_pred hCchhhhHHHHHhhCCCcch--hhhhhhcCCeEEEecCCCcEEEEEecC--CeEEcHHHHHHHHHHHHHHHHHHH
Confidence 48999999999999999987 56677889999987 678887776543 358999999999999999998753
No 13
>TIGR02350 prok_dnaK chaperone protein DnaK. Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved.
Probab=99.45 E-value=1.5e-13 Score=95.80 Aligned_cols=68 Identities=38% Similarity=0.763 Sum_probs=58.2
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEeCCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVNDCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
+||.||++++|||||+.+++ ++...+++||++..++|.+.+.+. .+.|+|+||+|++|++|++.|+.+
T Consensus 58 ~~p~~~i~~~Kr~iG~~~~~--~~~~~~~~~~~v~~~~~~~~~~v~----~~~~~peel~a~~L~~l~~~a~~~ 125 (595)
T TIGR02350 58 TNPENTIYSIKRFMGRRFDE--VTEEAKRVPYKVVGDGGDVRVKVD----GKEYTPQEISAMILQKLKKDAEAY 125 (595)
T ss_pred hCchhhhHHHHHHhCCCchH--HHHHhhcCCeeEEcCCCceEEEEC----CEEecHHHHHHHHHHHHHHHHHHH
Confidence 48999999999999999944 777788999996557888888773 468999999999999999999763
No 14
>TIGR01991 HscA Fe-S protein assembly chaperone HscA. The Heat Shock Cognate proteins HscA and HscB act together as chaperones. HscA resembles DnaK but belongs in a separate clade. The apparent function is to aid assembly of iron-sulfur cluster proteins. Homologs from Buchnera and Wolbachia are clearly in the same clade but are highly derived and score lower than some examples of DnaK.
Probab=99.41 E-value=3.3e-13 Score=94.49 Aligned_cols=67 Identities=31% Similarity=0.487 Sum_probs=56.2
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
+||.||++++|||||++++|+. . .+.+||+++. .+|.+.+.+.. ..++|+||+|++|++|++.|+.+
T Consensus 57 ~~p~~ti~~~Kr~iG~~~~d~~--~-~~~~~~~~~~~~~~~~~~~~~~----~~~~p~ei~a~iL~~lk~~a~~~ 124 (599)
T TIGR01991 57 EDPKNTISSVKRLMGRSIEDIK--T-FSILPYRFVDGPGEMVRLRTVQ----GTVTPVEVSAEILKKLKQRAEES 124 (599)
T ss_pred hChhhhHHHHHHHhCCCccchh--h-cccCCEEEEEcCCCceEEEeCC----CEEcHHHHHHHHHHHHHHHHHHH
Confidence 4799999999999999998853 3 5778999987 67888777642 37999999999999999999753
No 15
>CHL00094 dnaK heat shock protein 70
Probab=99.40 E-value=5.1e-13 Score=93.77 Aligned_cols=69 Identities=41% Similarity=0.631 Sum_probs=58.5
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhc
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALY 73 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~ 73 (74)
.||.||++++||+||+.++| ++...+.+||+++. .+|.+.+.+... .+.|+|+||++++|++|++.|+.
T Consensus 60 ~~p~~ti~~~KrliG~~~~~--~~~~~~~~~~~v~~~~~g~i~~~~~~~--~~~~s~eei~a~iL~~l~~~ae~ 129 (621)
T CHL00094 60 INPENTFYSVKRFIGRKFSE--ISEEAKQVSYKVKTDSNGNIKIECPAL--NKDFSPEEISAQVLRKLVEDASK 129 (621)
T ss_pred hCccceehhhHHhcCCChHH--HHhhhhcCCeEEEECCCCCEEEEEecC--CeEEcHHHHHHHHHHHHHHHHHH
Confidence 37999999999999999976 55666789999987 678877776543 46899999999999999999875
No 16
>PRK05183 hscA chaperone protein HscA; Provisional
Probab=99.37 E-value=8.9e-13 Score=92.59 Aligned_cols=68 Identities=32% Similarity=0.545 Sum_probs=57.3
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
+||.||++++|||||+.++| ++.....+||.+.. .+|.+.+.+. ...++|+||+|++|++|++.|+.+
T Consensus 76 ~~p~~ti~~~KrliG~~~~d--~~~~~~~~~~~~~~~~~g~~~~~~~----~~~~~p~ei~a~iL~~lk~~ae~~ 144 (616)
T PRK05183 76 QDPKNTISSVKRFMGRSLAD--IQQRYPHLPYQFVASENGMPLIRTA----QGLKSPVEVSAEILKALRQRAEET 144 (616)
T ss_pred hCchhhHHHHHHHhCCCchh--hhhhhhcCCeEEEecCCCceEEEec----CCeEcHHHHHHHHHHHHHHHHHHH
Confidence 47999999999999999987 45556789999887 6888888763 237899999999999999999763
No 17
>KOG0104|consensus
Probab=99.08 E-value=1.9e-10 Score=81.98 Aligned_cols=71 Identities=28% Similarity=0.456 Sum_probs=59.6
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCe-EEEeC--CCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPF-TVVND--CSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~-~i~~~--~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
++|++++..+|.|+|++.+||.++.+.+++|| .++.+ .+.+.|.+ .+ ...||+|||+||+|.+.+..||.|
T Consensus 80 r~P~~~~~~l~~llgk~~~~~~v~ly~~~~p~~e~v~d~~rstV~F~i--~d-~~~ysvEellAMil~~a~~~ae~~ 153 (902)
T KOG0104|consen 80 RFPQSTYRQLKDLLGKSLDDPTVDLYQKRFPFFELVEDPQRSTVVFKI--SD-QEEYSVEELLAMILQYAKSLAEEY 153 (902)
T ss_pred cCcHHHHHHHHHHhCcccCCcHHHHHHhcCCceeecccCccceEEEEe--CC-ccccCHHHHHHHHHHHHHHHHHHH
Confidence 47999999999999999999999999998885 57764 35555555 33 578999999999999999999865
No 18
>PRK01433 hscA chaperone protein HscA; Provisional
Probab=98.84 E-value=3.2e-09 Score=74.75 Aligned_cols=65 Identities=20% Similarity=0.249 Sum_probs=41.7
Q ss_pred chhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 6 TVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 6 ti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
|++++|||||+.++|................ .++...+. .. .+.|+|+||+|++|++||+.|+.+
T Consensus 71 ti~~~KrliG~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~--~~--~~~~speei~a~iL~~lk~~ae~~ 136 (595)
T PRK01433 71 GLRSIKRLFGKTLKEILNTPALFSLVKDYLDVNSSELKLN--FA--NKQLRIPEIAAEIFIYLKNQAEEQ 136 (595)
T ss_pred hHHHHHHHhCCCchhhccchhhHhhhhheeecCCCeeEEE--EC--CEEEcHHHHHHHHHHHHHHHHHHH
Confidence 7899999999999873211110001111122 23333343 33 468999999999999999999864
No 19
>COG0443 DnaK Molecular chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=98.73 E-value=1.5e-08 Score=71.18 Aligned_cols=51 Identities=47% Similarity=0.663 Sum_probs=40.5
Q ss_pred CCcccchhcchhhcCCCCCChHHHhhcccCCeEEEeCCCc-ceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 1 MNPKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVNDCSK-PKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 1 ~np~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~~~g~-~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
+||.||++++||+||+. .++. ..+.+ . .+.|+|+||+|++|.+||+.|+++
T Consensus 64 ~~p~~t~~~~kr~~G~~-------------------~~~~~~~~~~--~--~~~~~~eeisa~~L~~lk~~ae~~ 115 (579)
T COG0443 64 DNPENTIFSIKRKIGRG-------------------SNGLKISVEV--D--GKKYTPEEISAMILTKLKEDAEAY 115 (579)
T ss_pred hCCcceEEEEehhcCCC-------------------CCCCcceeee--C--CeeeCHHHHHHHHHHHHHHHHHHh
Confidence 58999999999999997 1121 23333 2 378999999999999999999875
No 20
>PRK11678 putative chaperone; Provisional
Probab=96.57 E-value=0.0025 Score=44.09 Aligned_cols=20 Identities=20% Similarity=0.230 Sum_probs=17.8
Q ss_pred chhhhHHHHHHHHHHHHhcC
Q psy6083 55 APEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 55 speev~a~iL~~lk~~ae~~ 74 (74)
.||+|++++|++||+.|+.+
T Consensus 125 ~~e~l~a~iL~~lk~~ae~~ 144 (450)
T PRK11678 125 LFEDLVCAMMLHIKQQAEAQ 144 (450)
T ss_pred CHHHHHHHHHHHHHHHHHHH
Confidence 38999999999999999863
No 21
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=86.18 E-value=0.97 Score=23.39 Aligned_cols=57 Identities=16% Similarity=0.175 Sum_probs=35.2
Q ss_pred hhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHH
Q psy6083 7 VFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVL 64 (74)
Q Consensus 7 i~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL 64 (74)
...+++++|..++...+...++++-|++.. .++...+.+..- ..=...+++|+-.++
T Consensus 8 ~~~i~~~lG~~i~~~~i~~~L~~lg~~~~~~~~~~~~v~vP~~-R~Di~~~~DliEEia 65 (70)
T PF03484_consen 8 LDKINKLLGIDISPEEIIKILKRLGFKVEKIDGDTLEVTVPSY-RFDIEHEEDLIEEIA 65 (70)
T ss_dssp HHHHHHHHTS---HHHHHHHHHHTT-EEEE-CTTEEEEEEETT-STT-SSHHHHHHHHH
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHCCCEEEECCCCEEEEEcCCC-cCCcCcccHHHHHHH
Confidence 456789999999988999999999999987 555555555421 011345666655554
No 22
>cd02426 Pol_gamma_b_Cterm C-terminal domain of mitochondrial DNA polymerase gamma B subunit, which is required for processivity. Polymerase gamma replicates and repairs mitochondrial DNA. The c-terminal domain of its B subunit is strikingly similar to the anticodon-binding domain of glycyl tRNA synthetase.
Probab=82.76 E-value=2.4 Score=24.56 Aligned_cols=43 Identities=12% Similarity=0.138 Sum_probs=27.1
Q ss_pred hhcccCCeEEE-e----CCCcceEEEEECCeeEEEchhhhHHHHHHHH
Q psy6083 25 QDMKHWPFTVV-N----DCSKPKIQVEFKGERKTFAPEEISSMVLTKM 67 (74)
Q Consensus 25 ~~~~~~p~~i~-~----~~g~~~~~v~~~~~~~~~speev~a~iL~~l 67 (74)
.+..-+||.|+ . .+|.+.+.-...++...++.+++...+...+
T Consensus 79 ~dliGiP~~I~IG~~~l~~g~vei~~Rdt~~k~~v~~~~l~~~i~~~~ 126 (128)
T cd02426 79 YDEMGVLFTLLISEQTLENGLLQLRSRDTTLKETIHISDLPDYLLRYI 126 (128)
T ss_pred hhhcCCCEEEEECCCcccCCEEEEEECCCCceEEEeHHHHHHHHHHHh
Confidence 34567899975 2 2555544444445567788888877665543
No 23
>PF12971 NAGLU_N: Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain; InterPro: IPR024240 Alpha-N-acetylglucosaminidase, is a lysosomal enzyme required for the stepwise degradation of heparan sulphate []. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations []. The structure shows that the enzyme is composed of three domains. This entry represents the N-terminal domain of Alpha-N-acetylglucosaminidase which has an alpha-beta fold [].; PDB: 4A4A_A 2VC9_A 2VCC_A 2VCB_A 2VCA_A.
Probab=72.21 E-value=9.7 Score=20.51 Aligned_cols=54 Identities=11% Similarity=0.137 Sum_probs=30.1
Q ss_pred chhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEE-CCeeEEE---chhhhHHHHHHHHHHHHh
Q psy6083 10 AKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEF-KGERKTF---APEEISSMVLTKMKETAL 72 (74)
Q Consensus 10 ~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~-~~~~~~~---speev~a~iL~~lk~~ae 72 (74)
++|++|....+ +-+++.. .+|.-.|++.. .++...+ |+..++.-+=.+||..+.
T Consensus 9 i~Rll~~~~~~---------f~~~~~~~~~~~d~F~l~~~~~gki~I~G~s~vala~Gl~~YLk~~c~ 67 (86)
T PF12971_consen 9 IERLLPEHASQ---------FTFELIPSSNGKDVFELSSADNGKIVIRGNSGVALASGLNWYLKYYCH 67 (86)
T ss_dssp HHHHC-GGGGG---------EEEEE---BTTBEEEEEEE-SSS-EEEEESSHHHHHHHHHHHHHHHS-
T ss_pred HHhhcccccce---------EEEEEecCCCCCCEEEEEeCCCCeEEEEeCCHHHHHHHHHHHHHHHhC
Confidence 45666653322 3455554 34777788775 4433333 677777777788887664
No 24
>PRK04081 hypothetical protein; Provisional
Probab=71.10 E-value=13 Score=23.58 Aligned_cols=38 Identities=13% Similarity=0.391 Sum_probs=26.3
Q ss_pred eEEEe--CCCcceEEEEE-CCeeEEEchhhhHHHHHHHHHH
Q psy6083 32 FTVVN--DCSKPKIQVEF-KGERKTFAPEEISSMVLTKMKE 69 (74)
Q Consensus 32 ~~i~~--~~g~~~~~v~~-~~~~~~~speev~a~iL~~lk~ 69 (74)
|+|++ +.....+.|.+ +|.++.++.||+-+.|=...+.
T Consensus 61 YKI~eE~Ps~~Trvilr~~dG~ER~LS~eE~dkLi~eE~~K 101 (207)
T PRK04081 61 YKILEEYPSSETRVVLRDLDGTERVLSQEEIDKLIKEEEAK 101 (207)
T ss_pred eEeeeecCCCcceEEEecCCCcccccCHHHHHHHHHHHHHh
Confidence 78775 44455555654 5678999999998877655443
No 25
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=69.86 E-value=15 Score=19.69 Aligned_cols=33 Identities=18% Similarity=0.220 Sum_probs=26.3
Q ss_pred CCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhc
Q psy6083 38 CSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALY 73 (74)
Q Consensus 38 ~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~ 73 (74)
.+...|.|..+| .++|.++...-++.|++.++.
T Consensus 53 ~d~~~~~VeT~G---s~~P~~al~~Ai~~L~~~~~~ 85 (86)
T cd00460 53 EDKFILRIETVG---SIPPEEALRRAVEILRKKLEH 85 (86)
T ss_pred CCeEEEEEEECC---CCCHHHHHHHHHHHHHHHHhh
Confidence 456778887655 489999999999999988765
No 26
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=68.27 E-value=12 Score=24.36 Aligned_cols=36 Identities=11% Similarity=0.060 Sum_probs=26.8
Q ss_pred hcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEE
Q psy6083 8 FDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQV 45 (74)
Q Consensus 8 ~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v 45 (74)
+.+-|+||+..+= ++.......|+|+- .||.+|+.-
T Consensus 155 ~kVpRvig~~~sm--~~~l~~~~~~~I~VG~NG~IWV~~ 191 (239)
T COG1097 155 SKVPRVIGKKGSM--LNMLKEKTGCEIIVGQNGRIWVDG 191 (239)
T ss_pred hhcceEecCCCcH--HHHhhhhcCeEEEEecCCEEEecC
Confidence 3456899998754 55556678999875 899988764
No 27
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=67.17 E-value=6.8 Score=19.86 Aligned_cols=30 Identities=23% Similarity=0.304 Sum_probs=24.8
Q ss_pred hhcchhhcCCCCCChHHHhhcccCCeEEEe
Q psy6083 7 VFDAKRLIGRKFDDPKIQQDMKHWPFTVVN 36 (74)
Q Consensus 7 i~~~KrliG~~~~d~~v~~~~~~~p~~i~~ 36 (74)
...+.+++|..+++..+...++++-|.+..
T Consensus 8 ~~~i~~llG~~i~~~ei~~~L~~lg~~~~~ 37 (71)
T smart00874 8 RERINRLLGLDLSAEEIEEILKRLGFEVEV 37 (71)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHCCCeEEe
Confidence 356789999999988888888888888754
No 28
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=65.46 E-value=22 Score=21.21 Aligned_cols=34 Identities=12% Similarity=0.243 Sum_probs=28.6
Q ss_pred CCcceEEEEECCeeEEEchhhhHHHHHHHHHHHH
Q psy6083 38 CSKPKIQVEFKGERKTFAPEEISSMVLTKMKETA 71 (74)
Q Consensus 38 ~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~a 71 (74)
...+||-++.+|+..++.|.+....++..+|..-
T Consensus 39 ~~EpWf~~De~~~~~~l~p~~~l~~Li~~~k~~~ 72 (137)
T PF10788_consen 39 ENEPWFIIDENNEEYVLLPQKSLQNLIESLKNAQ 72 (137)
T ss_pred CCCCeEEEcCCCCEEEEECHHHHHHHHHHHHHHH
Confidence 4568999888888889999999999999988754
No 29
>cd00862 ProRS_anticodon_zinc ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only, and an additional C-terminal zinc-binding domain specific to this subfamily of aaRSs.
Probab=64.11 E-value=32 Score=21.33 Aligned_cols=44 Identities=20% Similarity=0.205 Sum_probs=28.9
Q ss_pred hhcccCCeEEEe-----CCCcceEEEEECCeeEEEchhhhHHHHHHHHH
Q psy6083 25 QDMKHWPFTVVN-----DCSKPKIQVEFKGERKTFAPEEISSMVLTKMK 68 (74)
Q Consensus 25 ~~~~~~p~~i~~-----~~g~~~~~v~~~~~~~~~speev~a~iL~~lk 68 (74)
.+++.+||.|+- .+|.+.+.-...++...++.+++...+..-|.
T Consensus 63 ae~~GvP~~I~IG~~Ele~g~V~v~~Rd~~ek~~v~~~el~~~i~~ll~ 111 (202)
T cd00862 63 WELKGVPLRIEIGPRDLEKNTVVIVRRDTGEKKTVPLAELVEKVPELLD 111 (202)
T ss_pred HHhCCCCEEEEECcchhhCCEEEEEEecCCcceEEEHHHHHHHHHHHHH
Confidence 356788999752 25666665555566677888888776654444
No 30
>PF08127 Propeptide_C1: Peptidase family C1 propeptide; InterPro: IPR012599 This domain is found at the N-terminal of cathepsin B and cathepsin B-like peptidases that belong to MEROPS peptidase subfamily C1A. Cathepsin B are lysosomal cysteine proteinases belonging to the papain superfamily and are unique in their ability to act as both an endo- and an exopeptidases. They are synthesized as inactive zymogens. Activation of the peptidases occurs with the removal of the propeptide [, ]. ; GO: 0004197 cysteine-type endopeptidase activity, 0050790 regulation of catalytic activity; PDB: 1MIR_A 1PBH_A 2PBH_A 3PBH_A.
Probab=59.72 E-value=4.2 Score=19.11 Aligned_cols=16 Identities=31% Similarity=0.345 Sum_probs=9.5
Q ss_pred ccchhcchhhcCCCCC
Q psy6083 4 KNTVFDAKRLIGRKFD 19 (74)
Q Consensus 4 ~nti~~~KrliG~~~~ 19 (74)
.-++..+|||+|-.-+
T Consensus 24 ~~~~~~ik~LlGv~~~ 39 (41)
T PF08127_consen 24 NTSIEYIKRLLGVLPD 39 (41)
T ss_dssp SB-HHHHHHCS-B-TT
T ss_pred CCCHHHHHHHcCCCCC
Confidence 4567888999996544
No 31
>KOG1004|consensus
Probab=56.02 E-value=19 Score=23.21 Aligned_cols=35 Identities=23% Similarity=0.312 Sum_probs=26.5
Q ss_pred chhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEE
Q psy6083 10 AKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVE 46 (74)
Q Consensus 10 ~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~ 46 (74)
..+||- -+.|.+|..-+++||+|.- -||++|+...
T Consensus 158 ~R~Ll~--p~~~iLq~vGk~~~FEia~GlNGriWV~ae 193 (230)
T KOG1004|consen 158 CRKLLL--PDCPILQTVGKKYPFEIAFGLNGRIWVKAE 193 (230)
T ss_pred HHHHHc--CCCcHHHHhhcccceEEEEecCceEEEecc
Confidence 344443 3557888888999999976 7999998864
No 32
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=51.95 E-value=53 Score=20.96 Aligned_cols=35 Identities=17% Similarity=0.127 Sum_probs=23.7
Q ss_pred cchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEE
Q psy6083 9 DAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQV 45 (74)
Q Consensus 9 ~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v 45 (74)
-++|+||..- ..++.....++|+|.- .||.+|+.-
T Consensus 155 ~i~~lig~~g--~~i~~l~~~~~~~I~ig~NG~VwI~~ 190 (235)
T PRK04163 155 KVPRVIGKKG--SMINMLKEETGCDIIVGQNGRIWIKG 190 (235)
T ss_pred HHHhhcCCCC--hhHhhhhhhhCcEEEEcCCcEEEEee
Confidence 4678888643 2355555678999865 789887764
No 33
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=49.76 E-value=24 Score=22.59 Aligned_cols=60 Identities=20% Similarity=0.268 Sum_probs=37.7
Q ss_pred ccchhcchhhcCCCCCChHHHhhcccCCeEEEeCCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHH
Q psy6083 4 KNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVNDCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETA 71 (74)
Q Consensus 4 ~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~a 71 (74)
.+|.+-.|+|+|..++|........+..|.....-+.. ++. .=++-+.++.+.++..+.|
T Consensus 156 GsT~~vAk~l~G~~~~d~~~~~g~~~q~YPC~As~~~d-~~~-------~d~~~h~Ag~i~~~Ave~A 215 (217)
T PF02593_consen 156 GSTWFVAKRLIGKEVEDAPEKAGLAHQHYPCRASMGRD-FEL-------GDTILHKAGYIHKEAVEKA 215 (217)
T ss_pred ccHHHHHHHhcCCccchhhhhhhhhheecccccccccc-ccc-------ccchhhhhHHHHHHHHHHh
Confidence 57888999999999999877665554445443311110 111 1255567888887766655
No 34
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=45.35 E-value=55 Score=23.88 Aligned_cols=51 Identities=14% Similarity=0.201 Sum_probs=31.3
Q ss_pred hcCCCCCChHHHhhcccCCeEEEe-----CC-------CcceEEEEECCeeEEEchhhhHHHHHHHH
Q psy6083 13 LIGRKFDDPKIQQDMKHWPFTVVN-----DC-------SKPKIQVEFKGERKTFAPEEISSMVLTKM 67 (74)
Q Consensus 13 liG~~~~d~~v~~~~~~~p~~i~~-----~~-------g~~~~~v~~~~~~~~~speev~a~iL~~l 67 (74)
=||++|.+ .+....||-|+- .+ |.+.++-...++...++.+++.+.+..++
T Consensus 475 sIGKKyRr----aDeiGiPy~ITVD~~Tl~dGdkE~e~gTVTVR~RDs~eQ~rV~ideli~~L~~~~ 537 (539)
T PRK14894 475 AIGKLYRR----QDEIGTPFCITVDFDTIGQGKDPALAGTVTVRDRDTMAQERVPISELEAYLRDRV 537 (539)
T ss_pred CHhHHHHh----hhccCCCEEEEEeccccccccchhhcCeEEEEEeCCCeEEEEEHHHHHHHHHHHh
Confidence 35666643 234568998642 23 55555544444556788999887776654
No 35
>PF14847 Ras_bdg_2: Ras-binding domain of Byr2; PDB: 1I35_A 1K8R_B.
Probab=41.43 E-value=49 Score=18.69 Aligned_cols=28 Identities=25% Similarity=0.296 Sum_probs=17.0
Q ss_pred eCCCcceEEEEECCeeEEEchhhhHHHHHHHH
Q psy6083 36 NDCSKPKIQVEFKGERKTFAPEEISSMVLTKM 67 (74)
Q Consensus 36 ~~~g~~~~~v~~~~~~~~~speev~a~iL~~l 67 (74)
.++|.. -.|+.. ..+++++|...+|+|+
T Consensus 7 ~~dG~t-k~VNV~---~c~~a~eI~~rvLKKf 34 (105)
T PF14847_consen 7 LEDGST-KTVNVS---GCFNAQEIKRRVLKKF 34 (105)
T ss_dssp ETTTEE-EEEE-----S--HHHHHHHHHHHHH
T ss_pred CCCCcE-EEEEEC---CCCCHHHHHHHHHHHc
Confidence 345543 334433 4789999999999987
No 36
>TIGR00746 arcC carbamate kinase. The seed alignment for this model includes experimentally confirmed examples from a set of phylogenetically distinct species. In a neighbor-joining tree constructed from an alignment of candidate carbamate kinases and several acetylglutamate kinases, the latter group forms a clear outgroup which roots the tree of carbamate kinase-like proteins. This analysis suggests that in E. coli, the ArcC paralog YqeA may be a second isozyme, while the paralog YahI branches as an outlier and is less likely to be an authentic carbamate kinase. The homolog from Mycoplasma pneumoniae likewise branches outside the set containing known carbamate kinases and also scores below the trusted cutoff.
Probab=41.13 E-value=59 Score=21.80 Aligned_cols=33 Identities=12% Similarity=0.194 Sum_probs=22.4
Q ss_pred hhcchhhcCCCCCChHHHhhcccCCeEEEeCCC
Q psy6083 7 VFDAKRLIGRKFDDPKIQQDMKHWPFTVVNDCS 39 (74)
Q Consensus 7 i~~~KrliG~~~~d~~v~~~~~~~p~~i~~~~g 39 (74)
|.+-.+.||.-|+..+.+...+..++.+++++|
T Consensus 122 f~~p~k~ig~~y~~~~a~~~~~~~~~~~~~d~~ 154 (310)
T TIGR00746 122 FQNPTKPIGPFYTEEEAKRLAAEKGWIVKEDAG 154 (310)
T ss_pred ccCCCCcCCCCcCHHHHHHHHHHcCCeEeecCC
Confidence 556778899999887777666655665444333
No 37
>PF03646 FlaG: FlaG protein; InterPro: IPR005186 Although these proteins are known to be important for flagellar their exact function is unknown.; PDB: 2HC5_A.
Probab=40.89 E-value=63 Score=17.74 Aligned_cols=40 Identities=23% Similarity=0.406 Sum_probs=24.9
Q ss_pred CCeEEEeCCCcceEEEEECC--e-eEEEchhhhHHHHHHHHHHH
Q psy6083 30 WPFTVVNDCSKPKIQVEFKG--E-RKTFAPEEISSMVLTKMKET 70 (74)
Q Consensus 30 ~p~~i~~~~g~~~~~v~~~~--~-~~~~speev~a~iL~~lk~~ 70 (74)
+-|.+-++.|...+.|-... + -+.+.|++++.+. ++|++.
T Consensus 57 l~F~vde~~~~~vVkViD~~T~eVIRqIP~Ee~l~l~-~~l~e~ 99 (107)
T PF03646_consen 57 LRFSVDEESGRVVVKVIDKETGEVIRQIPPEELLDLA-KRLREL 99 (107)
T ss_dssp EEEEEEEETTEEEEEEEETTT-SEEEEE-HHHHHHHH-HHHHHH
T ss_pred eEEEEecCCCcEEEEEEECCCCcEEEeCCcHHHHHHH-HHHHHH
Confidence 33555556688888876542 2 2678999987765 555554
No 38
>PF12937 F-box-like: F-box-like; PDB: 1P22_A 2OVP_B 2OVR_B 2OVQ_B 1FS1_A 1FS2_C 1FQV_I 1LDK_E 2AST_B 2ASS_B.
Probab=40.84 E-value=7.9 Score=17.96 Aligned_cols=13 Identities=23% Similarity=0.457 Sum_probs=9.9
Q ss_pred chhhhHHHHHHHH
Q psy6083 55 APEEISSMVLTKM 67 (74)
Q Consensus 55 speev~a~iL~~l 67 (74)
-|.||...||.+|
T Consensus 4 LP~Eil~~If~~L 16 (47)
T PF12937_consen 4 LPDEILLEIFSYL 16 (47)
T ss_dssp S-HHHHHHHHTTS
T ss_pred hHHHHHHHHHhcC
Confidence 4889999998876
No 39
>KOG1434|consensus
Probab=39.94 E-value=40 Score=22.73 Aligned_cols=44 Identities=16% Similarity=0.218 Sum_probs=31.2
Q ss_pred CeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhcC
Q psy6083 31 PFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 31 p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~~ 74 (74)
-|.++- +.=...|+++|.|....=--.+.++.+|.+|..+|+.|
T Consensus 211 ~~rlvIVDsIma~FRvDy~grgeLseRqqkLn~ml~kl~~laeef 255 (335)
T KOG1434|consen 211 KYRLVIVDSIMALFRVDYDGRGELSERQQKLNQMLQKLNKLAEEF 255 (335)
T ss_pred cEEEEEEeceehheeecccccccHHHHHHHHHHHHHHHHHHHHhc
Confidence 355433 33345688888875555557889999999999999876
No 40
>COG4545 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=39.67 E-value=34 Score=18.55 Aligned_cols=21 Identities=14% Similarity=0.300 Sum_probs=14.7
Q ss_pred chhcchhhcCCCCCChHHHhh
Q psy6083 6 TVFDAKRLIGRKFDDPKIQQD 26 (74)
Q Consensus 6 ti~~~KrliG~~~~d~~v~~~ 26 (74)
.-.++||||-.+.+.|.+..-
T Consensus 37 Sm~NlKrFl~lRDs~~~Fd~v 57 (85)
T COG4545 37 SMANLKRFLHLRDSRPEFDEV 57 (85)
T ss_pred hhhhHHHHHhhhccchhHHhh
Confidence 346789998887777766543
No 41
>PRK08661 prolyl-tRNA synthetase; Provisional
Probab=39.39 E-value=1.1e+02 Score=21.65 Aligned_cols=46 Identities=15% Similarity=0.147 Sum_probs=29.2
Q ss_pred hhcccCCeEEEe-----CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHH
Q psy6083 25 QDMKHWPFTVVN-----DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKET 70 (74)
Q Consensus 25 ~~~~~~p~~i~~-----~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ 70 (74)
.++...|+.|+- .+|.+.+.-...++...++.+++...+-..|.++
T Consensus 340 ae~~GvP~~IiIG~~ele~~~V~ik~rdtgek~~v~~~el~~~l~~~l~~~ 390 (477)
T PRK08661 340 WELKGVPLRIEIGPRDLENNTVVLVRRDTLEKETVPLDELVEKVPELLEEI 390 (477)
T ss_pred HHHCCCCEEEEECcchhhcCeEEEEECCCCceEEEEHHHHHHHHHHHHHHH
Confidence 356778998752 2455555444455667788888887776655543
No 42
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=38.77 E-value=31 Score=21.19 Aligned_cols=28 Identities=14% Similarity=0.428 Sum_probs=19.7
Q ss_pred EeCCCcceEEEEE-CCeeEEEchhhhHHH
Q psy6083 35 VNDCSKPKIQVEF-KGERKTFAPEEISSM 62 (74)
Q Consensus 35 ~~~~g~~~~~v~~-~~~~~~~speev~a~ 62 (74)
.+.+|...|.|-. .++.+.+-|+||+++
T Consensus 139 fn~~G~~mfKiylgRDe~RqL~~eqvakF 167 (176)
T COG3721 139 FNAQGEAMFKIYLGRDEHRQLLPEQVAKF 167 (176)
T ss_pred ecccCceeeeeeeccchHhhhhHHHHHHH
Confidence 3467888888854 345677888887653
No 43
>PF04986 Y2_Tnp: Putative transposase; InterPro: IPR007069 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases IS1294 and IS801 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=37.58 E-value=82 Score=19.22 Aligned_cols=35 Identities=17% Similarity=0.215 Sum_probs=24.4
Q ss_pred EEEe-CCCcceEEEEEC----CeeEEEchhhhHHHHHHHH
Q psy6083 33 TVVN-DCSKPKIQVEFK----GERKTFAPEEISSMVLTKM 67 (74)
Q Consensus 33 ~i~~-~~g~~~~~v~~~----~~~~~~speev~a~iL~~l 67 (74)
.|.. ++|.+.+..... .+...++++|....+|.++
T Consensus 123 Ri~~~~~~~V~f~y~d~~~~~~~~~~l~~~efi~r~l~Hv 162 (183)
T PF04986_consen 123 RIVSYDDGTVTFRYKDHRTKKTKTLTLSAEEFIRRLLQHV 162 (183)
T ss_pred ceEEeccceeEEEEEcCCCCcEEEEEechHHHHHHHHhhc
Confidence 4555 667777765432 1346789999999999876
No 44
>PRK13669 hypothetical protein; Provisional
Probab=36.99 E-value=32 Score=18.54 Aligned_cols=16 Identities=25% Similarity=0.484 Sum_probs=14.1
Q ss_pred EchhhhHHHHHHHHHH
Q psy6083 54 FAPEEISSMVLTKMKE 69 (74)
Q Consensus 54 ~speev~a~iL~~lk~ 69 (74)
-||+|+...|.++|++
T Consensus 59 ~t~eeL~~kI~~~i~e 74 (78)
T PRK13669 59 ETPEELVENIYAHLEE 74 (78)
T ss_pred CCHHHHHHHHHHHHhh
Confidence 3899999999999987
No 45
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=36.90 E-value=39 Score=16.98 Aligned_cols=31 Identities=23% Similarity=0.311 Sum_probs=22.3
Q ss_pred CCcceEEEEECCeeEEEchhhhHHHHHHHHHHHH
Q psy6083 38 CSKPKIQVEFKGERKTFAPEEISSMVLTKMKETA 71 (74)
Q Consensus 38 ~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~a 71 (74)
.+...|.|..+| .++|.++...-++.|++..
T Consensus 35 ~~~~~~~IeT~g---~~~p~~~l~~A~~~l~~~~ 65 (66)
T PF01193_consen 35 EDKFVFRIETDG---SLTPKEALLKAIKILKEKL 65 (66)
T ss_dssp EEEEEEEEEEBS---SS-HHHHHHHHHHHHHHHH
T ss_pred CCEEEEEEEECC---CCCHHHHHHHHHHHHHHhc
Confidence 355677777554 4699999988888888765
No 46
>PF01614 IclR: Bacterial transcriptional regulator This Pfam family contains some of the members of the iclR family; InterPro: IPR014757 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 of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; PDB: 3MQ0_A 2IA2_D 3OBF_B 2G7U_C 3R4K_A 1TF1_D 1MKM_A 1YSP_A 3BJN_A 1TD5_A ....
Probab=36.42 E-value=51 Score=18.26 Aligned_cols=20 Identities=20% Similarity=0.321 Sum_probs=13.3
Q ss_pred EchhhhHHHHHHHHHHHHhc
Q psy6083 54 FAPEEISSMVLTKMKETALY 73 (74)
Q Consensus 54 ~speev~a~iL~~lk~~ae~ 73 (74)
++++.+...++..|++.|+.
T Consensus 106 ~~~~~~~~~~~~~l~~~A~~ 125 (129)
T PF01614_consen 106 FDEERLEERLAPALREAARE 125 (129)
T ss_dssp SHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHH
Confidence 44555555588888888763
No 47
>PF03129 HGTP_anticodon: Anticodon binding domain; InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [] it is probably the anticodon binding domain [].; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding; PDB: 1KOG_B 1EVL_D 1EVK_B 1QF6_A 1FYF_B 2I4O_A 2I4M_A 2I4N_A 2I4L_A 1HC7_D ....
Probab=35.61 E-value=53 Score=17.13 Aligned_cols=39 Identities=21% Similarity=0.328 Sum_probs=25.5
Q ss_pred hcccCCeEEE-e----CCCcceEEEEECCeeEEEchhhhHHHHH
Q psy6083 26 DMKHWPFTVV-N----DCSKPKIQVEFKGERKTFAPEEISSMVL 64 (74)
Q Consensus 26 ~~~~~p~~i~-~----~~g~~~~~v~~~~~~~~~speev~a~iL 64 (74)
.....||-++ . .+|.+.+.....+....++.+++...+.
T Consensus 49 ~~~g~p~~iiiG~~e~~~~~v~vk~~~~~~~~~v~~~el~~~l~ 92 (94)
T PF03129_consen 49 DKLGIPFIIIIGEKELENGTVTVKDRDTGEQETVSLEELIEYLK 92 (94)
T ss_dssp HHTTESEEEEEEHHHHHTTEEEEEETTTTEEEEEECCHHHHHHH
T ss_pred hhcCCeEEEEECchhHhCCEEEEEECCCCcEEEEEHHHHHHHHh
Confidence 4567899865 2 2566555544455677889998876654
No 48
>PF01913 FTR: Formylmethanofuran-tetrahydromethanopterin formyltransferase; InterPro: IPR022667 Formylmethanofuran:tetrahyromethanopterin formyltransferase (Ftr) is involved in C1 metabolism in methanogenic archaea, sulphate-reducing archaea and methylotrophic bacteria. It catalyses the following reversible reaction: N-formylmethanofuran + 5,6,7,8-tetrahydromethanopterin = methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterin Ftr from the thermophilic methanogen Methanopyrus kandleri (optimum growth temperature 98 degrees C) is a hyperthermophilic enzyme that is absolutely dependent on the presence of lyotropic salts for activity and thermostability. The crystal structure of Ftr, determined to a reveals a homotetramer composed essentially of two dimers. Each subunit is subdivided into two tightly associated lobes both consisting of a predominantly antiparallel beta sheet flanked by alpha helices forming an alpha/beta sandwich structure. The approximate location of the active site was detected in a region close to the dimer interface []. Ftr from the mesophilic methanogen Methanosarcina barkeri and the sulphate-reducing archaeon Archaeoglobus fulgidus have a similar structure []. In the methylotrophic bacterium Methylobacterium extorquens, Ftr interacts with three other polypeptides to form an Ftr/cyclohydrolase complex which catalyses the hydrolysis of formyl-tetrahydromethanopterin to formate during growth on C1 substrates [].; GO: 0016740 transferase activity, 0006730 one-carbon metabolic process; PDB: 1M5H_E 1M5S_C 1FTR_C 2FHJ_B 2FHK_D.
Probab=34.85 E-value=1e+02 Score=18.59 Aligned_cols=30 Identities=7% Similarity=0.244 Sum_probs=23.5
Q ss_pred CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHH
Q psy6083 37 DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKET 70 (74)
Q Consensus 37 ~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ 70 (74)
+||++++.|. --.++...+...++.++.+.
T Consensus 66 PDGRPGv~il----~f~~~~~~L~~~l~~RigQc 95 (144)
T PF01913_consen 66 PDGRPGVSIL----IFAMSKKKLEKQLLERIGQC 95 (144)
T ss_dssp TTSS-EEEEE----EEESSHHHHHHHHHHHHHHH
T ss_pred CCCCCcEEEE----EEeCCHHHHHHHHHHHccCc
Confidence 6999999985 34678889999999888775
No 49
>TIGR00408 proS_fam_I prolyl-tRNA synthetase, family I. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi. The other family includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae.
Probab=34.30 E-value=1.6e+02 Score=20.77 Aligned_cols=45 Identities=13% Similarity=0.236 Sum_probs=28.4
Q ss_pred hcccCCeEEEe-----CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHH
Q psy6083 26 DMKHWPFTVVN-----DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKET 70 (74)
Q Consensus 26 ~~~~~p~~i~~-----~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ 70 (74)
++...||.|+- .+|.+.+.-...++...++.+++...+-..|.++
T Consensus 335 e~~GvP~~IiIG~~Ele~~~V~ik~rdt~eq~~v~l~el~~~l~~~l~~~ 384 (472)
T TIGR00408 335 EIKGIPLRIEVGPNDIEKNIAVISRRDTGEKYQVSLDQLEERVVELLNNI 384 (472)
T ss_pred HHCCCCEEEEECcchhhCCeEEEEECCCCceEEEEHHHHHHHHHHHHHHH
Confidence 46678998752 2455555444455566788888877765555443
No 50
>PRK15322 invasion protein OrgB; Provisional
Probab=34.13 E-value=1.3e+02 Score=19.32 Aligned_cols=41 Identities=17% Similarity=0.460 Sum_probs=27.6
Q ss_pred ccCC--eEEEeCCCcceEEEEECCeeEEEchhhhHHHHHHHHHH
Q psy6083 28 KHWP--FTVVNDCSKPKIQVEFKGERKTFAPEEISSMVLTKMKE 69 (74)
Q Consensus 28 ~~~p--~~i~~~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~ 69 (74)
..|| |.|.-.+|. .|.+.++++--.|||+++.----++|+.
T Consensus 134 e~w~~~~~i~yhd~~-rFV~~~g~qIaEFsPq~~v~~a~~~l~~ 176 (210)
T PRK15322 134 ENWPGTFNLKYHQEQ-RFIMSCGDQIAEFSPEQFVETAVGVIKH 176 (210)
T ss_pred HhcCCCeEEEEcCCC-ceEEEeCCchhccCHHHHHHHHHHHHHh
Confidence 3567 666554443 5667777777889999987766666554
No 51
>PRK08868 flagellar protein FlaG; Provisional
Probab=33.90 E-value=1.1e+02 Score=18.42 Aligned_cols=41 Identities=15% Similarity=0.272 Sum_probs=26.9
Q ss_pred ccCCeEEEeCCCcceEEEEECCe---eEEEchhhhHHHHHHHHHH
Q psy6083 28 KHWPFTVVNDCSKPKIQVEFKGE---RKTFAPEEISSMVLTKMKE 69 (74)
Q Consensus 28 ~~~p~~i~~~~g~~~~~v~~~~~---~~~~speev~a~iL~~lk~ 69 (74)
..+-|.+-++-|...+.|-.... -+.+.||+++.+. ++|.+
T Consensus 89 ~~L~F~vdeetgr~VVkViD~~T~EVIRQIP~Ee~L~la-~~l~e 132 (144)
T PRK08868 89 KGLSFRVDEESGRDVVTIYEASTGDIIRQIPDEEMLEVL-RRLAE 132 (144)
T ss_pred CceEEEEecCCCCEEEEEEECCCCceeeeCCCHHHHHHH-HHHHH
Confidence 34567776677888888754321 3678999987664 44554
No 52
>PF02058 Guanylin: Guanylin precursor; InterPro: IPR000879 Guanylin, a 15-amino-acid peptide, is an endogenous ligand of the intestinal receptor guanylate cyclase-C, known as STaR [, ]. Upon receptor binding, guanylin increases the intracellular concentration of cGMP, it induces chloride secretion and decreases intestinal fluid absorption, ultimately causing diarrhoea []. The peptide stimulates the enzyme through the same receptor binding region as the heat-stable enterotoxins [].; GO: 0008047 enzyme activator activity; PDB: 1UYB_A 1UYA_A 1GNA_A 1O8R_A 1GNB_A.
Probab=33.41 E-value=47 Score=18.38 Aligned_cols=13 Identities=8% Similarity=0.365 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHh
Q psy6083 60 SSMVLTKMKETAL 72 (74)
Q Consensus 60 ~a~iL~~lk~~ae 72 (74)
+++||.+|..+|+
T Consensus 61 A~~if~rL~~Ia~ 73 (89)
T PF02058_consen 61 AASIFQRLRTIAQ 73 (89)
T ss_dssp HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHh
Confidence 7999999999987
No 53
>COG4844 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.40 E-value=37 Score=17.96 Aligned_cols=16 Identities=31% Similarity=0.528 Sum_probs=14.2
Q ss_pred chhhhHHHHHHHHHHH
Q psy6083 55 APEEISSMVLTKMKET 70 (74)
Q Consensus 55 speev~a~iL~~lk~~ 70 (74)
||||+..-|..+|++.
T Consensus 60 t~eeLv~NIY~~i~En 75 (78)
T COG4844 60 TPEELVENIYTFIEEN 75 (78)
T ss_pred CHHHHHHHHHHHHhcc
Confidence 8999999999998864
No 54
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and
Probab=33.10 E-value=1.1e+02 Score=19.31 Aligned_cols=39 Identities=13% Similarity=0.239 Sum_probs=27.6
Q ss_pred eEEEeCCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhc
Q psy6083 32 FTVVNDCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALY 73 (74)
Q Consensus 32 ~~i~~~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~ 73 (74)
|++....+...++|..+| .++|+++...-++-|++.++.
T Consensus 170 y~~~~~~d~li~~VeT~G---si~p~~~l~~A~~iL~~~~~~ 208 (212)
T cd07028 170 FRYDPVADTYIMNVESVG---SLPPDQVVVEAIKTLQKKVAS 208 (212)
T ss_pred EEEEccCCEEEEEEEecC---CcCHHHHHHHHHHHHHHHHHH
Confidence 444434566778887655 589999998888888876653
No 55
>smart00256 FBOX A Receptor for Ubiquitination Targets.
Probab=32.78 E-value=21 Score=15.43 Aligned_cols=12 Identities=42% Similarity=0.794 Sum_probs=8.8
Q ss_pred hhhhHHHHHHHH
Q psy6083 56 PEEISSMVLTKM 67 (74)
Q Consensus 56 peev~a~iL~~l 67 (74)
|.|+...||.++
T Consensus 2 P~~ll~~I~~~l 13 (41)
T smart00256 2 PDEILEEILSKL 13 (41)
T ss_pred CHHHHHHHHHcC
Confidence 667777777765
No 56
>PF00427 PBS_linker_poly: Phycobilisome Linker polypeptide; InterPro: IPR001297 Phycobilisomes (PBSs) are the major light-harvesting systems in cyanobacteria and red algae. PBS is a supercomplex that is composed of a core complex and multiple peripheral rod complexes. Typically, the core consists of two or five cylinders lying on the membrane with, in most cases, multiple rods radiating from the core to form a hemidiscoidal structure. The building units of the core cylinders and the peripheral rods are trimeric and hexameric discs, in which a monomer consists of a pair of related phycobiliproteins (PBPs), such as phycorerythrins, phycoerythrocyanins, phycocyanins, and allophycocyanins. The discs are connected to each other via specific linker polypeptides to form peripheral rods or core cylinders. Linker polypeptides share a conserved domain of ~180 residues, which can be present in one or multiple copies [, , , , ].; GO: 0015979 photosynthesis, 0030089 phycobilisome; PDB: 2L8V_A 2KY4_A 3OSJ_D 2L06_A 3NPH_B 2L3W_A 3PRU_C 3OHW_A.
Probab=30.82 E-value=24 Score=20.81 Aligned_cols=14 Identities=29% Similarity=0.389 Sum_probs=9.3
Q ss_pred hcchhhcCCCCCCh
Q psy6083 8 FDAKRLIGRKFDDP 21 (74)
Q Consensus 8 ~~~KrliG~~~~d~ 21 (74)
..+|+||||...++
T Consensus 76 l~~khlLGR~p~~~ 89 (131)
T PF00427_consen 76 LAFKHLLGRAPYNQ 89 (131)
T ss_dssp HHHHHHCSS--SSH
T ss_pred HHHHHHhCCCCCCH
Confidence 46899999977653
No 57
>PF08673 RsbU_N: Phosphoserine phosphatase RsbU, N-terminal domain; InterPro: IPR014787 The phosphoserine phosphatase RsbU acts as a positive regulator of the general stress-response factor of Gram-positive organisms, sigma-B. RsbU dephosphorylates rsbV in response to environmental stress conveyed from the rsbXST module. The phosphatase activity of RsbU is stimulated during the stress response by associating with the RsbT kinase. This association leads to the induction of sigmaB activity. The N-terminal domain forms a helix-swapped dimer that is otherwise similar to the KaiA domain dimer. Deletions in the N-terminal domain are deleterious to the activity of RsbU. The C-terminal domain of RsbU is similar to the catalytic domains of PP2C-type phosphatases [].; PDB: 2J6Y_D 2J6Z_A 2J70_A 1W53_A.
Probab=30.75 E-value=59 Score=17.28 Aligned_cols=21 Identities=29% Similarity=0.430 Sum_probs=14.4
Q ss_pred EEEchhhhHHHHHHHHHHHHh
Q psy6083 52 KTFAPEEISSMVLTKMKETAL 72 (74)
Q Consensus 52 ~~~speev~a~iL~~lk~~ae 72 (74)
+.++||||...-.+.+.+...
T Consensus 33 ~~I~PEeIv~iH~~~v~~l~~ 53 (77)
T PF08673_consen 33 KDISPEEIVEIHKSAVQELSP 53 (77)
T ss_dssp TT--HHHHHHHHHHHHHHH-T
T ss_pred cCCCHHHHHHHHHHHHHHHcc
Confidence 347999999998888877654
No 58
>PF12993 DUF3877: Domain of unknown function, E. rectale Gene description (DUF3877); InterPro: IPR024539 This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=30.50 E-value=52 Score=20.45 Aligned_cols=54 Identities=26% Similarity=0.442 Sum_probs=32.0
Q ss_pred hhcchhhcCCCCCChHHHhhcccCCeEEEeCCCcceEEEEECCeeEEE-chhhhHHH
Q psy6083 7 VFDAKRLIGRKFDDPKIQQDMKHWPFTVVNDCSKPKIQVEFKGERKTF-APEEISSM 62 (74)
Q Consensus 7 i~~~KrliG~~~~d~~v~~~~~~~p~~i~~~~g~~~~~v~~~~~~~~~-speev~a~ 62 (74)
..++++|+|...+....+..+..+|-.+...-|.+.+. .+++.-.+ -|++=+.+
T Consensus 32 lsSLn~~l~~e~~~~em~~~L~~f~~~~~~~lG~v~vs--~k~eRFCf~IP~~g~~Y 86 (175)
T PF12993_consen 32 LSSLNHFLGTEDDEEEMQEALEEFPEYVKDRLGEVEVS--HKGERFCFHIPEEGSEY 86 (175)
T ss_pred HHHHHHHhcccccHHHHHHHHHHhHHHHHhhhccEEEE--ecCcEEEEEcCcHHHHH
Confidence 46789999998877777777776665444444654443 34444333 34443333
No 59
>TIGR00472 pheT_bact phenylalanyl-tRNA synthetase, beta subunit, non-spirochete bacterial. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from Bacteria other than spirochetes, as well as a chloroplast-encoded form from Porphyra purpurea. The chloroplast-derived sequence is considerably shorter at the amino end, however.
Probab=29.72 E-value=59 Score=24.49 Aligned_cols=34 Identities=15% Similarity=0.337 Sum_probs=27.3
Q ss_pred chhcchhhcCCCCCChHHHhhcccCCeEEEeCCC
Q psy6083 6 TVFDAKRLIGRKFDDPKIQQDMKHWPFTVVNDCS 39 (74)
Q Consensus 6 ti~~~KrliG~~~~d~~v~~~~~~~p~~i~~~~g 39 (74)
+...+++++|..++..++...++++-|++...++
T Consensus 411 ~~~~i~~~lG~~i~~~ei~~iL~~Lgf~~~~~~~ 444 (798)
T TIGR00472 411 RIKKLNKILGISLSDEEVRDILKRLGFKVEKQKD 444 (798)
T ss_pred cHHHHHHHhCCccCHHHHHHHHHHCCCEEEecCC
Confidence 3456889999999998999999999998854333
No 60
>PRK07738 flagellar protein FlaG; Provisional
Probab=29.46 E-value=1.2e+02 Score=17.53 Aligned_cols=41 Identities=17% Similarity=0.216 Sum_probs=25.9
Q ss_pred cCCeEEEeCCCcceEEEEECCe---eEEEchhhhHHHHHHHHHHH
Q psy6083 29 HWPFTVVNDCSKPKIQVEFKGE---RKTFAPEEISSMVLTKMKET 70 (74)
Q Consensus 29 ~~p~~i~~~~g~~~~~v~~~~~---~~~~speev~a~iL~~lk~~ 70 (74)
.+-|.+-++.|.+.+.|-.... -+.+.|++++.+ +.+|.+.
T Consensus 65 ~L~F~vdeet~~~vVkVvD~~T~EVIRQIPpEe~L~l-~~~m~e~ 108 (117)
T PRK07738 65 SLKFELHEKLNEYYVQVVDERTNEVIREIPPKKLLDM-YAAMMEF 108 (117)
T ss_pred ceEEEEecCCCcEEEEEEECCCCeeeeeCCCHHHHHH-HHHHHHH
Confidence 4457776667888888764322 266788888665 4455544
No 61
>PF10178 DUF2372: Uncharacterised conserved protein (DUF2372); InterPro: IPR018788 Proteasome assembly chaperone 3 (PSMG3) promotes assembly of the 20S proteasome []. It may cooperate with PSMG1-PSMG2 heterodimers to orchestrate the correct assembly of proteasomes.; PDB: 2Z5E_A.
Probab=29.21 E-value=19 Score=19.81 Aligned_cols=25 Identities=28% Similarity=0.586 Sum_probs=14.6
Q ss_pred ccchhcchhhcCCCCCChHHHhhcccC
Q psy6083 4 KNTVFDAKRLIGRKFDDPKIQQDMKHW 30 (74)
Q Consensus 4 ~nti~~~KrliG~~~~d~~v~~~~~~~ 30 (74)
.+..+++|-++|+ |||.+....+++
T Consensus 27 ~~p~f~v~vllG~--dep~l~v~Ar~L 51 (90)
T PF10178_consen 27 DNPTFTVKVLLGK--DEPLLHVYARQL 51 (90)
T ss_dssp CS--EEEEEEES-----HHHHHHHHHH
T ss_pred CCCcceEEEEecC--CcHHHHHHHHHH
Confidence 3566888899999 888887665543
No 62
>PF10726 DUF2518: Protein of function (DUF2518); InterPro: IPR019664 This entry contains the Ycf51 protein family, which is conserved in Cyanobacteria. The function is not known.
Probab=28.43 E-value=1.2e+02 Score=18.33 Aligned_cols=29 Identities=14% Similarity=0.381 Sum_probs=18.1
Q ss_pred CeEEEeCCCcceEEEEECCeeEEEchhhhHHH
Q psy6083 31 PFTVVNDCSKPKIQVEFKGERKTFAPEEISSM 62 (74)
Q Consensus 31 p~~i~~~~g~~~~~v~~~~~~~~~speev~a~ 62 (74)
.|.++-+||...+.+... -.++|+++-+-
T Consensus 71 ~~~~VyDnG~~~vVi~v~---~~i~~~~leaT 99 (145)
T PF10726_consen 71 RYPIVYDNGADQVVIAVP---PDITPEALEAT 99 (145)
T ss_pred EeeEEEECCCcEEEEEcC---CCCCHHHHHHH
Confidence 466666777666655433 35788887554
No 63
>PF13280 WYL: WYL domain
Probab=28.33 E-value=80 Score=17.95 Aligned_cols=21 Identities=10% Similarity=0.309 Sum_probs=17.3
Q ss_pred eEEEchhhhHHHHHHHHHHHH
Q psy6083 51 RKTFAPEEISSMVLTKMKETA 71 (74)
Q Consensus 51 ~~~~speev~a~iL~~lk~~a 71 (74)
-+.++|+++-..+..+++++|
T Consensus 152 v~Vl~P~~lr~~~~~~l~~~l 172 (172)
T PF13280_consen 152 VEVLEPESLRQRLKERLEKML 172 (172)
T ss_pred EEEECCHHHHHHHHHHHHHhC
Confidence 478899999988888888764
No 64
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=28.14 E-value=31 Score=16.04 Aligned_cols=15 Identities=33% Similarity=0.494 Sum_probs=9.1
Q ss_pred hHHHHHHHHHHHHhc
Q psy6083 59 ISSMVLTKMKETALY 73 (74)
Q Consensus 59 v~a~iL~~lk~~ae~ 73 (74)
+-++-+..|+++|+.
T Consensus 2 L~~~~~~eL~~iAk~ 16 (43)
T PF07498_consen 2 LKSMTLSELREIAKE 16 (43)
T ss_dssp HHCS-HHHHHHHHHC
T ss_pred cccCCHHHHHHHHHH
Confidence 344556777777765
No 65
>KOG3493|consensus
Probab=28.07 E-value=25 Score=18.48 Aligned_cols=17 Identities=35% Similarity=0.464 Sum_probs=14.1
Q ss_pred CcccchhcchhhcCCCC
Q psy6083 2 NPKNTVFDAKRLIGRKF 18 (74)
Q Consensus 2 np~nti~~~KrliG~~~ 18 (74)
||..||-++|.||...-
T Consensus 19 n~dDtiGD~KKliaaQt 35 (73)
T KOG3493|consen 19 NTDDTIGDLKKLIAAQT 35 (73)
T ss_pred CCcccccCHHHHHHHhh
Confidence 78899999999986543
No 66
>PF00646 F-box: F-box domain; InterPro: IPR001810 The F-box domain was first described as a sequence motif found in cyclin-F that interacts with the protein SKP1 [, ]. This relatively conserved structural motif is present in numerous proteins and serves as a link between a target protein and a ubiquitin-conjugating enzyme. The SCF complex (e.g., Skp1-Cullin-F-box) plays a similar role as an E3 ligase in the ubiquitin protein degradation pathway [, ]. Different F-box proteins as a part of SCF complex recruit particular substrates for ubiquitination through specific protein-protein interaction domains. Many mammalian F-box domains contain leucine-rich or WD-40 repeats (IPR001680 from INTERPRO). However, several F-box proteins either have other previously described domains such as Sec7 domain found in FBS protein or do not contain defined protein-protein interaction domains or motifs.; GO: 0005515 protein binding; PDB: 2E32_A 2E31_A 3V7D_B 1NEX_B 3MKS_D 3L2O_B.
Probab=28.02 E-value=24 Score=16.09 Aligned_cols=13 Identities=31% Similarity=0.611 Sum_probs=8.4
Q ss_pred hhhhHHHHHHHHH
Q psy6083 56 PEEISSMVLTKMK 68 (74)
Q Consensus 56 peev~a~iL~~lk 68 (74)
|+|+...||.+|-
T Consensus 7 P~~il~~Il~~l~ 19 (48)
T PF00646_consen 7 PDEILQEILSYLD 19 (48)
T ss_dssp -HHHHHHHHHTS-
T ss_pred CHHHHHHHHHHCc
Confidence 6778888887653
No 67
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=28.01 E-value=68 Score=21.81 Aligned_cols=56 Identities=14% Similarity=0.132 Sum_probs=33.5
Q ss_pred ccchhcchhhcCCCCCChHHHhhcccCC--eEEEe-CCCcceEEEEECCeeEEEchhhhHH
Q psy6083 4 KNTVFDAKRLIGRKFDDPKIQQDMKHWP--FTVVN-DCSKPKIQVEFKGERKTFAPEEISS 61 (74)
Q Consensus 4 ~nti~~~KrliG~~~~d~~v~~~~~~~p--~~i~~-~~g~~~~~v~~~~~~~~~speev~a 61 (74)
-..|..+|+-+|...|= .......+| |.++. .+|...+++..-+.+--+|.-|..+
T Consensus 120 L~ki~~l~~dLGLP~Df--~~~lv~~yP~~Frvv~~~~~~~~LeLv~Wd~~LAvs~~E~~~ 178 (335)
T PF11955_consen 120 LSKIAHLRRDLGLPDDF--RDSLVPKYPDYFRVVDLEDGGRYLELVSWDPELAVSALEKRA 178 (335)
T ss_pred HHHHHHHHHHcCCChhh--ccchhhhCCCCcEEeecCCCCCEEEEeecCCccCcCccchhh
Confidence 34577888899986532 222234556 88888 7788888875433333344444433
No 68
>TIGR00471 pheT_arch phenylalanyl-tRNA synthetase, beta subunit. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from eukaryotic cytosol, the Archaea, and spirochetes.
Probab=27.97 E-value=79 Score=22.78 Aligned_cols=30 Identities=20% Similarity=0.308 Sum_probs=24.9
Q ss_pred hhcchhhcCCCCCChHHHhhcccCCeEEEe
Q psy6083 7 VFDAKRLIGRKFDDPKIQQDMKHWPFTVVN 36 (74)
Q Consensus 7 i~~~KrliG~~~~d~~v~~~~~~~p~~i~~ 36 (74)
...+.|++|..++...+...++++-|++..
T Consensus 284 ~~~i~~~lG~~l~~~ei~~iL~~Lg~~v~~ 313 (551)
T TIGR00471 284 VEYINSLLGLNLSADEIAHSLKKMRLDAVQ 313 (551)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHhCCCeEe
Confidence 456789999999988888888888888754
No 69
>PRK05339 PEP synthetase regulatory protein; Provisional
Probab=27.53 E-value=22 Score=23.52 Aligned_cols=28 Identities=21% Similarity=0.190 Sum_probs=20.6
Q ss_pred CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHH
Q psy6083 37 DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKET 70 (74)
Q Consensus 37 ~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ 70 (74)
..|.+.+.|. .-|.||.++.|+..+...
T Consensus 238 k~~~pvIdvT------~kSIEEtA~~Il~~~~~~ 265 (269)
T PRK05339 238 REGIPVIDVT------NKSIEETAAKILEILGLR 265 (269)
T ss_pred HcCCCEEECC------CCcHHHHHHHHHHHHHhh
Confidence 3566666553 469999999999988653
No 70
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=27.41 E-value=1e+02 Score=16.14 Aligned_cols=38 Identities=18% Similarity=0.247 Sum_probs=26.7
Q ss_pred eEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHh
Q psy6083 32 FTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETAL 72 (74)
Q Consensus 32 ~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae 72 (74)
|.+-- -...+.+.|+.++ ..+|.++....+..|.++++
T Consensus 33 Y~vpHPl~~~i~l~Iqt~~---~~~p~~~l~~a~~~l~~~~~ 71 (77)
T PF13656_consen 33 YRVPHPLENKINLRIQTKG---GITPIEALKKALEDLIKICE 71 (77)
T ss_dssp EEESETTSSEEEEEEEEST---TS-HHHHHHHHHHHHHHHHH
T ss_pred eccCCCCCCceEEEEEECC---CCCHHHHHHHHHHHHHHHHH
Confidence 45532 2567888887654 25899999999999888765
No 71
>PF05965 FYRC: F/Y rich C-terminus; InterPro: IPR003889 The "FY-rich" domain C-terminal region is sometimes closely juxtaposed with the N-terminal region (IPR003888 from INTERPRO), but sometimes is far distant. It is of unknown function, but occurs frequently in chromatin-associated proteins like trithorax and its homologues.; GO: 0005634 nucleus; PDB: 2WZO_A.
Probab=27.12 E-value=1.1e+02 Score=16.15 Aligned_cols=32 Identities=22% Similarity=0.285 Sum_probs=20.6
Q ss_pred CcceEEEEECC--e--eEEEchhhhHHHHHHHHHHH
Q psy6083 39 SKPKIQVEFKG--E--RKTFAPEEISSMVLTKMKET 70 (74)
Q Consensus 39 g~~~~~v~~~~--~--~~~~speev~a~iL~~lk~~ 70 (74)
|.+.|+|...+ + -.--||.+.=..|++.+.+.
T Consensus 2 ~~P~F~Vt~~d~p~~~~~g~s~~~~W~~i~~~v~~~ 37 (86)
T PF05965_consen 2 GGPLFEVTSEDDPGEVFEGSSPTEAWSEILERVNEA 37 (86)
T ss_dssp -SEEEEEEETT-GGG-EEESSHHHHHHHHHHHHHHH
T ss_pred CCCEEEEEECCCCCCEEEeCCHHHHHHHHHHHHHHH
Confidence 45566665543 1 13458999999999888763
No 72
>PRK09616 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=26.85 E-value=82 Score=22.69 Aligned_cols=30 Identities=13% Similarity=0.189 Sum_probs=24.9
Q ss_pred hhcchhhcCCCCCChHHHhhcccCCeEEEe
Q psy6083 7 VFDAKRLIGRKFDDPKIQQDMKHWPFTVVN 36 (74)
Q Consensus 7 i~~~KrliG~~~~d~~v~~~~~~~p~~i~~ 36 (74)
...+++++|...+...+...++++-|++..
T Consensus 281 ~~~i~~~lG~~i~~~~i~~iL~~Lgf~~~~ 310 (552)
T PRK09616 281 VEYINKLLGIDLSAEEIIELLERMRYDAEI 310 (552)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHcCCCcEe
Confidence 456789999999988888888888888754
No 73
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=26.74 E-value=1.1e+02 Score=16.39 Aligned_cols=33 Identities=15% Similarity=0.222 Sum_probs=25.9
Q ss_pred CCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhc
Q psy6083 38 CSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALY 73 (74)
Q Consensus 38 ~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~ 73 (74)
.+.+.+.|+..+ ..+|.++...-+..|.+.++.
T Consensus 50 ~~~~~lrIqt~~---~~~p~~al~~a~~~L~~~~~~ 82 (85)
T PRK01146 50 ISNPVLKIKTDG---GIDPLEALKEAAKRIIDLCDE 82 (85)
T ss_pred CCccEEEEEECC---CCCHHHHHHHHHHHHHHHHHH
Confidence 467888887653 468999999999999887764
No 74
>PF07293 DUF1450: Protein of unknown function (DUF1450); InterPro: IPR009910 This entry consists of several hypothetical bacterial proteins of around 80 residues in length representing two families. Members contain four highly conserved cysteine residues and their function is unknown.
Probab=26.70 E-value=54 Score=17.56 Aligned_cols=16 Identities=25% Similarity=0.407 Sum_probs=13.8
Q ss_pred chhhhHHHHHHHHHHH
Q psy6083 55 APEEISSMVLTKMKET 70 (74)
Q Consensus 55 speev~a~iL~~lk~~ 70 (74)
||+|+...|.++|++.
T Consensus 60 t~eeL~~kI~~~i~e~ 75 (78)
T PF07293_consen 60 TAEELLEKIKEKIEEN 75 (78)
T ss_pred CHHHHHHHHHHHHhcc
Confidence 8999999999988763
No 75
>PF08171 Mad3_BUB1_II: Mad3/BUB1 homology region 2; InterPro: IPR012572 This domain is required for cell cycle arrest induced by spindle assembly checkpoint (SPC) activation. It is also involved in the nuclear accumulation and kinetochore targeting of proteins Bub1p, Bub3p and Mad3p [].; GO: 0000075 cell cycle checkpoint, 0005634 nucleus; PDB: 2I3T_D 2I3S_F.
Probab=26.65 E-value=24 Score=18.49 Aligned_cols=17 Identities=18% Similarity=0.479 Sum_probs=10.6
Q ss_pred ECCeeEEEchhhhHHHH
Q psy6083 47 FKGERKTFAPEEISSMV 63 (74)
Q Consensus 47 ~~~~~~~~speev~a~i 63 (74)
|.+....|+.+||+|+-
T Consensus 37 Yp~~~eE~s~eEiLA~s 53 (68)
T PF08171_consen 37 YPDDEEEYSLEEILAIS 53 (68)
T ss_dssp CTTSSSB--HHHHHHHH
T ss_pred ecCCCceecHHHHHHHH
Confidence 34545689999999864
No 76
>TIGR00409 proS_fam_II prolyl-tRNA synthetase, family II. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent groups. This group includes enzymes from Escherichia coli, Bacillus subtilis, Aquifex aeolicus, the spirochete Treponema pallidum, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. The other group includes the Pro-specific domain of a human multifunctional tRNA ligase and the prolyl-tRNA synthetases from the Archaea, the Mycoplasmas, and the spirochete Borrelia burgdorferi.
Probab=26.00 E-value=70 Score=23.25 Aligned_cols=39 Identities=18% Similarity=0.324 Sum_probs=25.2
Q ss_pred hcccCCeEEEe-----CCCcceEEEEECCeeEEEchhhhHHHHH
Q psy6083 26 DMKHWPFTVVN-----DCSKPKIQVEFKGERKTFAPEEISSMVL 64 (74)
Q Consensus 26 ~~~~~p~~i~~-----~~g~~~~~v~~~~~~~~~speev~a~iL 64 (74)
++...||.|+- .+|.+.+.....++...++.+++.+.+.
T Consensus 523 dliGiP~~i~vG~~~l~~~~Vei~~R~~~~~~~v~~~~l~~~i~ 566 (568)
T TIGR00409 523 ELIGIPLRVVVGKKNLDNGEIEVKKRRNGEKQLIKKDELVECLE 566 (568)
T ss_pred hhcCCCEEEEECCCcccCCeEEEEEcCCCceEEEEHHHHHHHHh
Confidence 45678998753 2555555544455667788888877654
No 77
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=25.82 E-value=1.2e+02 Score=16.11 Aligned_cols=48 Identities=17% Similarity=0.299 Sum_probs=27.4
Q ss_pred HHhhcccCCeEEEeCCCcceEEEEECCeeEE----------EchhhhHHHHHHHHHHH
Q psy6083 23 IQQDMKHWPFTVVNDCSKPKIQVEFKGERKT----------FAPEEISSMVLTKMKET 70 (74)
Q Consensus 23 v~~~~~~~p~~i~~~~g~~~~~v~~~~~~~~----------~speev~a~iL~~lk~~ 70 (74)
++..+....|.....+|.+.+.|+-.|+-.. ..|++|...|+.-+.+.
T Consensus 14 ~~~~l~~~~~~~~s~~g~V~V~v~g~g~v~~i~i~~~~~~~~~~~~L~~~I~~A~n~A 71 (93)
T PF02575_consen 14 AQEELAEIEVTGTSGDGLVTVTVNGNGEVVDIEIDPSALRPLDPEELEDLIVEAVNDA 71 (93)
T ss_dssp HHHHHHHSEEEEEETCCTEEEEEETTS-EEEEEE-GGGGCTS-HHHHHHHHHHHHHHH
T ss_pred HHHHHhcCEEEEEECCCEEEEEEecCceEEEEEEehHhhccCCHHHHHHHHHHHHHHH
Confidence 3444555566666667777776664442211 45777777777666553
No 78
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=25.24 E-value=1.4e+02 Score=18.83 Aligned_cols=36 Identities=17% Similarity=0.183 Sum_probs=18.0
Q ss_pred CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHh
Q psy6083 37 DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETAL 72 (74)
Q Consensus 37 ~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae 72 (74)
.+|.+...+...+-...+++++....++..|++.|.
T Consensus 207 ~~g~~~aalsv~~p~~r~~~~~~~~~~~~~l~~aa~ 242 (248)
T TIGR02431 207 ARGQVVAALNVSTHAARTTPEELVERILPLLLEAAR 242 (248)
T ss_pred CCCCEEEEEEEeeecccCCHHHHHHHHHHHHHHHHH
Confidence 345444333332222335666555566777776654
No 79
>PF04407 DUF531: Protein of unknown function (DUF531); InterPro: IPR007501 This is a family of hypothetical archaeal proteins.
Probab=24.90 E-value=37 Score=20.93 Aligned_cols=19 Identities=37% Similarity=0.628 Sum_probs=15.3
Q ss_pred ECCeeEEEchhhhHHHHHH
Q psy6083 47 FKGERKTFAPEEISSMVLT 65 (74)
Q Consensus 47 ~~~~~~~~speev~a~iL~ 65 (74)
-.++.+..||.|++.++|+
T Consensus 100 kPd~~K~i~p~e~a~~~l~ 118 (173)
T PF04407_consen 100 KPDEKKAISPEEVAEMALR 118 (173)
T ss_pred CCCCCCCCCHHHHHHHHhc
Confidence 3556788999999988774
No 80
>PF14756 Pdase_C33_assoc: Peptidase_C33-associated domain
Probab=24.84 E-value=46 Score=19.55 Aligned_cols=21 Identities=14% Similarity=0.324 Sum_probs=16.6
Q ss_pred eEEEchhhhHHHHHHHHHHHH
Q psy6083 51 RKTFAPEEISSMVLTKMKETA 71 (74)
Q Consensus 51 ~~~~speev~a~iL~~lk~~a 71 (74)
....+||||++.|=.+|+..+
T Consensus 92 tnr~tpeeva~kidqYlrgA~ 112 (147)
T PF14756_consen 92 TNRATPEEVAAKIDQYLRGAT 112 (147)
T ss_pred ccCCCHHHHHHHHHHHHhccc
Confidence 345799999999988887643
No 81
>PF05047 L51_S25_CI-B8: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain ; InterPro: IPR007741 Proteins containing this domain are located in the mitochondrion and include ribosomal protein L51, and S25. This domain is also found in mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) 1.6.5.3 from EC. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.; PDB: 1S3A_A.
Probab=23.46 E-value=99 Score=14.53 Aligned_cols=37 Identities=22% Similarity=0.365 Sum_probs=17.3
Q ss_pred hHHHhhcccCCeEEEeCCC-cceEEEEEC-CeeEEEchh
Q psy6083 21 PKIQQDMKHWPFTVVNDCS-KPKIQVEFK-GERKTFAPE 57 (74)
Q Consensus 21 ~~v~~~~~~~p~~i~~~~g-~~~~~v~~~-~~~~~~spe 57 (74)
|.++.....+++.+....| .+.+.+.|. |..+.++..
T Consensus 10 p~l~~~NP~v~~~v~~~~~~~P~~~~~y~~G~~~~i~~~ 48 (52)
T PF05047_consen 10 PTLKYHNPQVQFEVRRRRGRHPFLTAEYLNGREKTIDVK 48 (52)
T ss_dssp HHHHHHSTT--EEEE---SSS-EEEEEESS--EEEEE-T
T ss_pred HHHHHHCCCcEEEEEECCCCCCEEEEEEcCCCEEEEECC
Confidence 3455556667777766444 588888775 344555543
No 82
>cd01786 STE50_RA Ubiquitin-like domain of STE50_RA. STE50_RA The fungal adaptor protein STE50 is an essential component of three MAPK-mediated signalling pathways, which control the mating response, invasive/filamentous growth and osmotolerance (HOG pathway), respectively. STE50 functions in cell signalling between the activated G protein and STE11. The domain architecture of STE50 includes an amino-terminal SAM (sterile alpha motif) domain in addition to the carboxy-terminal ubiquitin-like RA (RAS-associated) domain. While the SAM domain interacts with STE11, the RA domain interacts with CDC42 and RAS. Modulation of signal transduction by STE50 specifically affects the pheromone-response pathway in yeast.
Probab=23.43 E-value=1.5e+02 Score=16.62 Aligned_cols=28 Identities=7% Similarity=0.345 Sum_probs=23.4
Q ss_pred EEEEECCeeEEEchhhhHHHHHHHHHHH
Q psy6083 43 IQVEFKGERKTFAPEEISSMVLTKMKET 70 (74)
Q Consensus 43 ~~v~~~~~~~~~speev~a~iL~~lk~~ 70 (74)
+-|.|.++++.+.-+|==-.||+.|++.
T Consensus 60 L~I~YgdqER~L~ldEKPl~lFk~L~~~ 87 (98)
T cd01786 60 LVICYGDQERILDLDEKPVIIFKNLKQQ 87 (98)
T ss_pred EEEEeCCeeeeccccccHHHHHHHHHHc
Confidence 4466888899999888888999999875
No 83
>PLN02975 complex I subunit
Probab=23.30 E-value=52 Score=18.47 Aligned_cols=19 Identities=21% Similarity=0.218 Sum_probs=14.8
Q ss_pred hcchhhcCCCCCChHHHhh
Q psy6083 8 FDAKRLIGRKFDDPKIQQD 26 (74)
Q Consensus 8 ~~~KrliG~~~~d~~v~~~ 26 (74)
.+.+||+|-.-++.+|+..
T Consensus 77 ~S~~Rf~G~~EN~rEV~~~ 95 (97)
T PLN02975 77 NSAGRLMGFFPNEGEVARY 95 (97)
T ss_pred ccchhhcCCCCCHHHHHhc
Confidence 4678999998888777754
No 84
>PRK14537 50S ribosomal protein L20/unknown domain fusion protein; Provisional
Probab=22.89 E-value=73 Score=20.66 Aligned_cols=18 Identities=28% Similarity=0.394 Sum_probs=15.1
Q ss_pred hhhHHHHHHHHHHHHhcC
Q psy6083 57 EEISSMVLTKMKETALYQ 74 (74)
Q Consensus 57 eev~a~iL~~lk~~ae~~ 74 (74)
..+++|.+..||+.|..+
T Consensus 189 ~~l~~m~~~elk~lak~~ 206 (230)
T PRK14537 189 IDLSKMLLKELKKLAKEH 206 (230)
T ss_pred ccHHHhhHHHHHHHHHHh
Confidence 359999999999999753
No 85
>COG0072 PheT Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis]
Probab=22.62 E-value=82 Score=23.33 Aligned_cols=31 Identities=23% Similarity=0.340 Sum_probs=26.7
Q ss_pred chhcchhhcCCCCCChHHHhhcccCCeEEEe
Q psy6083 6 TVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN 36 (74)
Q Consensus 6 ti~~~KrliG~~~~d~~v~~~~~~~p~~i~~ 36 (74)
.+..+.|++|..++..++...++++-|.+..
T Consensus 270 ~~~~i~~llG~~ls~eei~~iL~rLg~~~~~ 300 (650)
T COG0072 270 RLERINRLLGLELSAEEIEKILKRLGFKVEV 300 (650)
T ss_pred cHHHHHHHhCCCCCHHHHHHHHHHcCCeeEe
Confidence 3457889999999999999999999998765
No 86
>PRK00629 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=22.42 E-value=1e+02 Score=23.25 Aligned_cols=30 Identities=27% Similarity=0.431 Sum_probs=25.7
Q ss_pred hhcchhhcCCCCCChHHHhhcccCCeEEEe
Q psy6083 7 VFDAKRLIGRKFDDPKIQQDMKHWPFTVVN 36 (74)
Q Consensus 7 i~~~KrliG~~~~d~~v~~~~~~~p~~i~~ 36 (74)
...+++++|..+++..+...++++-|++..
T Consensus 407 ~~~i~~ilG~~i~~~~i~~iL~~Lgf~~~~ 436 (791)
T PRK00629 407 LERINRLLGTEISDEEIVDILKRLGFEVTE 436 (791)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHCCCEEEe
Confidence 456889999999998898889999999864
No 87
>COG3172 NadR Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]
Probab=22.32 E-value=2.1e+02 Score=17.95 Aligned_cols=39 Identities=21% Similarity=0.273 Sum_probs=27.5
Q ss_pred cccchhcchhhcCCCCCChHHHhhcccCCeEEE--eCCCcceE
Q psy6083 3 PKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVV--NDCSKPKI 43 (74)
Q Consensus 3 p~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~--~~~g~~~~ 43 (74)
+-.|..-.|-+.|| .+|-++......||.++ -++..+++
T Consensus 88 ~itT~~~~~~y~gr--~~P~~~~~i~~~r~DL~lLl~p~t~wv 128 (187)
T COG3172 88 FLTTQAFCKKYEGR--EHPFLQALIAEYRFDLTLLLEPNTPWV 128 (187)
T ss_pred HHHHHHHHHHHccc--CCchHHHHHhhcccceEEEcCCCCcee
Confidence 33455566788898 67889999999999864 24445554
No 88
>PF02831 gpW: gpW; InterPro: IPR004174 GpW is a 68 residue protein known to be present in phage particles. Extracts of phage-infected cells lacking GpW contain DNA-filled heads, and active tails, but no infectious virions. GpW is required for the addition of GpFII to the head, which is, in turn, required for the attachment of tails. Since GpFII and tails are known to be attached at the connector, GpW is also likely to assemble at this site. The addition of GpW to filled heads increases the DNase resistance of the packaged DNA, suggesting that GpW either forms a plug at the connector to prevent ejection of the DNA, or binds directly to the DNA. The large number of positively charged residues in GpW (its calculated pI is 10.8) is consistent with a role in DNA interaction [].; GO: 0019067 viral assembly, maturation, egress, and release; PDB: 2L6Q_A 2L6R_A 1HYW_A.
Probab=22.28 E-value=1.3e+02 Score=15.61 Aligned_cols=31 Identities=13% Similarity=0.235 Sum_probs=19.9
Q ss_pred CCcceEEEEECCeeEEEchhhhHHHHHHHHHH
Q psy6083 38 CSKPKIQVEFKGERKTFAPEEISSMVLTKMKE 69 (74)
Q Consensus 38 ~g~~~~~v~~~~~~~~~speev~a~iL~~lk~ 69 (74)
.|.-.+++..+|..-.|++..+. .+..++.+
T Consensus 19 tG~~vvsv~~dgrsV~Yt~a~i~-~L~~yI~~ 49 (68)
T PF02831_consen 19 TGQRVVSVQGDGRSVTYTQANIG-DLRAYIQQ 49 (68)
T ss_dssp CS-SEEEEEETTEEEEEEGGGHH-HHHHHHHH
T ss_pred hCCceeEeecCCeEEEEecCCHH-HHHHHHHH
Confidence 36666778888877888888773 34444443
No 89
>PRK14645 hypothetical protein; Provisional
Probab=22.23 E-value=89 Score=18.81 Aligned_cols=55 Identities=15% Similarity=0.175 Sum_probs=31.7
Q ss_pred cccchhcchhhcCCCCCChHHHhhcccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHH
Q psy6083 3 PKNTVFDAKRLIGRKFDDPKIQQDMKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSM 62 (74)
Q Consensus 3 p~nti~~~KrliG~~~~d~~v~~~~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~ 62 (74)
|=.+..+++|++|+... +....+.+--.+.. +++.+.+ ...++...+.-.+|.+.
T Consensus 90 pL~~~~df~r~~G~~v~---v~~~~k~~~G~L~~~~d~~i~l--~~~~~~~~i~~~~I~~~ 145 (154)
T PRK14645 90 PLFTARHFERFAGLKAK---VRGPGENFTGRIKAVSGDQVTF--DVGGEDRTLRIGTFQAN 145 (154)
T ss_pred CCCCHHHHHHhCCCEEE---EEcCCeEEEEEEEEEeCCEEEE--EECCeEEEEEHHHhhhh
Confidence 33456788999998542 22233444445555 4555444 45566777777777543
No 90
>TIGR02529 EutJ ethanolamine utilization protein EutJ family protein.
Probab=22.05 E-value=72 Score=20.24 Aligned_cols=21 Identities=10% Similarity=-0.018 Sum_probs=16.8
Q ss_pred EEchhhhHHHHHHHHHHHHhc
Q psy6083 53 TFAPEEISSMVLTKMKETALY 73 (74)
Q Consensus 53 ~~speev~a~iL~~lk~~ae~ 73 (74)
.+.--+.++++|++|++.|+.
T Consensus 35 ~I~d~~~~~~~l~~l~~~a~~ 55 (239)
T TIGR02529 35 IVVDFLGAVEIVRRLKDTLEQ 55 (239)
T ss_pred eEEEhHHHHHHHHHHHHHHHH
Confidence 456667889999999998864
No 91
>PF14053 DUF4248: Domain of unknown function (DUF4248)
Probab=21.97 E-value=78 Score=16.44 Aligned_cols=17 Identities=12% Similarity=0.677 Sum_probs=11.2
Q ss_pred eeEEEchhhhHHHHHHHH
Q psy6083 50 ERKTFAPEEISSMVLTKM 67 (74)
Q Consensus 50 ~~~~~speev~a~iL~~l 67 (74)
..+.|||-||. .|+.+|
T Consensus 50 ~~r~~TP~QV~-lIv~~L 66 (69)
T PF14053_consen 50 RQRSFTPRQVR-LIVRYL 66 (69)
T ss_pred CCEecCHHHHH-HHHHHc
Confidence 46789999984 444443
No 92
>KOG1584|consensus
Probab=21.93 E-value=12 Score=25.03 Aligned_cols=24 Identities=17% Similarity=0.403 Sum_probs=20.1
Q ss_pred CcccchhcchhhcCCCCCChHHHh
Q psy6083 2 NPKNTVFDAKRLIGRKFDDPKIQQ 25 (74)
Q Consensus 2 np~nti~~~KrliG~~~~d~~v~~ 25 (74)
+|...|..+-+|||+.+.+.+.+.
T Consensus 201 dp~~~ikrlaeFLg~~~~~Ee~~~ 224 (297)
T KOG1584|consen 201 DPKGEIKKLAEFLGCPFTKEEEDK 224 (297)
T ss_pred CHHHHHHHHHHHhCCCCCHHHHhh
Confidence 678888999999999998876554
No 93
>COG4302 EutC Ethanolamine ammonia-lyase, small subunit [Amino acid transport and metabolism]
Probab=21.91 E-value=69 Score=21.30 Aligned_cols=20 Identities=15% Similarity=0.318 Sum_probs=15.2
Q ss_pred cchhhcCCCCCChHHHhhcc
Q psy6083 9 DAKRLIGRKFDDPKIQQDMK 28 (74)
Q Consensus 9 ~~KrliG~~~~d~~v~~~~~ 28 (74)
-...-|||.++++.++..+.
T Consensus 134 ltRPDLGRrldeesv~~lk~ 153 (294)
T COG4302 134 LTRPDLGRRLDEESVEALKA 153 (294)
T ss_pred ecCcccccccCHHHHHHHHH
Confidence 34456899999999987654
No 94
>PF09545 RE_AccI: AccI restriction endonuclease; InterPro: IPR019054 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the restriction endonuclease AccI, which recognises and cleaves the double-stranded sequence GT^MKAC.
Probab=21.89 E-value=2e+02 Score=19.76 Aligned_cols=26 Identities=23% Similarity=0.322 Sum_probs=20.0
Q ss_pred CCCcceEEEEECCeeEEEchhhhHHH
Q psy6083 37 DCSKPKIQVEFKGERKTFAPEEISSM 62 (74)
Q Consensus 37 ~~g~~~~~v~~~~~~~~~speev~a~ 62 (74)
++|.+.+-|...|+...++-+-+.+.
T Consensus 333 ~~Gril~yV~F~GG~a~l~~e~l~~~ 358 (366)
T PF09545_consen 333 KNGRILPYVTFEGGTATLDEENLRSI 358 (366)
T ss_pred cCCcEEEEEEEecCeEEEeHHHHHHH
Confidence 57999999998887777777766554
No 95
>PF11918 DUF3436: Domain of unknown function (DUF3436); InterPro: IPR024591 This uncharacterised N-terminal domain is associated with the interphotoreceptor retinol-binding protein family. It is about 50 amino acids in length and has two conserved sequence motifs: DPRL and SYEP.
Probab=21.87 E-value=46 Score=16.76 Aligned_cols=16 Identities=25% Similarity=0.588 Sum_probs=11.9
Q ss_pred EEchhhhHHHHHHHHH
Q psy6083 53 TFAPEEISSMVLTKMK 68 (74)
Q Consensus 53 ~~speev~a~iL~~lk 68 (74)
.+++||++|++=+.+|
T Consensus 37 ~Lt~EqLla~lq~~ik 52 (55)
T PF11918_consen 37 NLTPEQLLAMLQKSIK 52 (55)
T ss_pred CcCHHHHHHHHHhhee
Confidence 5799999988755443
No 96
>PF01202 SKI: Shikimate kinase; InterPro: IPR000623 Shikimate kinase (2.7.1.71 from EC) catalyses the fifth step in the biosynthesis of aromatic amino acids from chorismate (the so-called shikimate pathway) []. The enzyme catalyses the following reaction: ATP + shikimate = ADP + shikimate-3-phosphate The protein is found in bacteria (gene aroK or aroL), plants and fungi (where it is part of a multifunctional enzyme that catalyses five consecutive steps in this pathway). In 1994, the 3D structure of shikimate kinase was predicted to be very close to that of adenylate kinase, suggesting a functional similarity as well as an evolutionary relationship []. This prediction has since been confirmed experimentally. The protein is reported to possess an alpha/beta fold, consisting of a central sheet of five parallel beta-strands flanked by alpha-helices. Such a topology is very similar to that of adenylate kinase [].; GO: 0004765 shikimate kinase activity, 0005524 ATP binding; PDB: 3VAA_C 1KO8_B 1KO4_B 1KO1_A 1KOF_A 1KNQ_A 1KO5_A 1KAG_A 2PT5_D 1SHK_A ....
Probab=21.60 E-value=67 Score=18.73 Aligned_cols=15 Identities=40% Similarity=0.563 Sum_probs=12.0
Q ss_pred EchhhhHHHHHHHHH
Q psy6083 54 FAPEEISSMVLTKMK 68 (74)
Q Consensus 54 ~speev~a~iL~~lk 68 (74)
-+|++++..|+..||
T Consensus 144 ~~~~~i~~~i~~~l~ 158 (158)
T PF01202_consen 144 SPPEEIAEEILEFLK 158 (158)
T ss_dssp CHHHHHHHHHHHHH-
T ss_pred CCHHHHHHHHHHHhC
Confidence 467999999999886
No 97
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer.
Probab=20.98 E-value=1.5e+02 Score=15.80 Aligned_cols=33 Identities=15% Similarity=0.227 Sum_probs=25.6
Q ss_pred CCcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhc
Q psy6083 38 CSKPKIQVEFKGERKTFAPEEISSMVLTKMKETALY 73 (74)
Q Consensus 38 ~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~ 73 (74)
...+.+.|+..+. .+|.++...-+..|.+.++.
T Consensus 48 ~~~~~lrIqT~~~---~~p~~al~~a~~~l~~~~~~ 80 (83)
T cd06927 48 LSNPVLKIKTDGG---VDPLEALKEAAKRLIDLCEE 80 (83)
T ss_pred CCccEEEEEeCCC---CCHHHHHHHHHHHHHHHHHH
Confidence 4678888876542 69999999989888887764
No 98
>PF07671 DUF1601: Protein of unknown function (DUF1601); InterPro: IPR011632 This repeat is found in a small number of proteins and is apparently limited to Coxiella burnetii.
Probab=20.75 E-value=1.1e+02 Score=14.00 Aligned_cols=22 Identities=14% Similarity=0.175 Sum_probs=16.4
Q ss_pred EEchhhhHHHHHHHHHHHHhcC
Q psy6083 53 TFAPEEISSMVLTKMKETALYQ 74 (74)
Q Consensus 53 ~~speev~a~iL~~lk~~ae~~ 74 (74)
.+-+.+++..++..+...|+.|
T Consensus 7 ~l~~q~L~~~L~~aV~~~a~~F 28 (37)
T PF07671_consen 7 YLEEQRLSDRLLDAVRRNAEQF 28 (37)
T ss_pred hhhhccchHHHHHHHHHHHHHc
Confidence 3456678888888888887765
No 99
>PF12321 DUF3634: Protein of unknown function (DUF3634); InterPro: IPR022090 This family of proteins is found in bacteria. Proteins in this family are typically between 103 and 114 amino acids in length.
Probab=20.63 E-value=1.8e+02 Score=16.59 Aligned_cols=14 Identities=14% Similarity=0.052 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHhcC
Q psy6083 61 SMVLTKMKETALYQ 74 (74)
Q Consensus 61 a~iL~~lk~~ae~~ 74 (74)
.-++..++++|+.+
T Consensus 44 ~~F~~~c~dIa~~~ 57 (108)
T PF12321_consen 44 PGFLHNCRDIARRY 57 (108)
T ss_pred hHHHHHHHHHHHhC
Confidence 45788888888754
No 100
>PLN02496 probable phosphopantothenoylcysteine decarboxylase
Probab=20.62 E-value=1.1e+02 Score=19.43 Aligned_cols=52 Identities=13% Similarity=0.210 Sum_probs=34.8
Q ss_pred CCChHHHhh---cccCCeEEEe-CCCcceEEEEECCeeEEEchhhhHHHHHHHHHHHH
Q psy6083 18 FDDPKIQQD---MKHWPFTVVN-DCSKPKIQVEFKGERKTFAPEEISSMVLTKMKETA 71 (74)
Q Consensus 18 ~~d~~v~~~---~~~~p~~i~~-~~g~~~~~v~~~~~~~~~speev~a~iL~~lk~~a 71 (74)
+++|.+|.. ++.+.+.++. ..|. +.....|..+.-.|++|...++..|+...
T Consensus 146 w~~Pat~~nl~~L~~~G~~vi~P~~g~--lAcg~~G~Grm~ep~~I~~~i~~~l~~~~ 201 (209)
T PLN02496 146 WNNPFTERHLMSIDELGISLIPPVTKR--LACGDYGNGAMAEPSLIYSTVRLFLESRA 201 (209)
T ss_pred HhCHHHHHHHHHHHHCCCEEECCCcCc--ccCCCcCCCCCCCHHHHHHHHHHHHhhcc
Confidence 566766653 3455777776 4554 22333456678899999999999887643
No 101
>cd08031 LARP_4_5_like La RNA-binding domain of proteins similar to La-related proteins 4 and 5. This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes.
Probab=20.57 E-value=69 Score=16.95 Aligned_cols=29 Identities=17% Similarity=0.187 Sum_probs=15.6
Q ss_pred cccchhcchhhcCCCCCChHHHhhcccCC
Q psy6083 3 PKNTVFDAKRLIGRKFDDPKIQQDMKHWP 31 (74)
Q Consensus 3 p~nti~~~KrliG~~~~d~~v~~~~~~~p 31 (74)
|=.+|.+|+|+-...-+-..+....+..+
T Consensus 34 pl~~i~~F~rmk~lt~d~~~i~~Al~~S~ 62 (75)
T cd08031 34 PIWTIANFNKIKKLTTDIDLIVEALRESP 62 (75)
T ss_pred EHHHHhCchhHHHHcCCHHHHHHHHHhCC
Confidence 34577888887655433333444444344
No 102
>PF10407 Cytokin_check_N: Cdc14 phosphatase binding protein N-terminus ; InterPro: IPR018844 Cytokinesis in yeasts involves a family of proteins whose essential function is to bind Cdc14-family phosphatase and prevent this from being sequestered and inhibited in the nucleolus. This is the highly conserved N terminus of a family of proteins which act as cytokinesis checkpoint controls by allowing cells to cope with cytokinesis defects. These proteins are required for rDNA silencing and mini-chromosome maintenance [].
Probab=20.27 E-value=55 Score=17.31 Aligned_cols=22 Identities=32% Similarity=0.425 Sum_probs=15.2
Q ss_pred CcccchhcchhhcCCCCCChHHHhhcccCC
Q psy6083 2 NPKNTVFDAKRLIGRKFDDPKIQQDMKHWP 31 (74)
Q Consensus 2 np~nti~~~KrliG~~~~d~~v~~~~~~~p 31 (74)
.|.||+..+++-| .+...+.+|
T Consensus 10 ~~~~tl~~L~~eI--------~~~f~kLYP 31 (73)
T PF10407_consen 10 DPNNTLSQLKEEI--------EERFKKLYP 31 (73)
T ss_pred CCCCcHHHHHHHH--------HHHHHHHCC
Confidence 5788888888754 555556565
No 103
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=20.21 E-value=2.4e+02 Score=17.84 Aligned_cols=32 Identities=28% Similarity=0.270 Sum_probs=23.9
Q ss_pred CcceEEEEECCeeEEEchhhhHHHHHHHHHHHHhc
Q psy6083 39 SKPKIQVEFKGERKTFAPEEISSMVLTKMKETALY 73 (74)
Q Consensus 39 g~~~~~v~~~~~~~~~speev~a~iL~~lk~~ae~ 73 (74)
+...|+|..+| .++|+++...-++-|++.++.
T Consensus 192 d~l~f~IeT~G---~i~p~~al~~A~~iL~~k~~~ 223 (224)
T smart00662 192 DKLIFDVETNG---SLKPEEAVLEAAKILKEKLEA 223 (224)
T ss_pred CEEEEEEEecC---CcCHHHHHHHHHHHHHHHHhh
Confidence 44567776554 689999999888888887654
No 104
>PLN02720 complex II
Probab=20.13 E-value=71 Score=19.02 Aligned_cols=25 Identities=16% Similarity=0.276 Sum_probs=17.8
Q ss_pred hhcchhhcCC-----CCCChHHHhhcccCC
Q psy6083 7 VFDAKRLIGR-----KFDDPKIQQDMKHWP 31 (74)
Q Consensus 7 i~~~KrliG~-----~~~d~~v~~~~~~~p 31 (74)
+.+.||+++| +++|.+|++.+..=|
T Consensus 24 l~~y~~~~~rdkPLP~Ws~sDVeeFIaSDP 53 (140)
T PLN02720 24 LENYARFSKRDKPLPPWSDSDVDEFIASDP 53 (140)
T ss_pred HHHHHHhhcCCCCCCCCchhhHHHHHhcCC
Confidence 4567889888 467777887766545
Done!