Query 040282
Match_columns 161
No_of_seqs 104 out of 144
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 06:51:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040282.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040282hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00463 SMR Small MutS-rela 99.7 6.5E-18 1.4E-22 118.3 7.6 78 71-148 2-80 (80)
2 PF01713 Smr: Smr domain; Int 99.7 1.5E-16 3.2E-21 112.1 5.6 72 73-147 1-82 (83)
3 PF08590 DUF1771: Domain of un 98.7 2.1E-09 4.6E-14 73.9 0.4 38 31-68 29-66 (66)
4 COG2840 Uncharacterized protei 98.5 4E-07 8.7E-12 74.8 7.1 77 71-149 97-180 (184)
5 PRK04946 hypothetical protein; 98.4 9.4E-07 2E-11 72.2 7.5 74 71-150 96-175 (181)
6 PRK00409 recombination and DNA 98.0 1.4E-05 3.1E-10 77.1 7.6 72 70-147 704-781 (782)
7 TIGR01069 mutS2 MutS2 family p 98.0 1.8E-05 3.9E-10 76.3 7.2 72 70-147 693-770 (771)
8 KOG2401 Predicted MutS-related 92.2 0.05 1.1E-06 49.5 0.6 106 31-137 270-378 (448)
9 COG1193 Mismatch repair ATPase 89.6 0.7 1.5E-05 45.3 5.7 71 70-146 676-752 (753)
10 cd00291 SirA_YedF_YeeD SirA, Y 85.4 6.2 0.00013 25.9 6.8 66 72-147 1-67 (69)
11 PF01206 TusA: Sulfurtransfera 82.9 7.8 0.00017 25.8 6.5 66 72-147 2-68 (70)
12 PLN03218 maturation of RBCL 1; 81.9 3.3 7.1E-05 42.1 6.1 75 71-146 922-1011(1060)
13 cd03421 SirA_like_N SirA_like_ 80.5 12 0.00027 24.8 6.8 65 72-147 1-65 (67)
14 cd03420 SirA_RHOD_Pry_redox Si 76.7 13 0.00028 25.2 6.0 66 72-147 1-67 (69)
15 KOG2401 Predicted MutS-related 70.6 2.6 5.6E-05 38.4 1.8 37 101-137 393-429 (448)
16 cd03423 SirA SirA (also known 70.4 26 0.00056 23.6 6.3 65 73-147 2-67 (69)
17 TIGR00090 iojap_ybeB iojap-lik 67.6 27 0.00058 25.6 6.3 72 59-150 6-80 (99)
18 cd00248 Mth938-like Mth938-lik 59.9 12 0.00027 27.7 3.4 31 104-137 55-85 (109)
19 PF04430 DUF498: Protein of un 57.3 17 0.00036 26.8 3.7 31 104-137 56-86 (110)
20 PF11506 DUF3217: Protein of u 54.2 15 0.00032 27.6 2.9 26 17-42 31-56 (104)
21 cd05125 Mth938_2P1-like Mth938 52.9 18 0.0004 27.4 3.3 51 83-137 37-87 (114)
22 PRK00299 sulfur transfer prote 52.7 78 0.0017 22.1 6.8 67 71-147 10-77 (81)
23 PRK10629 EnvZ/OmpR regulon mod 51.4 15 0.00032 28.5 2.7 32 120-151 52-84 (127)
24 PF13721 SecD-TM1: SecD export 49.6 17 0.00038 26.8 2.7 31 121-151 49-80 (101)
25 COG1665 Predicted nucleotidylt 49.6 26 0.00056 31.3 4.1 85 56-157 57-143 (315)
26 PRK13498 chemoreceptor glutami 49.2 97 0.0021 25.0 7.1 72 76-149 64-150 (167)
27 cd05560 Xcc1710_like Xcc1710_l 47.3 30 0.00064 25.7 3.7 31 104-137 55-85 (109)
28 TIGR01038 L22_arch ribosomal p 46.0 46 0.001 26.6 4.8 38 75-115 33-70 (150)
29 cd05126 Mth938 Mth938 domain. 45.4 57 0.0012 24.7 5.0 52 73-137 41-92 (117)
30 PRK13488 chemoreceptor glutami 43.6 1.1E+02 0.0025 24.3 6.7 59 77-137 60-126 (157)
31 PRK13494 chemoreceptor glutami 43.0 1.3E+02 0.0028 24.4 6.9 59 77-137 69-133 (163)
32 PF13986 DUF4224: Domain of un 42.9 40 0.00086 21.8 3.3 28 118-146 15-42 (47)
33 COG3414 SgaB Phosphotransferas 42.4 26 0.00057 25.7 2.7 34 103-136 2-35 (93)
34 PLN03199 delta6-acyl-lipid des 41.6 15 0.00032 34.0 1.5 22 117-138 434-455 (485)
35 PF10137 TIR-like: Predicted n 41.6 9.7 0.00021 29.4 0.3 33 105-141 2-37 (125)
36 COG0096 RpsH Ribosomal protein 41.3 42 0.00091 26.5 3.8 36 115-150 28-67 (132)
37 PF01171 ATP_bind_3: PP-loop f 41.0 39 0.00085 26.4 3.6 60 71-138 98-167 (182)
38 PRK13489 chemoreceptor glutami 40.6 1.2E+02 0.0026 26.1 6.7 58 75-134 77-141 (233)
39 PRK13487 chemoreceptor glutami 39.5 1.6E+02 0.0034 24.6 7.1 59 76-136 80-145 (201)
40 PF14201 DUF4318: Domain of un 38.9 49 0.0011 23.6 3.5 31 119-149 20-50 (74)
41 PF10006 DUF2249: Uncharacteri 38.7 1.2E+02 0.0026 20.2 6.8 64 72-147 1-67 (69)
42 COG1504 Uncharacterized conser 37.3 98 0.0021 24.2 5.2 48 76-136 47-94 (121)
43 KOG2192 PolyC-binding hnRNP-K 36.9 82 0.0018 28.4 5.3 57 29-97 136-194 (390)
44 PRK04223 rpl22p 50S ribosomal 36.2 76 0.0017 25.4 4.6 37 75-114 37-73 (153)
45 PRK13490 chemoreceptor glutami 35.8 2.3E+02 0.005 22.7 7.4 58 76-135 62-129 (162)
46 KOG3363 Uncharacterized conser 34.4 42 0.00091 28.0 2.9 31 105-136 115-145 (196)
47 TIGR00322 diphth2_R diphthamid 33.9 95 0.0021 27.5 5.3 65 82-155 214-278 (332)
48 PF13060 DUF3921: Protein of u 33.2 29 0.00062 23.6 1.5 26 71-96 22-47 (58)
49 PRK13495 chemoreceptor glutami 32.8 2.1E+02 0.0047 22.9 6.7 60 75-136 58-123 (159)
50 cd00495 Ribosomal_L25_TL5_CTC 32.6 1.4E+02 0.003 21.2 5.1 38 89-131 17-54 (91)
51 PRK11018 hypothetical protein; 32.1 1.7E+02 0.0038 20.2 7.7 67 71-147 9-76 (78)
52 PF06372 Gemin6: Gemin6 protei 31.8 15 0.00034 29.9 0.0 30 116-145 98-128 (166)
53 PRK05943 50S ribosomal protein 30.5 1.5E+02 0.0032 21.4 5.0 38 89-131 18-55 (94)
54 PF03975 CheD: CheD chemotacti 29.6 2.3E+02 0.0051 20.9 6.6 61 74-136 13-82 (114)
55 PRK11104 hemG protoporphyrinog 29.1 1.8E+02 0.0038 23.0 5.7 122 25-160 5-135 (177)
56 PRK13491 chemoreceptor glutami 28.9 2.4E+02 0.0052 23.7 6.6 57 77-135 71-132 (199)
57 PF12090 Spt20: Spt20 family; 27.8 80 0.0017 25.7 3.5 29 117-149 53-81 (182)
58 COG5520 O-Glycosyl hydrolase [ 27.5 77 0.0017 29.5 3.7 58 101-161 42-111 (433)
59 KOG3758 Uncharacterized conser 27.5 1.3E+02 0.0027 29.7 5.2 54 44-98 185-238 (655)
60 PF11360 DUF3110: Protein of u 27.4 58 0.0013 23.6 2.4 30 115-145 51-82 (86)
61 PRK12360 4-hydroxy-3-methylbut 27.2 1.1E+02 0.0023 26.9 4.4 69 79-159 14-88 (281)
62 TIGR03527 selenium_YedF seleni 27.0 3.2E+02 0.0068 22.4 6.9 67 73-149 1-68 (194)
63 COG3139 Uncharacterized protei 26.3 53 0.0011 24.4 2.0 49 44-93 30-81 (90)
64 PF08727 P3A: Poliovirus 3A pr 26.1 38 0.00082 23.3 1.1 14 120-133 29-42 (57)
65 PF02410 Oligomerisation: Olig 25.7 1.5E+02 0.0032 21.5 4.3 45 105-149 32-80 (100)
66 PF11126 Phage_DsbA: Transcrip 25.7 81 0.0018 22.5 2.8 34 34-68 23-57 (69)
67 TIGR01689 EcbF-BcbF capsule bi 24.3 1.4E+02 0.0031 22.8 4.2 37 101-137 41-83 (126)
68 cd03422 YedF YedF is a bacteri 24.2 2.3E+02 0.0049 19.0 6.8 65 73-147 2-67 (69)
69 TIGR03682 arCOG04112 arCOG0411 24.1 1.8E+02 0.004 25.4 5.3 66 81-155 193-258 (308)
70 PF10150 RNase_E_G: Ribonuclea 24.0 3.9E+02 0.0085 22.8 7.2 50 46-95 192-245 (271)
71 smart00536 AXH domain in Ataxi 23.9 34 0.00074 26.5 0.7 11 17-27 71-81 (116)
72 PRK13497 chemoreceptor glutami 23.8 3.9E+02 0.0085 22.0 6.9 59 76-136 67-130 (184)
73 PF07660 STN: Secretin and Ton 23.5 83 0.0018 19.5 2.3 28 117-146 23-50 (52)
74 PRK12613 galactose-6-phosphate 23.2 89 0.0019 24.7 2.9 31 104-137 2-32 (141)
75 PF02563 Poly_export: Polysacc 23.2 1.7E+02 0.0036 20.2 4.0 28 71-98 47-74 (82)
76 COG1825 RplY Ribosomal protein 22.9 2.5E+02 0.0054 20.6 5.1 38 89-131 18-55 (93)
77 PLN03198 delta6-acyl-lipid des 22.6 44 0.00096 31.5 1.2 20 118-137 479-498 (526)
78 PF08800 VirE_N: VirE N-termin 22.6 88 0.0019 24.0 2.7 85 71-158 34-128 (136)
79 COG2403 Predicted GTPase [Gene 22.1 3.9E+02 0.0085 25.2 7.1 78 57-135 72-159 (449)
80 PRK13493 chemoreceptor glutami 21.7 4E+02 0.0086 22.4 6.7 58 76-135 94-156 (213)
81 PRK07193 fliF flagellar MS-rin 21.2 41 0.00088 32.1 0.7 37 121-157 66-102 (552)
82 PHA02754 hypothetical protein; 21.1 1.5E+02 0.0033 20.7 3.4 32 79-112 15-46 (67)
83 PF09585 Lin0512_fam: Conserve 20.9 50 0.0011 25.5 1.0 22 71-92 9-31 (113)
84 PF02817 E3_binding: e3 bindin 20.9 58 0.0013 20.3 1.1 20 118-137 4-23 (39)
85 TIGR00731 ctc_TL5 ribosomal pr 20.5 2.3E+02 0.0051 22.7 4.9 38 89-131 15-52 (176)
86 COG3002 Uncharacterized protei 20.5 1.9E+02 0.0041 29.1 5.0 61 77-137 538-623 (880)
87 PRK12800 fliF flagellar MS-rin 20.4 44 0.00094 32.0 0.7 35 121-155 71-105 (574)
88 PF04153 NOT2_3_5: NOT2 / NOT3 20.4 82 0.0018 24.2 2.1 31 20-50 54-87 (134)
89 COG2454 Uncharacterized conser 20.2 2.9E+02 0.0063 23.6 5.5 50 78-133 110-159 (211)
90 TIGR03176 AllC allantoate amid 20.2 1.7E+02 0.0037 26.0 4.4 33 120-153 36-68 (406)
91 KOG2617 Citrate synthase [Ener 20.2 76 0.0016 29.8 2.2 57 74-130 288-356 (458)
No 1
>smart00463 SMR Small MutS-related domain.
Probab=99.74 E-value=6.5e-18 Score=118.30 Aligned_cols=78 Identities=23% Similarity=0.362 Sum_probs=70.4
Q ss_pred ceeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCC-ccccchHHHHHHHHhCCCcEEecCCCeEEEEEEc
Q 040282 71 MTLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDS-KKEAQKRMIKKLLKKESIEWTEDGNGQAILIQVD 148 (161)
Q Consensus 71 ~~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~-g~~kiKpaV~klL~e~gi~~~e~~n~G~IlI~L~ 148 (161)
++|||||++++||+..|+..|..+...+....+.||||+|+||. |+.+++|+|.++|...++.|.++.|+|+++|.|.
T Consensus 2 ~~lDLHG~~~~eA~~~l~~~l~~~~~~~~~~~~~II~G~G~~s~~g~~~i~~~l~~~l~~~~~~~~~~~~~G~~~v~l~ 80 (80)
T smart00463 2 WSLDLHGLTVEEALTALDKFLNNARLKGLEQKLVIITGKGKHSLGGKSGVKPALKEHLRVESFRFAEEGNSGVLVVKLK 80 (80)
T ss_pred CeEEcCCCCHHHHHHHHHHHHHHHHHcCCCceEEEEEcccCCCccchhhHHHHHHhchhhcccccCCCCCCeEEEEEeC
Confidence 68999999999999999999999987663268999999999996 6788999999999999999988569999999873
No 2
>PF01713 Smr: Smr domain; InterPro: IPR002625 This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 (P23909 from SWISSPROT) protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2, P94545 from SWISSPROT [].; PDB: 3QD7_X 2D9I_A 3FAU_A 2VKC_A 2ZQE_A.
Probab=99.66 E-value=1.5e-16 Score=112.10 Aligned_cols=72 Identities=25% Similarity=0.454 Sum_probs=58.5
Q ss_pred eecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEe----------cCCCeE
Q 040282 73 LDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTE----------DGNGQA 142 (161)
Q Consensus 73 IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e----------~~n~G~ 142 (161)
|||||++++||++.|++.|..+...+ ...+.||||+|+||.+.. +||+|.++|++ +++|.+ +.|+|+
T Consensus 1 iDLHG~~~~eA~~~l~~~l~~~~~~~-~~~~~II~G~G~hS~~g~-Lk~~V~~~L~~-~~~~~~v~~~~~~~~~~g~~G~ 77 (83)
T PF01713_consen 1 IDLHGLTVEEALRALEEFLDEARQRG-IRELRIITGKGNHSKGGV-LKRAVRRWLEE-GYQYEEVLAYRDAEPEDGNSGA 77 (83)
T ss_dssp EE-TTS-HHHHHHHHHHHHHHHHHTT-HSEEEEE--STCTCCTSH-HHHHHHHHHHH-THCCTTEEEEEE--CCCTGGGE
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHHcC-CCEEEEEeccCCCCCCCc-HHHHHHHHHHh-hhccchhheeeecCCCCCCCeE
Confidence 89999999999999999999987665 489999999999997654 99999999988 766543 129999
Q ss_pred EEEEE
Q 040282 143 ILIQV 147 (161)
Q Consensus 143 IlI~L 147 (161)
++|.|
T Consensus 78 ~~V~l 82 (83)
T PF01713_consen 78 TIVYL 82 (83)
T ss_dssp EEEEE
T ss_pred EEEEe
Confidence 99987
No 3
>PF08590 DUF1771: Domain of unknown function (DUF1771); InterPro: IPR013899 This domain is almost always found adjacent to IPR002625 from INTERPRO. ; PDB: 2VKC_A.
Probab=98.74 E-value=2.1e-09 Score=73.85 Aligned_cols=38 Identities=26% Similarity=0.299 Sum_probs=15.2
Q ss_pred eeCchHHHHHHHHhHHHHHHHHHHHHHHHHHHHhhhCC
Q 040282 31 IACSSFLILLNLQGHFFRQKASEADRKSAEKLVKTRNN 68 (161)
Q Consensus 31 ~~~~s~A~~LSeqGk~~~~ka~ean~kAa~~IF~~rN~ 68 (161)
-|+++.|++||++||.|.++|+++|.+||+.||..||+
T Consensus 29 ~Gd~~~A~~ls~~gk~~~~~~~~~n~~AA~~I~~~~N~ 66 (66)
T PF08590_consen 29 RGDKAAAKELSEEGKQHNEKMKEANRQAAEAIFEERNA 66 (66)
T ss_dssp ----------------------SHHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 48999999999999999999999999999999999984
No 4
>COG2840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.48 E-value=4e-07 Score=74.78 Aligned_cols=77 Identities=13% Similarity=0.210 Sum_probs=64.5
Q ss_pred ceeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCc-cccchHHHHHHHHhCCC--cEEecC----CCeEE
Q 040282 71 MTLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSK-KEAQKRMIKKLLKKESI--EWTEDG----NGQAI 143 (161)
Q Consensus 71 ~~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g-~~kiKpaV~klL~e~gi--~~~e~~----n~G~I 143 (161)
..|||||+.++||-..|-.-|..+.... .....||+|+|. |.| .+-+|++|-.+|.+.-- -|.+.. ..|.|
T Consensus 97 ~~LDLHG~tq~eAr~~L~~Fi~~a~~~~-~rcv~VihGkG~-s~g~~~vLK~~Vp~WL~qhp~V~a~~~a~~~hGG~GAl 174 (184)
T COG2840 97 ARLDLHGLTQEEARQELGAFIARARAEG-LRCVLVIHGKGR-SKGSKPVLKSQVPRWLTQHPDVLAFHQAPRRHGGDGAL 174 (184)
T ss_pred eeeeccCCCHHHHHHHHHHHHHHHHHhC-CcEEEEEeCCCc-CCCCchhHHHHHHHHHHhChHHHhhcccchhcCCceEE
Confidence 8999999999999999999999998665 478999999999 988 56789999999999544 255543 66788
Q ss_pred EEEEcc
Q 040282 144 LIQVDV 149 (161)
Q Consensus 144 lI~L~~ 149 (161)
+|.|.-
T Consensus 175 yVlL~~ 180 (184)
T COG2840 175 YVLLRR 180 (184)
T ss_pred EEEEec
Confidence 888753
No 5
>PRK04946 hypothetical protein; Provisional
Probab=98.41 E-value=9.4e-07 Score=72.21 Aligned_cols=74 Identities=14% Similarity=0.194 Sum_probs=62.4
Q ss_pred ceeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCC--cEEec----CCCeEEE
Q 040282 71 MTLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESI--EWTED----GNGQAIL 144 (161)
Q Consensus 71 ~~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi--~~~e~----~n~G~Il 144 (161)
.+|||||+.++||...|...|..+...+ ...+.||.|+|. +.+|.+|..+|.+.-. .|..- +..|.++
T Consensus 96 ~~LDLhG~~~eeA~~~L~~fl~~a~~~g-~r~v~IIHGkG~-----gvLk~~V~~wL~q~~~V~af~~A~~~~GG~GA~~ 169 (181)
T PRK04946 96 LFLDLHGLTQLQAKQELGALIAACRKEH-VFCACVMHGHGK-----HILKQQTPLWLAQHPDVMAFHQAPKEWGGDAALL 169 (181)
T ss_pred eEEECCCCCHHHHHHHHHHHHHHHHHcC-CCEEEEEcCCCH-----hHHHHHHHHHHcCCchhheeeccCcccCCceEEE
Confidence 8999999999999999999999987655 478999999995 6799999999988655 46542 2789999
Q ss_pred EEEccc
Q 040282 145 IQVDVI 150 (161)
Q Consensus 145 I~L~~~ 150 (161)
|.|...
T Consensus 170 VlLk~~ 175 (181)
T PRK04946 170 VLIEIE 175 (181)
T ss_pred EEEecC
Confidence 998654
No 6
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=98.02 E-value=1.4e-05 Score=77.08 Aligned_cols=72 Identities=14% Similarity=0.189 Sum_probs=61.0
Q ss_pred cceeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCC--cEEecC----CCeEE
Q 040282 70 VMTLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESI--EWTEDG----NGQAI 143 (161)
Q Consensus 70 ~~~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi--~~~e~~----n~G~I 143 (161)
..+|||||+.++||+..|+..|..+...+ ...+.||.|+|. |.+|.+|.+||.+.-. .|+..+ +.|+.
T Consensus 704 ~~~lDL~G~~~eeA~~~l~~fl~~a~~~g-~~~v~IIHGkGt-----G~Lr~~v~~~L~~~~~V~~f~~a~~~~GG~Gat 777 (782)
T PRK00409 704 SLELDLRGMRYEEALERLDKYLDDALLAG-YGEVLIIHGKGT-----GKLRKGVQEFLKKHPSVKSFRDAPPNEGGFGVT 777 (782)
T ss_pred CceEECCCCCHHHHHHHHHHHHHHHHHcC-CCEEEEEcCCCh-----hHHHHHHHHHHcCCCceeeeeecCcccCCCeEE
Confidence 38999999999999999999999887655 489999999985 5899999999998876 365532 78888
Q ss_pred EEEE
Q 040282 144 LIQV 147 (161)
Q Consensus 144 lI~L 147 (161)
+|.|
T Consensus 778 ~V~l 781 (782)
T PRK00409 778 IVEL 781 (782)
T ss_pred EEEE
Confidence 8876
No 7
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=97.97 E-value=1.8e-05 Score=76.35 Aligned_cols=72 Identities=15% Similarity=0.220 Sum_probs=60.7
Q ss_pred cceeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCC--cEEecC----CCeEE
Q 040282 70 VMTLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESI--EWTEDG----NGQAI 143 (161)
Q Consensus 70 ~~~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi--~~~e~~----n~G~I 143 (161)
..+|||||+.++||+..|+..|..+.-.+ ...++||-|+|. |.+|++|.+||++... .|+..+ ..|+.
T Consensus 693 ~~~ldl~G~~~~eA~~~l~~~ld~a~~~g-~~~v~IIHGkGt-----G~Lr~~v~~~L~~~~~V~~f~~a~~~~GG~G~t 766 (771)
T TIGR01069 693 SLTLDLRGQRSEEALDRLEKFLNDALLAG-YEVVLIIHGKGS-----GKLRKGVQELLKNHPKVKSFRDAPPNDGGSGVT 766 (771)
T ss_pred CceEECCCCCHHHHHHHHHHHHHHHHHCC-CCEEEEEcCCCh-----hHHHHHHHHHhcCCcceeeecccCcccCCceEE
Confidence 38999999999999999999999987655 479999999995 6799999999999876 354432 67888
Q ss_pred EEEE
Q 040282 144 LIQV 147 (161)
Q Consensus 144 lI~L 147 (161)
+|.|
T Consensus 767 ~V~l 770 (771)
T TIGR01069 767 IVYL 770 (771)
T ss_pred EEEE
Confidence 8876
No 8
>KOG2401 consensus Predicted MutS-related protein involved in mismatch repair [Replication, recombination and repair]
Probab=92.24 E-value=0.05 Score=49.45 Aligned_cols=106 Identities=12% Similarity=0.029 Sum_probs=92.9
Q ss_pred eeCchHHHHHHHHhHHHHHHHHHHHHHHHHHHHhhhCCCc--ceeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEe
Q 040282 31 IACSSFLILLNLQGHFFRQKASEADRKSAEKLVKTRNNEV--MTLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVG 108 (161)
Q Consensus 31 ~~~~s~A~~LSeqGk~~~~ka~ean~kAa~~IF~~rN~~~--~~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG 108 (161)
-+|...++.++.+.+.....++.++.++....|...+... ..+|.|+++++.|...+...+......+ ..++.++.+
T Consensus 270 ~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~ 348 (448)
T KOG2401|consen 270 GKCLRKRHELSDKPRGVLQAEDDYNADELSDEFGNKESIKSEREIDNQRLYKKAAEQKAQPEIEDAINLQ-ASELKPKVS 348 (448)
T ss_pred cchhhhhhhhhhhhhhhhhcccccchhhhhhhhhhhhhhhhhHHhhhhhHHHHHHHhhhhhhhhhhhhhh-hhhhchhhh
Confidence 4788899999999999999999999999999999888764 9999999999999999999888776655 479999999
Q ss_pred eCCCCC-ccccchHHHHHHHHhCCCcEEec
Q 040282 109 TSDEDS-KKEAQKRMIKKLLKKESIEWTED 137 (161)
Q Consensus 109 ~G~HS~-g~~kiKpaV~klL~e~gi~~~e~ 137 (161)
.+.++. +..+++|+....+....+.-...
T Consensus 349 ~~~~~~~~v~~~~~a~~~~~~~~~~~r~~~ 378 (448)
T KOG2401|consen 349 LAVKGSYAVAKLKPATQWKLDNEEIERRSE 378 (448)
T ss_pred hcccccchhhhcchHHHHHHhhhhhhcccc
Confidence 999994 67889999999999888865443
No 9
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=89.63 E-value=0.7 Score=45.31 Aligned_cols=71 Identities=13% Similarity=0.167 Sum_probs=54.3
Q ss_pred cceeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCC--cEEecC----CCeEE
Q 040282 70 VMTLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESI--EWTEDG----NGQAI 143 (161)
Q Consensus 70 ~~~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi--~~~e~~----n~G~I 143 (161)
..++||+|.-+.||+..|+.-+..+--.+ ...+.||=|+| .|+++..|.++|+++-- .|+..+ ..|+=
T Consensus 676 ~~~ldLrg~r~e~a~~~l~k~i~eail~~-~~~v~iihgkG-----tG~lre~v~~~Lk~~~~v~~~~~~~~~~GG~G~t 749 (753)
T COG1193 676 SNRLDLRGERSEEALDELDKSIDEAILEG-YEKVSIIHGKG-----TGKLREGVQEYLKKHKKVKSFRDAPPNEGGSGVT 749 (753)
T ss_pred cccccccccccHHHHHHHHhhhHHHHHcC-CcceeEEeeee-----chHHHHHHHHHHHhCCCccCcCCCCcCCCCCCee
Confidence 37999999999999999999999876444 46788987765 46799999999999865 244432 45555
Q ss_pred EEE
Q 040282 144 LIQ 146 (161)
Q Consensus 144 lI~ 146 (161)
+|.
T Consensus 750 iv~ 752 (753)
T COG1193 750 IVE 752 (753)
T ss_pred EEe
Confidence 554
No 10
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=85.43 E-value=6.2 Score=25.93 Aligned_cols=66 Identities=20% Similarity=0.144 Sum_probs=46.8
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEecC-CCeEEEEEE
Q 040282 72 TLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTEDG-NGQAILIQV 147 (161)
Q Consensus 72 ~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~~-n~G~IlI~L 147 (161)
+||+.|+--=+-+-.++..|..+. +...|.|++.... -..-|.++|++.|+++.+.+ ..|...|.+
T Consensus 1 ~lD~rg~~CP~Pl~~~~~~l~~l~---~g~~l~v~~d~~~-------~~~~i~~~~~~~g~~~~~~~~~~~~~~i~i 67 (69)
T cd00291 1 TLDLRGLPCPLPVLKTKKALEKLK---SGEVLEVLLDDPG-------AVEDIPAWAKETGHEVLEVEEEGGVYRILI 67 (69)
T ss_pred CccccCCcCCHHHHHHHHHHhcCC---CCCEEEEEecCCc-------HHHHHHHHHHHcCCEEEEEEEeCCEEEEEE
Confidence 489999988888888888888764 2467888865321 24468899999999986543 445555544
No 11
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=82.95 E-value=7.8 Score=25.79 Aligned_cols=66 Identities=18% Similarity=0.160 Sum_probs=46.9
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEecC-CCeEEEEEE
Q 040282 72 TLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTEDG-NGQAILIQV 147 (161)
Q Consensus 72 ~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~~-n~G~IlI~L 147 (161)
+||+-|+.==.-+-.+++.|..+.. .+.|.|++.... -..-|.++|++.|+++.+.+ ..|.+.|.+
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~---G~~l~v~~d~~~-------~~~di~~~~~~~g~~~~~~~~~~~~~~i~I 68 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPP---GEVLEVLVDDPA-------AVEDIPRWCEENGYEVVEVEEEGGEYRILI 68 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGT---T-EEEEEESSTT-------HHHHHHHHHHHHTEEEEEEEESSSSEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCC---CCEEEEEECCcc-------HHHHHHHHHHHCCCEEEEEEEeCCEEEEEE
Confidence 7999998888888888888888753 368888874221 23568899999999865543 566666554
No 12
>PLN03218 maturation of RBCL 1; Provisional
Probab=81.92 E-value=3.3 Score=42.05 Aligned_cols=75 Identities=11% Similarity=0.191 Sum_probs=54.6
Q ss_pred ceeecCCCCHHHHHHH-------HHHHHHhhcCCCCcceE-------EEEEeeCCCCCcc-ccchHHHHHHHHhCCCcEE
Q 040282 71 MTLDWHSIEPKEVVCL-------LRVHLTSLSGIPTIKHL-------RIVVGTSDEDSKK-EAQKRMIKKLLKKESIEWT 135 (161)
Q Consensus 71 ~~IDLHGLhVkEAi~i-------Lk~~L~~l~~~~s~~~L-------~VItG~G~HS~g~-~kiKpaV~klL~e~gi~~~ 135 (161)
+.+|+|++-|.-|.-. |++++......|. -.+ .+.+|+|+|+... +++-.+|..+|++.+++|.
T Consensus 922 ~~~d~~~~~~~aa~~~l~~wl~~~~~~~~~g~~lp~-~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~l~~l~~~~~ 1000 (1060)
T PLN03218 922 IVIDAEELPVFAAEVYLLTILKGLKHRLAAGAKLPN-VTILLPTEKKEIYTPKGEKTINLAGRVGQAVAALLRRLGLPYQ 1000 (1060)
T ss_pred eEEEcccCcchhHHHHHHHHHHHHHHHHhccCcCCc-ceeeeccccceeeccCCchhHHHHHHHHHHHHHHHHHhCCCCC
Confidence 9999999999988654 4556655555563 122 2667777776554 3467899999999999998
Q ss_pred ecCCCeEEEEE
Q 040282 136 EDGNGQAILIQ 146 (161)
Q Consensus 136 e~~n~G~IlI~ 146 (161)
+.+..|.|.+.
T Consensus 1001 ~~~~~g~~~~~ 1011 (1060)
T PLN03218 1001 GSESHGKLRIN 1011 (1060)
T ss_pred CCCCCCeEEec
Confidence 87755988764
No 13
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=80.48 E-value=12 Score=24.76 Aligned_cols=65 Identities=15% Similarity=0.236 Sum_probs=44.9
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEecCCCeEEEEEE
Q 040282 72 TLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTEDGNGQAILIQV 147 (161)
Q Consensus 72 ~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~~n~G~IlI~L 147 (161)
+||+-|+.==+-+-.+++.| .+.. .+.|.|++.. .. -+.-|..+|++.|+++...++.|.+.|.+
T Consensus 1 ~lD~rG~~CP~P~l~~k~al-~~~~---g~~l~v~~d~-~~------s~~~i~~~~~~~G~~~~~~~~~~~~~i~I 65 (67)
T cd03421 1 TIDARGLACPQPVIKTKKAL-ELEA---GGEIEVLVDN-EV------AKENVSRFAESRGYEVSVEEKGGEFEITI 65 (67)
T ss_pred CcccCCCCCCHHHHHHHHHH-hcCC---CCEEEEEEcC-hh------HHHHHHHHHHHcCCEEEEEecCCEEEEEE
Confidence 48999998888888888888 5532 3578887431 11 23468899999999996454555666654
No 14
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=76.67 E-value=13 Score=25.18 Aligned_cols=66 Identities=9% Similarity=0.042 Sum_probs=46.8
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEecC-CCeEEEEEE
Q 040282 72 TLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTEDG-NGQAILIQV 147 (161)
Q Consensus 72 ~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~~-n~G~IlI~L 147 (161)
+||+.|+.==.-+-.++..|..+.. .+.|.|++.-. . -..-|..||++.|+++...+ ..|.+.+.+
T Consensus 1 ~lD~rG~~CP~Pvl~~kkal~~l~~---G~~l~V~~d~~-~------a~~di~~~~~~~G~~~~~~~~~~~~~~~~I 67 (69)
T cd03420 1 EVDACGLQCPGPILKLKKEIDKLQD---GEQLEVKASDP-G------FARDAQAWCKSTGNTLISLETEKGKVKAVI 67 (69)
T ss_pred CcccCCCcCCHHHHHHHHHHHcCCC---CCEEEEEECCc-c------HHHHHHHHHHHcCCEEEEEEecCCEEEEEE
Confidence 4788888877777778888887752 35888887622 1 23457899999999986432 567776655
No 15
>KOG2401 consensus Predicted MutS-related protein involved in mismatch repair [Replication, recombination and repair]
Probab=70.65 E-value=2.6 Score=38.39 Aligned_cols=37 Identities=14% Similarity=0.217 Sum_probs=29.6
Q ss_pred ceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEec
Q 040282 101 KHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTED 137 (161)
Q Consensus 101 ~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~ 137 (161)
..+.|++|.|.||.+...+.++..+..+..+..+.+.
T Consensus 393 ~~~qv~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~ 429 (448)
T KOG2401|consen 393 LKLQVLFGRGIHSRGEARLPRAEKRSYEDPPQGFVEE 429 (448)
T ss_pred ccccccccccccCccchhhhhhhhhhccCCccceeee
Confidence 4577999999999998888888888788887765443
No 16
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=70.45 E-value=26 Score=23.61 Aligned_cols=65 Identities=15% Similarity=0.139 Sum_probs=44.6
Q ss_pred eecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEecC-CCeEEEEEE
Q 040282 73 LDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTEDG-NGQAILIQV 147 (161)
Q Consensus 73 IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~~-n~G~IlI~L 147 (161)
||+-|+.==.=+-.++..|..+. +.+.|.|++.-. . -..-|..+|++.|++..+.+ ++|.+.+.+
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~---~G~~l~V~~dd~-~------s~~di~~~~~~~g~~~~~~~~~~~~~~~~I 67 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMK---PGDTLLVLATDP-S------TTRDIPKFCTFLGHELLAQETEDEPYRYLI 67 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCC---CCCEEEEEeCCC-c------hHHHHHHHHHHcCCEEEEEEEcCCEEEEEE
Confidence 67777776666677788887764 236788887522 2 23457899999999986533 567666554
No 17
>TIGR00090 iojap_ybeB iojap-like ribosome-associated protein. This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown.
Probab=67.57 E-value=27 Score=25.62 Aligned_cols=72 Identities=17% Similarity=0.273 Sum_probs=47.2
Q ss_pred HHHHHhhhCCCcceeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcE--Ee
Q 040282 59 AEKLVKTRNNEVMTLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEW--TE 136 (161)
Q Consensus 59 a~~IF~~rN~~~~~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~--~e 136 (161)
++.+-+.+-.|...|||.+... . ..+ +|+++|+...-..++-..|.+.+++.|++. .|
T Consensus 6 ~~~l~~kka~dI~vldv~~~~~----------------~--~dy--~VI~Tg~S~rh~~aia~~v~~~~k~~~~~~~~~E 65 (99)
T TIGR00090 6 VEALDDKKAEDIVVLDVRGKSS----------------I--ADY--FVIASGTSSRHVKAIADNVEEELKEAGLKPLGVE 65 (99)
T ss_pred HHHHHHcCCCCEEEEECCCCCc----------------c--cCE--EEEEEeCCHHHHHHHHHHHHHHHHHcCCCccccc
Confidence 3333333444558888887541 1 133 778888776666678888999999999975 44
Q ss_pred cC-CCeEEEEEEccc
Q 040282 137 DG-NGQAILIQVDVI 150 (161)
Q Consensus 137 ~~-n~G~IlI~L~~~ 150 (161)
.. +++-++++..++
T Consensus 66 G~~~~~WillD~g~i 80 (99)
T TIGR00090 66 GLEEGDWVLVDLGDV 80 (99)
T ss_pred CCCCCCEEEEECCCE
Confidence 32 667888877653
No 18
>cd00248 Mth938-like Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. 2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined.
Probab=59.85 E-value=12 Score=27.70 Aligned_cols=31 Identities=19% Similarity=0.217 Sum_probs=25.6
Q ss_pred EEEEeeCCCCCccccchHHHHHHHHhCCCcEEec
Q 040282 104 RIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTED 137 (161)
Q Consensus 104 ~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~ 137 (161)
-||+|+|.+. ..+.|.+.++|.+.|+..+.-
T Consensus 55 iliiGTG~~~---~~~~~~~~~~l~~~gI~vE~m 85 (109)
T cd00248 55 ILLIGTGAEI---AFLPRALRAALRAAGIGVEVM 85 (109)
T ss_pred EEEEcCCCCC---CcCCHHHHHHHHHcCCeEEEe
Confidence 5899999876 246899999999999987654
No 19
>PF04430 DUF498: Protein of unknown function (DUF498/DUF598); InterPro: IPR007523 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This is entry represents an essential factor for the assembly of mitochondrial NADH:ubiquinone oxidoreductase complex (complex I) []. The crystal structure of this protein revealed a 3-layer beta+alpha/beta/alpha topology [].; PDB: 2K2E_A 2Q4Q_B 2AB1_A 2FVT_A 2CYJ_A 1IHN_B 2GM2_A 3CPK_A 2FI9_A.
Probab=57.33 E-value=17 Score=26.79 Aligned_cols=31 Identities=16% Similarity=0.244 Sum_probs=23.6
Q ss_pred EEEEeeCCCCCccccchHHHHHHHHhCCCcEEec
Q 040282 104 RIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTED 137 (161)
Q Consensus 104 ~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~ 137 (161)
-+|+|+|.. ...+.|.++++|++.|+.-..-
T Consensus 56 ~liiGtG~~---~~~~~~~~~~~l~~~GI~ve~m 86 (110)
T PF04430_consen 56 VLIIGTGKR---QLFLPPELREYLRKKGIGVEVM 86 (110)
T ss_dssp EEEEEETTS----SECTHHHHHHHHTTT-EEEEE
T ss_pred EEEEccCCc---cccCCHHHHHHHHHcCCeEEEE
Confidence 489999976 4457899999999999976543
No 20
>PF11506 DUF3217: Protein of unknown function (DUF3217); InterPro: IPR024506 This family of proteins with unknown function appears to be restricted to Mycoplasma.; PDB: 2HQL_E.
Probab=54.21 E-value=15 Score=27.61 Aligned_cols=26 Identities=27% Similarity=0.437 Sum_probs=22.7
Q ss_pred hhccCceeEEEEEeeeCchHHHHHHH
Q 040282 17 EVFSDHSFYVYYSIIACSSFLILLNL 42 (161)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~s~A~~LSe 42 (161)
..|...+|--||-|-+|+++|-+|-.
T Consensus 31 R~FG~r~FTDyyViYAN~QL~~ELEk 56 (104)
T PF11506_consen 31 RKFGERTFTDYYVIYANGQLAFELEK 56 (104)
T ss_dssp EEETTEEEEEEEEEEEEHHHHHHHHH
T ss_pred hhhccccceeEEEEEECCeeehhHHH
Confidence 46888999999999999999999854
No 21
>cd05125 Mth938_2P1-like Mth938_2P1-like domain. This model contains sequences that are similar to 2P1, a partially characterized nuclear protein, which is homologous to E3-3 from rat and known to be alternatively spliced. Its function is unknown. This family is part of the Mth938 family, for which structures, but no functional data are available.
Probab=52.93 E-value=18 Score=27.36 Aligned_cols=51 Identities=16% Similarity=0.147 Sum_probs=34.0
Q ss_pred HHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEec
Q 040282 83 VVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTED 137 (161)
Q Consensus 83 Ai~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~ 137 (161)
..++-..+|..+..... +.=-+|+|+|.. ...+.|.+.++|++.|+....-
T Consensus 37 ~~~l~~~~l~~l~~~~~-~peiliiGtG~~---~~~~~~~~~~~l~~~gi~vevm 87 (114)
T cd05125 37 FEDITEESLSLFELLEP-RPEILVIGTGRK---SRPLSPELRKYFKKLGIAVEVV 87 (114)
T ss_pred hhhCCHHHHHHHHhccC-CCCEEEEccCCC---CCcCCHHHHHHHHHcCCEEEEE
Confidence 44445556665543211 233489999987 3457889999999999986543
No 22
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=52.66 E-value=78 Score=22.14 Aligned_cols=67 Identities=16% Similarity=0.123 Sum_probs=48.1
Q ss_pred ceeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEecC-CCeEEEEEE
Q 040282 71 MTLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTEDG-NGQAILIQV 147 (161)
Q Consensus 71 ~~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~~-n~G~IlI~L 147 (161)
.+||+-|+.==.=+-.+++.|..+.. .+.|.|++.- .. -+.-|..+|++.|.+..+.+ ..|.+.+.+
T Consensus 10 ~~lD~~Gl~CP~Pll~~kk~l~~l~~---G~~l~V~~dd-~~------~~~di~~~~~~~G~~~~~~~~~~g~~~~~I 77 (81)
T PRK00299 10 HTLDALGLRCPEPVMMVRKTVRNMQP---GETLLIIADD-PA------TTRDIPSFCRFMDHELLAQETEQLPYRYLI 77 (81)
T ss_pred eEEecCCCCCCHHHHHHHHHHHcCCC---CCEEEEEeCC-cc------HHHHHHHHHHHcCCEEEEEEecCCEEEEEE
Confidence 78999999877777788888887742 3688888752 11 24457789999999985433 567666654
No 23
>PRK10629 EnvZ/OmpR regulon moderator; Provisional
Probab=51.41 E-value=15 Score=28.48 Aligned_cols=32 Identities=16% Similarity=0.200 Sum_probs=25.5
Q ss_pred hHHHHHHHHhCCCcEEecC-CCeEEEEEEcccC
Q 040282 120 KRMIKKLLKKESIEWTEDG-NGQAILIQVDVID 151 (161)
Q Consensus 120 KpaV~klL~e~gi~~~e~~-n~G~IlI~L~~~~ 151 (161)
.-.|.+.|+++||.....+ ..+.++|++++.|
T Consensus 52 ~~~v~~~L~~~gI~~ksi~~~~~~~~irf~~~~ 84 (127)
T PRK10629 52 GFYVYQHLDANGIHIKSITPENDSLLIRFDSPE 84 (127)
T ss_pred HHHHHHHHHHCCCCcceEEeeCCEEEEEECCHH
Confidence 4479999999999875543 6779999998754
No 24
>PF13721 SecD-TM1: SecD export protein N-terminal TM region
Probab=49.63 E-value=17 Score=26.82 Aligned_cols=31 Identities=26% Similarity=0.371 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCCcEEecC-CCeEEEEEEcccC
Q 040282 121 RMIKKLLKKESIEWTEDG-NGQAILIQVDVID 151 (161)
Q Consensus 121 paV~klL~e~gi~~~e~~-n~G~IlI~L~~~~ 151 (161)
-.|.+.|+++||....-+ ..|.++|++++.+
T Consensus 49 ~~v~~~L~~~~I~~k~i~~~~~~llirf~~~~ 80 (101)
T PF13721_consen 49 FQVEQALKAAGIAVKSIEQEGDSLLIRFDSTD 80 (101)
T ss_pred HHHHHHHHHCCCCcceEEeeCCEEEEEECCHH
Confidence 389999999999875443 7899999998753
No 25
>COG1665 Predicted nucleotidyltransferase [General function prediction only]
Probab=49.58 E-value=26 Score=31.33 Aligned_cols=85 Identities=20% Similarity=0.264 Sum_probs=63.3
Q ss_pred HHHHHHHHhhhCCCcceeecCCCCHHHHHHHHH--HHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCc
Q 040282 56 RKSAEKLVKTRNNEVMTLDWHSIEPKEVVCLLR--VHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIE 133 (161)
Q Consensus 56 ~kAa~~IF~~rN~~~~~IDLHGLhVkEAi~iLk--~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~ 133 (161)
.+.|..+.+++.+.-.-=+.|+.-..+..++|+ +||..+-..|+. -++-+|+.++|++.|++
T Consensus 57 ~~~a~~fl~e~~peYl~~~~~~Vp~~~V~~iLrPeeRl~eil~s~~~----------------~~~~rai~~~led~gVp 120 (315)
T COG1665 57 FKIAFRFLEESHPEYLRSVVHVVPLSDVERILRPEERLEEILESPSS----------------ESKARAIVEFLEDAGVP 120 (315)
T ss_pred hhhHHHHHHhcchhhhhhcccccCHHHHHHhcCHHHHHHHHHhCccc----------------HHHHHHHHHHHHHcCCc
Confidence 556666666666553223389999999999997 688877665541 33567899999999999
Q ss_pred EEecCCCeEEEEEEcccCCCcccc
Q 040282 134 WTEDGNGQAILIQVDVIDPKRLSF 157 (161)
Q Consensus 134 ~~e~~n~G~IlI~L~~~~~~~l~~ 157 (161)
|+.-+=+|.|+.-|.+.+ +.|.|
T Consensus 121 ~~~mGVTGSiL~gl~~~n-SDIDf 143 (315)
T COG1665 121 VNSMGVTGSILLGLYDEN-SDIDF 143 (315)
T ss_pred hhhccccccccccccCCC-CCceE
Confidence 988778999999999944 44544
No 26
>PRK13498 chemoreceptor glutamine deamidase CheD; Provisional
Probab=49.21 E-value=97 Score=25.03 Aligned_cols=72 Identities=11% Similarity=0.126 Sum_probs=47.2
Q ss_pred CCCCHHHHHHHHHHHHHhhcCCCCcceEE-EEEeeCCC---------CCccccch-HHHHHHHHhCCCcEEecC----CC
Q 040282 76 HSIEPKEVVCLLRVHLTSLSGIPTIKHLR-IVVGTSDE---------DSKKEAQK-RMIKKLLKKESIEWTEDG----NG 140 (161)
Q Consensus 76 HGLhVkEAi~iLk~~L~~l~~~~s~~~L~-VItG~G~H---------S~g~~kiK-paV~klL~e~gi~~~e~~----n~ 140 (161)
-|-|++.||+.|-+.|......++ .|. -|.|=++- +...+.+. .+++++|+++||+-..++ .+
T Consensus 64 ~~rY~d~ai~~Ll~~m~~~Ga~~~--~l~aKifGGA~m~~~~~~~~~~~~IG~rNi~~a~~~L~~~gi~i~a~DvGG~~g 141 (167)
T PRK13498 64 DGRYADEAMELLIRHALANGTPPE--DYQVKLFGGGNMFPELQQDLHTLNVADKNIHAALALAEQNGLHLKAQDLGSTGH 141 (167)
T ss_pred CcCcHHHHHHHHHHHHHHcCCCHH--HEEEEEEECcccccccccCcccCChHHHHHHHHHHHHHHCCCcEEEEeCCCCCC
Confidence 477999999999999999987664 555 34442221 12344443 489999999999854442 22
Q ss_pred eEEEEEEcc
Q 040282 141 QAILIQVDV 149 (161)
Q Consensus 141 G~IlI~L~~ 149 (161)
-+|....+.
T Consensus 142 R~i~f~~~t 150 (167)
T PRK13498 142 RSIIFDLWN 150 (167)
T ss_pred cEEEEECCC
Confidence 355555544
No 27
>cd05560 Xcc1710_like Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. Their three-dimensional structures have been determined, but their functions are unknown.
Probab=47.34 E-value=30 Score=25.74 Aligned_cols=31 Identities=16% Similarity=0.111 Sum_probs=24.7
Q ss_pred EEEEeeCCCCCccccchHHHHHHHHhCCCcEEec
Q 040282 104 RIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTED 137 (161)
Q Consensus 104 ~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~ 137 (161)
-+|+|+|.+.. -+.|++.++|++.|+..+.-
T Consensus 55 iliiGTG~~~~---~~~~~~~~~l~~~gi~vE~m 85 (109)
T cd05560 55 VILLGTGERQR---FPPPALLAPLLARGIGVEVM 85 (109)
T ss_pred EEEEecCCCCC---cCCHHHHHHHHHcCCeEEEE
Confidence 68999998743 23689999999999987654
No 28
>TIGR01038 L22_arch ribosomal protein L22(archaeal)/L17(eukaryotic/archaeal). This model describes the ribosomal protein of the eukaryotic cytosol and of the Archaea, variously designated as L17, L22, and L23. The corresponding bacterial homolog, described by a separate model, is designated L22.
Probab=46.05 E-value=46 Score=26.59 Aligned_cols=38 Identities=11% Similarity=0.038 Sum_probs=30.4
Q ss_pred cCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCc
Q 040282 75 WHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSK 115 (161)
Q Consensus 75 LHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g 115 (161)
+-|..+.+|+.+|+..|..-...| .-+---|.|+|+..
T Consensus 33 IrG~~v~~A~~~L~~V~~~k~~vP---f~r~~~~~g~~~~~ 70 (150)
T TIGR01038 33 IRGMELDKARKYLEDVIEMKRAVP---FRRYNGKVGHRRGL 70 (150)
T ss_pred HcCCcHHHHHHHHHHHHhcccccc---eeeecCCccccccc
Confidence 369999999999999988877766 45566678888864
No 29
>cd05126 Mth938 Mth938 domain. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. The function of the protein has not been determined.
Probab=45.44 E-value=57 Score=24.70 Aligned_cols=52 Identities=23% Similarity=0.178 Sum_probs=38.0
Q ss_pred eecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEec
Q 040282 73 LDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTED 137 (161)
Q Consensus 73 IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~ 137 (161)
-+.|.+...+..++|.. .| + -||+|+|..- .-.+.|++.++|.+.|+....-
T Consensus 41 ~~~~~l~~~~l~~ll~~-------~p--e--ivliGTG~~~--~~~~~~~~~~~l~~~Gi~ve~m 92 (117)
T cd05126 41 GTSHGLQPEELEELLEE-------GV--E--VIVIGTGQSG--ALKVPPETVEKLEKRGVEVLVL 92 (117)
T ss_pred CCcccCCHHHHHHHHhc-------CC--C--EEEEcCCCCc--cccCCHHHHHHHHhcCCEEEEc
Confidence 37788888887777642 13 2 6999999763 2246889999999999987663
No 30
>PRK13488 chemoreceptor glutamine deamidase CheD; Provisional
Probab=43.62 E-value=1.1e+02 Score=24.31 Aligned_cols=59 Identities=17% Similarity=0.160 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHHHHHhhcCCCCcceEEE-EEeeCCCCC------ccccch-HHHHHHHHhCCCcEEec
Q 040282 77 SIEPKEVVCLLRVHLTSLSGIPTIKHLRI-VVGTSDEDS------KKEAQK-RMIKKLLKKESIEWTED 137 (161)
Q Consensus 77 GLhVkEAi~iLk~~L~~l~~~~s~~~L~V-ItG~G~HS~------g~~kiK-paV~klL~e~gi~~~e~ 137 (161)
+-|++.|++.|=+.|......++ .|++ |.|=++--. +.+.+. .++.++|+++||+-..+
T Consensus 60 ~rY~d~ai~~li~~m~~~Ga~~~--~l~akifGGA~m~~~~~~~~~IG~rNi~~a~~~L~~~gi~i~a~ 126 (157)
T PRK13488 60 GKYADTAIPLLIEEMVKLGARKS--KLEAKLAGGAAMFDFSSNNLNIGERNIESAKETLKKLGIRIVAE 126 (157)
T ss_pred cccHHHHHHHHHHHHHHcCCCHH--HEEEEEEeCcccccCCCccCChHHHHHHHHHHHHHHCCCcEEEE
Confidence 67999999999999999987764 4543 333333211 234442 48999999999985443
No 31
>PRK13494 chemoreceptor glutamine deamidase CheD; Provisional
Probab=42.95 E-value=1.3e+02 Score=24.36 Aligned_cols=59 Identities=12% Similarity=0.036 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHHHhhcCCCCcceEEE-EEeeCCCC----Cccccch-HHHHHHHHhCCCcEEec
Q 040282 77 SIEPKEVVCLLRVHLTSLSGIPTIKHLRI-VVGTSDED----SKKEAQK-RMIKKLLKKESIEWTED 137 (161)
Q Consensus 77 GLhVkEAi~iLk~~L~~l~~~~s~~~L~V-ItG~G~HS----~g~~kiK-paV~klL~e~gi~~~e~ 137 (161)
|-|++.|++.|=+.|......++ .|.+ |.|=++-= ...+.+. .++.++|+++||+-..+
T Consensus 69 ~rY~d~ai~~Ll~~m~~~Ga~~~--~l~aKifGGa~m~~~~~~~IG~rNv~~a~~~L~~~gI~i~a~ 133 (163)
T PRK13494 69 GRYGVYAIPMLIDAMLENGASKS--NLKAKLFGGTNFMAKGTIKVGLENSEFAVNTLNKYGIPILAK 133 (163)
T ss_pred cccHHHHHHHHHHHHHHcCCCHH--HeEEEEEeCcccCCcccCChHHHHHHHHHHHHHHcCCcEEEE
Confidence 67999999999999999887664 5553 44444322 2234442 48999999999985443
No 32
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=42.91 E-value=40 Score=21.77 Aligned_cols=28 Identities=7% Similarity=0.169 Sum_probs=21.5
Q ss_pred cchHHHHHHHHhCCCcEEecCCCeEEEEE
Q 040282 118 AQKRMIKKLLKKESIEWTEDGNGQAILIQ 146 (161)
Q Consensus 118 kiKpaV~klL~e~gi~~~e~~n~G~IlI~ 146 (161)
|.+.+-.+.|+++||.|... ..|..+|.
T Consensus 15 k~~~~Q~~~L~~~Gi~~~~~-~~G~p~V~ 42 (47)
T PF13986_consen 15 KRPSKQIRWLRRNGIPFVVR-ADGRPIVT 42 (47)
T ss_pred CCHHHHHHHHHHCCCeeEEC-CCCCEEee
Confidence 35567889999999999987 56765553
No 33
>COG3414 SgaB Phosphotransferase system, galactitol-specific IIB component [Carbohydrate transport and metabolism]
Probab=42.44 E-value=26 Score=25.73 Aligned_cols=34 Identities=15% Similarity=0.235 Sum_probs=24.4
Q ss_pred EEEEEeeCCCCCccccchHHHHHHHHhCCCcEEe
Q 040282 103 LRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTE 136 (161)
Q Consensus 103 L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e 136 (161)
.+|++-+|+.=...--++-+|+++|++.||+.+.
T Consensus 2 ~KIL~aCG~GvgSS~~ik~kve~~l~~~gi~~~~ 35 (93)
T COG3414 2 IKILAACGNGVGSSTMIKMKVEEVLKELGIDVDV 35 (93)
T ss_pred cEEEEECCCCccHHHHHHHHHHHHHHHcCCCcee
Confidence 4677777765222334799999999999997543
No 34
>PLN03199 delta6-acyl-lipid desaturase-like protein; Provisional
Probab=41.62 E-value=15 Score=34.02 Aligned_cols=22 Identities=9% Similarity=0.258 Sum_probs=19.0
Q ss_pred ccchHHHHHHHHhCCCcEEecC
Q 040282 117 EAQKRMIKKLLKKESIEWTEDG 138 (161)
Q Consensus 117 ~kiKpaV~klL~e~gi~~~e~~ 138 (161)
.++.|.|+++|+|.|++|++.+
T Consensus 434 ~~i~piVk~~C~k~glpY~~~~ 455 (485)
T PLN03199 434 AKCHALVESFCKEWGVKYHEAD 455 (485)
T ss_pred HhhhHHHHHHHHHhCCCccccC
Confidence 3578999999999999998863
No 35
>PF10137 TIR-like: Predicted nucleotide-binding protein containing TIR-like domain; InterPro: IPR019302 This entry represents a TIR-like domain found in a family of prokaryotic predicted nucleotide-binding proteins. Their exact function has not, as yet, been defined.
Probab=41.55 E-value=9.7 Score=29.37 Aligned_cols=33 Identities=24% Similarity=0.448 Sum_probs=16.7
Q ss_pred EEEeeCCCCCccccchHHHHHHHHhCCCc---EEecCCCe
Q 040282 105 IVVGTSDEDSKKEAQKRMIKKLLKKESIE---WTEDGNGQ 141 (161)
Q Consensus 105 VItG~G~HS~g~~kiKpaV~klL~e~gi~---~~e~~n~G 141 (161)
|.+|-| |+. +.+.+|..+|++.+++ |.+..+.|
T Consensus 2 VFIvhg-~~~---~~~~~v~~~L~~~~~ep~i~~~~~~~g 37 (125)
T PF10137_consen 2 VFIVHG-RDL---AAAEAVERFLEKLGLEPIIWHEQPNLG 37 (125)
T ss_pred EEEEeC-CCH---HHHHHHHHHHHhCCCceEEeecCCCCC
Confidence 445544 332 2445566666665553 55544443
No 36
>COG0096 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis]
Probab=41.31 E-value=42 Score=26.52 Aligned_cols=36 Identities=28% Similarity=0.333 Sum_probs=29.3
Q ss_pred ccccchHHHHHHHHhCCC--c--EEecCCCeEEEEEEccc
Q 040282 115 KKEAQKRMIKKLLKKESI--E--WTEDGNGQAILIQVDVI 150 (161)
Q Consensus 115 g~~kiKpaV~klL~e~gi--~--~~e~~n~G~IlI~L~~~ 150 (161)
..+|++.+|.+.|.++|| . +.|+.+.|.+.|.|...
T Consensus 28 P~SKl~~~il~vLk~eGYI~~f~~~~~~~~~~~~v~Lky~ 67 (132)
T COG0096 28 PASKLKGAILKVLKKEGYIKDFEVIDDGRKGKLRVQLKYR 67 (132)
T ss_pred chHHHHHHHHHHHHHcCCcceEEEEeCCcceEEEEEEEec
Confidence 456889999999999999 3 45545899999999874
No 37
>PF01171 ATP_bind_3: PP-loop family; InterPro: IPR011063 This entry represents the PP-loop motif superfamily [,]. The PP-loop motif appears to be a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding []. Named PP-motif, since it appears to be a part of a previously uncharacterised ATP pyrophophatase domain. ATP sulfurylases, Escherichia coli NtrL, and Bacillus subtilis OutB consist of this domain alone. In other proteins, the pyrophosphatase domain is associated with amidotransferase domains (type I or type II), a putative citrulline-aspartate ligase domain or a nitrilase/amidase domain.; PDB: 3A2K_A 2E89_B 2E21_D 1WY5_B 1NI5_A.
Probab=40.97 E-value=39 Score=26.38 Aligned_cols=60 Identities=13% Similarity=0.108 Sum_probs=32.4
Q ss_pred ceeecCCCCHHHHHHHHHHHHHhhcCCCC---cceEEEEEeeCCCCCccccchH-------HHHHHHHhCCCcEEecC
Q 040282 71 MTLDWHSIEPKEVVCLLRVHLTSLSGIPT---IKHLRIVVGTSDEDSKKEAQKR-------MIKKLLKKESIEWTEDG 138 (161)
Q Consensus 71 ~~IDLHGLhVkEAi~iLk~~L~~l~~~~s---~~~L~VItG~G~HS~g~~kiKp-------aV~klL~e~gi~~~e~~ 138 (161)
+.| +=|+|.++.++-+=.++...++... ..+..-. .+..-+|| -+.+||++.|++|.+++
T Consensus 98 ~~i-~~GHh~dD~~ET~l~~l~rg~~~~~l~~~~~~~~~-------~~~~~iRPLl~~~k~ei~~~~~~~~i~~~~D~ 167 (182)
T PF01171_consen 98 NKI-ALGHHLDDQAETFLMNLLRGSGLRGLAGMPPVSPF-------KGIKLIRPLLYVSKDEIRAYAKENGIPYVEDP 167 (182)
T ss_dssp CEE-E---BHHHHHHHHHHHHHHT--CCCCC-S-SEEEE-------TTCEEE-GGGCS-HHHHHHHHHHTT-SSBS-C
T ss_pred cce-eecCcCCccHHHHHHHHHHhccchhhccccccccc-------cCcccCCcchhCCHHHHHHHHHHCCCcEEECc
Confidence 344 6699999888877777666543311 1221111 23334577 49999999999998875
No 38
>PRK13489 chemoreceptor glutamine deamidase CheD; Provisional
Probab=40.62 E-value=1.2e+02 Score=26.10 Aligned_cols=58 Identities=14% Similarity=0.095 Sum_probs=42.6
Q ss_pred cCCCCHHHHHHHHHHHHHhhcCCCCcceEEE-EEeeCCCCC-----ccccch-HHHHHHHHhCCCcE
Q 040282 75 WHSIEPKEVVCLLRVHLTSLSGIPTIKHLRI-VVGTSDEDS-----KKEAQK-RMIKKLLKKESIEW 134 (161)
Q Consensus 75 LHGLhVkEAi~iLk~~L~~l~~~~s~~~L~V-ItG~G~HS~-----g~~kiK-paV~klL~e~gi~~ 134 (161)
.-+-|++.||+.|=+.|......+ ..|.+ |.|=++-=. +.|.+. .++.++|.++||+-
T Consensus 77 ~~~rYgd~Ame~Li~~m~~~Ga~r--~~L~AKifGGA~m~~~~~~~~IG~RNieaa~~~L~~~gI~I 141 (233)
T PRK13489 77 ESMRYGAYAMEVLINELIKAGGRR--ERFEAKVFGGAAVLAGMTTINIGDRNADFVRRYLALERIRI 141 (233)
T ss_pred CCcccHHHHHHHHHHHHHHcCCCH--HHEEEEEEECccccCCCCcCChhHHHHHHHHHHHHHcCCcE
Confidence 347799999999999999988765 47776 556554311 234442 48999999999974
No 39
>PRK13487 chemoreceptor glutamine deamidase CheD; Provisional
Probab=39.53 E-value=1.6e+02 Score=24.61 Aligned_cols=59 Identities=17% Similarity=0.155 Sum_probs=41.8
Q ss_pred CCCCHHHHHHHHHHHHHhhcCCCCcceEEE-EEeeCCCC-----Cccccch-HHHHHHHHhCCCcEEe
Q 040282 76 HSIEPKEVVCLLRVHLTSLSGIPTIKHLRI-VVGTSDED-----SKKEAQK-RMIKKLLKKESIEWTE 136 (161)
Q Consensus 76 HGLhVkEAi~iLk~~L~~l~~~~s~~~L~V-ItG~G~HS-----~g~~kiK-paV~klL~e~gi~~~e 136 (161)
=+-|++.||+.|=+.|......++ .|++ |.|=++-- .+.|.+. .++.++|+++||+-..
T Consensus 80 ~~rY~d~A~~~Li~~m~~~Ga~~~--~l~aKlfGGA~m~~~~~~~~IG~rNi~~a~~~L~~~gI~iva 145 (201)
T PRK13487 80 SARYGSYAMELLINDLLKLGARRE--NLEAKVFGGGNVLRGFTSMNVGERNAEFVRDYLQTERIPIVA 145 (201)
T ss_pred CcccHHHHHHHHHHHHHHcCCCHH--HEEEEEEeCCcccCCCccCCchHHHHHHHHHHHHHcCCcEEE
Confidence 478999999999999999987764 5553 44433221 2344443 5899999999998543
No 40
>PF14201 DUF4318: Domain of unknown function (DUF4318)
Probab=38.91 E-value=49 Score=23.60 Aligned_cols=31 Identities=16% Similarity=0.063 Sum_probs=20.6
Q ss_pred chHHHHHHHHhCCCcEEecCCCeEEEEEEcc
Q 040282 119 QKRMIKKLLKKESIEWTEDGNGQAILIQVDV 149 (161)
Q Consensus 119 iKpaV~klL~e~gi~~~e~~n~G~IlI~L~~ 149 (161)
+=-+|++||.++|.+..-.+..-=+.+.|||
T Consensus 20 i~~aIE~YC~~~~~~l~Fisr~~Pi~~~idg 50 (74)
T PF14201_consen 20 ICEAIEKYCIKNGESLEFISRDKPITFKIDG 50 (74)
T ss_pred HHHHHHHHHHHcCCceEEEecCCcEEEEECC
Confidence 4459999999999976444333335555655
No 41
>PF10006 DUF2249: Uncharacterized conserved protein (DUF2249); InterPro: IPR018720 This domain is found in a number of hypothetical bacterial and archaeal proteins with no known function. It is also found in proteins described as cupin 2 and hemerythrin. It represents a conserved region that shows distant similarity to the SirA protein (see IPR001455 from INTERPRO).
Probab=38.73 E-value=1.2e+02 Score=20.24 Aligned_cols=64 Identities=16% Similarity=0.233 Sum_probs=43.0
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhC-CC-cEEecC-CCeEEEEEE
Q 040282 72 TLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKE-SI-EWTEDG-NGQAILIQV 147 (161)
Q Consensus 72 ~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~-gi-~~~e~~-n~G~IlI~L 147 (161)
+||+.|+...+.+..+-..+..+.. .+.|.++.-.. -.| ....|++. |+ .|+-.+ .+|...|.+
T Consensus 1 ~LDvR~l~~~~p~~~il~~~~~L~~---Ge~l~lv~d~~--------P~p-L~~~l~~~~g~~~~~~~~~~~~~w~v~i 67 (69)
T PF10006_consen 1 VLDVRGLPPPEPHERILEALDELPP---GETLELVNDHD--------PRP-LYPQLEERRGFFSWEYEEQGPGEWRVRI 67 (69)
T ss_pred CEECCCCCCcChHHHHHHHHHcCCC---CCEEEEEeCCC--------CHH-HHHHHHHhCCCceEEEEEcCCCEEEEEE
Confidence 5899999888888888888777753 35677664221 123 44555666 88 885543 788777765
No 42
>COG1504 Uncharacterized conserved protein [Function unknown]
Probab=37.28 E-value=98 Score=24.22 Aligned_cols=48 Identities=25% Similarity=0.266 Sum_probs=34.5
Q ss_pred CCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEe
Q 040282 76 HSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTE 136 (161)
Q Consensus 76 HGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e 136 (161)
|-+..+|+.++|++. .=.+++|+|.+ |.-.+-|++.+||++.+..-.+
T Consensus 47 Hkl~~eEle~~lee~-----------~E~ivvGTG~~--G~l~l~~ea~e~~r~k~~~vi~ 94 (121)
T COG1504 47 HKLALEELEELLEEG-----------PEVIVVGTGQS--GMLELSEEAREFFRKKGCEVIE 94 (121)
T ss_pred cccCHHHHHHHHhcC-----------CcEEEEecCce--eEEEeCHHHHHHHHhcCCeEEE
Confidence 557778888887732 23488999976 4445788999999999865433
No 43
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=36.87 E-value=82 Score=28.37 Aligned_cols=57 Identities=19% Similarity=0.105 Sum_probs=45.7
Q ss_pred Eeee-CchHHHHHHHHhHHHHHHHHHHHHHHHHHHHhhhCCCc-ceeecCCCCHHHHHHHHHHHHHhhcCC
Q 040282 29 SIIA-CSSFLILLNLQGHFFRQKASEADRKSAEKLVKTRNNEV-MTLDWHSIEPKEVVCLLRVHLTSLSGI 97 (161)
Q Consensus 29 ~~~~-~~s~A~~LSeqGk~~~~ka~ean~kAa~~IF~~rN~~~-~~IDLHGLhVkEAi~iLk~~L~~l~~~ 97 (161)
.||| |+|+-++|.|+-- |.-+||.++-+.+ +.+=|-|-..+..+.+++..|..++.+
T Consensus 136 ~iigrngskikelrekcs------------arlkift~c~p~stdrv~l~~g~~k~v~~~i~~il~~i~e~ 194 (390)
T KOG2192|consen 136 GIIGRNGSKIKELREKCS------------ARLKIFTECCPHSTDRVVLIGGKPKRVVECIKIILDLISES 194 (390)
T ss_pred ceecccchhHHHHHHhhh------------hhhhhhhccCCCCcceEEEecCCcchHHHHHHHHHHHhhcC
Confidence 3666 8888888877632 4458999999876 888899999999999999998887644
No 44
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=36.17 E-value=76 Score=25.43 Aligned_cols=37 Identities=11% Similarity=0.099 Sum_probs=28.0
Q ss_pred cCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCC
Q 040282 75 WHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDS 114 (161)
Q Consensus 75 LHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~ 114 (161)
+-|..+++|+.+|+..|..-...| ..+-.=|.|.++.
T Consensus 37 IRG~~v~~A~~~L~~V~~~k~~vP---f~r~~~~~g~~~~ 73 (153)
T PRK04223 37 IRGMKLDEAKAYLEDVIALKRAVP---FKRHNKKVGHRKG 73 (153)
T ss_pred HcCCcHHHHHHHHHHHHhcccccc---eeeecCCcccccc
Confidence 369999999999999888776665 3444556777764
No 45
>PRK13490 chemoreceptor glutamine deamidase CheD; Provisional
Probab=35.78 E-value=2.3e+02 Score=22.70 Aligned_cols=58 Identities=17% Similarity=0.137 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHHHHhhcCCCCcceEEE-EEeeCCCC--------Cccccch-HHHHHHHHhCCCcEE
Q 040282 76 HSIEPKEVVCLLRVHLTSLSGIPTIKHLRI-VVGTSDED--------SKKEAQK-RMIKKLLKKESIEWT 135 (161)
Q Consensus 76 HGLhVkEAi~iLk~~L~~l~~~~s~~~L~V-ItG~G~HS--------~g~~kiK-paV~klL~e~gi~~~ 135 (161)
-+-|++.||+.|=+.|......++ .|++ |.|=++-- ...+.+. .++.++|+++||+-.
T Consensus 62 ~~rY~d~ai~~Li~~m~~~Ga~~~--~l~aKifGGA~m~~~~~~~~~~~IG~rNv~~a~~~L~~~gI~i~ 129 (162)
T PRK13490 62 PMKFADLAIPILIEKMEKLGANKR--NLKAKIAGGASMFNFSDKSMVMDIGNRNGKAVKKKLKELSIPIL 129 (162)
T ss_pred CccCHHHHHHHHHHHHHHcCCCHH--HEEEEEEeCccccCCCCccccCChhHHHHHHHHHHHHHcCCcEE
Confidence 478999999999999999987664 5553 44444321 1233332 479999999999853
No 46
>KOG3363 consensus Uncharacterized conserved nuclear protein [Function unknown]
Probab=34.40 E-value=42 Score=28.01 Aligned_cols=31 Identities=16% Similarity=0.431 Sum_probs=24.7
Q ss_pred EEEeeCCCCCccccchHHHHHHHHhCCCcEEe
Q 040282 105 IVVGTSDEDSKKEAQKRMIKKLLKKESIEWTE 136 (161)
Q Consensus 105 VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e 136 (161)
.|+|+|..- .-.|++|.|.+|+++.+++-+.
T Consensus 115 LIvG~Gd~~-~p~~v~~~V~~F~k~~ki~lEi 145 (196)
T KOG3363|consen 115 LIVGCGDKK-HPDKVRPSVRQFVKSHKIKLEI 145 (196)
T ss_pred EEEecCCcC-CchhcCHHHHHHHHHhCcceEE
Confidence 688999763 3456899999999999998544
No 47
>TIGR00322 diphth2_R diphthamide biosynthesis protein 2-related domain. Because archaeal species are known to have the diphthamide modification to the conserved His of archaeal and eukaryotic EF-2, it may be that the lone homolog of YKL191W in M. jannaschii, A. fulgidus, and M. thermoautotrophicum is orthologous. However, each of these is considerably shorter than YKL191W and seems more closely related to the uncharacterized protein YIL103W than to YKL191W.
Probab=33.86 E-value=95 Score=27.51 Aligned_cols=65 Identities=15% Similarity=0.241 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEecCCCeEEEEEEcccCCCcc
Q 040282 82 EVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTEDGNGQAILIQVDVIDPKRL 155 (161)
Q Consensus 82 EAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~~n~G~IlI~L~~~~~~~l 155 (161)
++-++|++|......-...+..=||+|+=.- +|.-.+-.+++++|+++|.++. +|-++.++|.+|
T Consensus 214 ~~~~~l~rR~~~I~ka~~A~~vGIlvgTl~~-q~~~~~~~~l~~ll~~~gkk~y--------~i~~~~in~~kL 278 (332)
T TIGR00322 214 DAKQFVKVRALAISKARKGKKFGVVLSSKGG-QGRLRLAKNLKKNLEEAGKTVL--------IILLSNVSPAKL 278 (332)
T ss_pred cHHHHHHHHHHHHHHHhcCCEEEEEEecCcc-CCCHHHHHHHHHHHHHcCCcEE--------EEEeCCCCHHHH
Confidence 4678888887765432223677788885321 2223345678899999988763 456666766665
No 48
>PF13060 DUF3921: Protein of unknown function (DUF3921)
Probab=33.17 E-value=29 Score=23.57 Aligned_cols=26 Identities=19% Similarity=0.199 Sum_probs=22.3
Q ss_pred ceeecCCCCHHHHHHHHHHHHHhhcC
Q 040282 71 MTLDWHSIEPKEVVCLLRVHLTSLSG 96 (161)
Q Consensus 71 ~~IDLHGLhVkEAi~iLk~~L~~l~~ 96 (161)
-+|||||.-++|-.+.-++.|..++.
T Consensus 22 kei~~~g~~~d~i~kaqeeylsals~ 47 (58)
T PF13060_consen 22 KEIDLQGVIADEIQKAQEEYLSALSH 47 (58)
T ss_pred HHhhhcchHHHHHHHHHHHHHHHhhH
Confidence 57999999999988888888888763
No 49
>PRK13495 chemoreceptor glutamine deamidase CheD; Provisional
Probab=32.81 E-value=2.1e+02 Score=22.87 Aligned_cols=60 Identities=17% Similarity=0.124 Sum_probs=41.7
Q ss_pred cCCCCHHHHHHHHHHHHHhhcCCCCcceEEE-EEeeCCCCC----ccccch-HHHHHHHHhCCCcEEe
Q 040282 75 WHSIEPKEVVCLLRVHLTSLSGIPTIKHLRI-VVGTSDEDS----KKEAQK-RMIKKLLKKESIEWTE 136 (161)
Q Consensus 75 LHGLhVkEAi~iLk~~L~~l~~~~s~~~L~V-ItG~G~HS~----g~~kiK-paV~klL~e~gi~~~e 136 (161)
.=+-|++.|++.|=+.|......++ .|++ |.|=++--. +.+.+. .++.++|+++||+-..
T Consensus 58 ~~~rY~d~ai~~Li~~m~~~Ga~~~--~l~aKifGGA~m~~~~~~~IG~rNi~~a~~~L~~~gI~i~a 123 (159)
T PRK13495 58 KPGKYADTAIKTLVEELKKMGAKVE--RLEAKIAGGASMFESSGMNIGARNVEAVKKHLKDFGIKLVA 123 (159)
T ss_pred CCccCHHHHHHHHHHHHHHcCCCHH--HEEEEEEeCCccCCCCCCChHHHHHHHHHHHHHHcCCcEEE
Confidence 3478999999999999999987664 5554 344333222 233342 4899999999998533
No 50
>cd00495 Ribosomal_L25_TL5_CTC Ribosomal_L25_TL5_CTC: Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain. L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC, which each contain two domains. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had impaired protein synthesis capability. In Bacillus subtilis, CTC is induced under stress conditions and located in the ribosome; it has been proposed that CTC may be necessary for accurate translation under stress conditions. Ribosomal_L25_TL5_CTC is found only in bacteria and some plastids. Due to its limited taxonomic diversity and the viability of cells deleted for L25, this protein is not believed to be necessary for ribosomal assembly. Eukaryotes contain a protein called L25, which is not homologous to bacterial L
Probab=32.60 E-value=1.4e+02 Score=21.15 Aligned_cols=38 Identities=24% Similarity=0.454 Sum_probs=25.2
Q ss_pred HHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCC
Q 040282 89 VHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKES 131 (161)
Q Consensus 89 ~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~g 131 (161)
++|+....+|. ||+|.|..+....--...+.+++.+.|
T Consensus 17 r~lR~~G~iPa-----vvYG~~~~~~~i~v~~~~l~k~l~~~~ 54 (91)
T cd00495 17 RRLRRAGKVPA-----VIYGKGKEPISISVDEKELEKLLRKEG 54 (91)
T ss_pred HHHHHCCCCCE-----EEECCCCCCEEEEEcHHHHHHHHhhcC
Confidence 35555556676 999999654433323567888888776
No 51
>PRK11018 hypothetical protein; Provisional
Probab=32.11 E-value=1.7e+02 Score=20.19 Aligned_cols=67 Identities=13% Similarity=0.013 Sum_probs=45.6
Q ss_pred ceeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEec-CCCeEEEEEE
Q 040282 71 MTLDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTED-GNGQAILIQV 147 (161)
Q Consensus 71 ~~IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~-~n~G~IlI~L 147 (161)
.+||+-|+.==.=+-.++..|..+. +.+.|.|++-- .. -..-|..+|++.|++.... +..|.+.+.+
T Consensus 9 ~~lD~rG~~CP~Pvl~~kk~l~~l~---~G~~L~V~~d~-~~------a~~di~~~~~~~G~~v~~~~~~~g~~~~~I 76 (78)
T PRK11018 9 YRLDMVGEPCPYPAVATLEALPQLK---KGEILEVVSDC-PQ------SINNIPLDARNHGYTVLDIQQDGPTIRYLI 76 (78)
T ss_pred eeEECCCCcCCHHHHHHHHHHHhCC---CCCEEEEEeCC-cc------HHHHHHHHHHHcCCEEEEEEecCCeEEEEE
Confidence 6899999976666666677777664 23678887642 11 2346889999999998542 2567666654
No 52
>PF06372 Gemin6: Gemin6 protein; InterPro: IPR009422 This family consists of several mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the Survival of motor neuron complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles [].; GO: 0000245 spliceosome assembly, 0005634 nucleus; PDB: 1Y96_A.
Probab=31.79 E-value=15 Score=29.88 Aligned_cols=30 Identities=30% Similarity=0.428 Sum_probs=0.0
Q ss_pred cccchHHHHHHHHhCCCcEEecC-CCeEEEE
Q 040282 116 KEAQKRMIKKLLKKESIEWTEDG-NGQAILI 145 (161)
Q Consensus 116 ~~kiKpaV~klL~e~gi~~~e~~-n~G~IlI 145 (161)
..+||-.|+++|+++.|..+|.. ..|+++|
T Consensus 98 l~~RK~~l~~wL~~N~ipV~E~g~~~~~l~V 128 (166)
T PF06372_consen 98 LEKRKESLKQWLEKNRIPVTEQGDPDGTLCV 128 (166)
T ss_dssp -------------------------------
T ss_pred HHHHHHHHHHHHHHCCCceEeecCCCCeEEE
Confidence 45678899999999999999975 3555544
No 53
>PRK05943 50S ribosomal protein L25; Reviewed
Probab=30.45 E-value=1.5e+02 Score=21.36 Aligned_cols=38 Identities=16% Similarity=0.232 Sum_probs=24.8
Q ss_pred HHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCC
Q 040282 89 VHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKES 131 (161)
Q Consensus 89 ~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~g 131 (161)
++|+.....|. ||+|+|..+....--...+.+++.+.+
T Consensus 18 r~lR~~G~vPa-----ViYG~~~~~~~i~v~~~el~k~l~~~~ 55 (94)
T PRK05943 18 RRLRRAGKFPA-----IIYGGNEAPVSIVLDHKDVINLQAKAE 55 (94)
T ss_pred HHHHHCCCCCE-----EEECCCCCcEEEEEcHHHHHHHHhcCC
Confidence 35555556666 999999876443333567888887554
No 54
>PF03975 CheD: CheD chemotactic sensory transduction; InterPro: IPR005659 CheD deamidates glutamine residues to glutamate on methyl-accepting chemotaxis receptors (MCPs). CheD-mediated MCP deamidation is required for productive communication of the conformational signals of the chemoreceptors to the cheA kinase []. CheC is a CheY-P phosphatase (CheY controls flagellar rotation and is activated by phosphorylation). The activity of CheC is enhanced by its interaction with CheD, forming a CheC-CheD heterodimer. It is suggested that CheC exerts its effect on MCP methylation in Bacillus subtilis by controlling the binding of CheD to the MCPs [].; GO: 0050568 protein-glutamine glutaminase activity, 0006935 chemotaxis; PDB: 2F9Z_D.
Probab=29.57 E-value=2.3e+02 Score=20.92 Aligned_cols=61 Identities=15% Similarity=0.147 Sum_probs=36.0
Q ss_pred ecCCCCHHHHHHHHHHHHHhhcCCCCcceEEE-EEeeCC-CC------Cccccch-HHHHHHHHhCCCcEEe
Q 040282 74 DWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRI-VVGTSD-ED------SKKEAQK-RMIKKLLKKESIEWTE 136 (161)
Q Consensus 74 DLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~V-ItG~G~-HS------~g~~kiK-paV~klL~e~gi~~~e 136 (161)
..-+-|++.||+.|=..|......++ .|.+ |.|=++ -+ ...+.+. .++.++|.++||+-..
T Consensus 13 ~~~~rY~d~ai~~ll~~m~~~Ga~~~--~l~aklfGGa~m~~~~~~~~~~IG~rNv~~a~~~L~~~gi~I~a 82 (114)
T PF03975_consen 13 SNPGRYGDTAIELLLDEMEKRGARPS--RLEAKLFGGANMFPGMNSSSFNIGERNVEAARELLAEEGIPIVA 82 (114)
T ss_dssp -SCCCBHHHHHHHHHHHHHTTT--GG--G-EEEEEE----S------SS-HHHHHHHHHHHHHHHTT--EEE
T ss_pred CCCccCHHHHHHHHHHHHHHcCCCHH--HeEEEEeeCcccccccccccCCHHHHHHHHHHHHHHHCCCcEEE
Confidence 46788999999999999998876664 4443 333222 11 1233332 4799999999997533
No 55
>PRK11104 hemG protoporphyrinogen oxidase; Provisional
Probab=29.12 E-value=1.8e+02 Score=23.01 Aligned_cols=122 Identities=10% Similarity=0.060 Sum_probs=63.6
Q ss_pred EEEEEeeeCchH-HHHHHHHhHHHHHHHHHHHHHHHHHHHhhhCCCc----ceeecCCCCHHHHHHHHHHHHHhhcCCCC
Q 040282 25 YVYYSIIACSSF-LILLNLQGHFFRQKASEADRKSAEKLVKTRNNEV----MTLDWHSIEPKEVVCLLRVHLTSLSGIPT 99 (161)
Q Consensus 25 ~~~~~~~~~~s~-A~~LSeqGk~~~~ka~ean~kAa~~IF~~rN~~~----~~IDLHGLhVkEAi~iLk~~L~~l~~~~s 99 (161)
-+|+|..||-.. |..++++=.. ....+-.+-.-+. ...-.+-|. --+ -.|....+...+|++++..+.+.+.
T Consensus 5 IvY~S~~G~T~~iA~~Ia~~l~~-g~~v~~~~~~~~~-~~~l~~yD~vIlGspi-~~G~~~~~~~~fl~~~~~~l~~K~v 81 (177)
T PRK11104 5 ILYSSRDGQTRKIASYIASELKE-GIQCDVVNLHRIE-EPDLSDYDRVVIGASI-RYGHFHSALYKFVKKHATQLNQMPS 81 (177)
T ss_pred EEEECCCChHHHHHHHHHHHhCC-CCeEEEEEhhhcC-ccCHHHCCEEEEECcc-ccCCcCHHHHHHHHHHHHHhCCCeE
Confidence 489999999776 6666665321 1111111100000 000001111 112 2577788888999998887765442
Q ss_pred cceEEEEEeeCCCCCc----cccchHHHHHHHHhCCCcEEecCCCeEEEEEEcccCCCccccccc
Q 040282 100 IKHLRIVVGTSDEDSK----KEAQKRMIKKLLKKESIEWTEDGNGQAILIQVDVIDPKRLSFFRK 160 (161)
Q Consensus 100 ~~~L~VItG~G~HS~g----~~kiKpaV~klL~e~gi~~~e~~n~G~IlI~L~~~~~~~l~~~~~ 160 (161)
.+.+.|..+.. ..-.++.+.+++.+..++-... -+-=..+++++++|..|
T Consensus 82 -----~~F~v~l~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~------~~f~G~l~~~k~~f~~r 135 (177)
T PRK11104 82 -----AFFSVNLTARKPEKRTPQTNSYARKFLMNSPWQPDLC------AVFAGALRYPRYRWFDR 135 (177)
T ss_pred -----EEEEechhhcCCCCCChhhhHHHHHHHHhCCCCCcee------EEEeeeecCCcCCHHHH
Confidence 45555543321 1225688888888876543222 11123356778887653
No 56
>PRK13491 chemoreceptor glutamine deamidase CheD; Provisional
Probab=28.89 E-value=2.4e+02 Score=23.68 Aligned_cols=57 Identities=14% Similarity=0.090 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCC----ccccch-HHHHHHHHhCCCcEE
Q 040282 77 SIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDS----KKEAQK-RMIKKLLKKESIEWT 135 (161)
Q Consensus 77 GLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~----g~~kiK-paV~klL~e~gi~~~ 135 (161)
+-|++.||+.|=+.|......+ ..|++-+==|-+-. +.|.+. .++.++|+++||+-.
T Consensus 71 ~rYgd~Ai~~Li~~m~~~Ga~~--~~L~AKifGGA~M~~~~~~IG~rNie~a~~~L~~~GI~iv 132 (199)
T PRK13491 71 LRYGSHAMELLINALLKLGAAR--QRIEAKIFGGAMMTPQLGAIGQANAAFARRYLRDEGIRCT 132 (199)
T ss_pred cccHHHHHHHHHHHHHHcCCCH--HHeEEEEEeCcccccccccHHHHHHHHHHHHHHHcCCcEE
Confidence 7899999999999999987765 46664433333322 234443 489999999999853
No 57
>PF12090 Spt20: Spt20 family; InterPro: IPR021950 This presumed domain is found in the Spt20 proteins from both human and yeast. The Spt20 protein is part of the SAGA complex which is a large cmplex mediating histone deacetylation. Yeast Spt20 has been shown to play a role in structural integrity of the SAGA complex as as no intact SAGA could be purified in spt20 deletion strains.
Probab=27.81 E-value=80 Score=25.66 Aligned_cols=29 Identities=10% Similarity=0.268 Sum_probs=24.2
Q ss_pred ccchHHHHHHHHhCCCcEEecCCCeEEEEEEcc
Q 040282 117 EAQKRMIKKLLKKESIEWTEDGNGQAILIQVDV 149 (161)
Q Consensus 117 ~kiKpaV~klL~e~gi~~~e~~n~G~IlI~L~~ 149 (161)
+.+.+...++|++.+++|.| |+|+|++-.
T Consensus 53 ~~iP~~Lle~l~~~~v~FYd----GClIveV~D 81 (182)
T PF12090_consen 53 GEIPHDLLELLDDANVPFYD----GCLIVEVRD 81 (182)
T ss_pred CCCCHHHHHHHHhCCCeeEc----CEEEEEEec
Confidence 45678899999999999998 689998854
No 58
>COG5520 O-Glycosyl hydrolase [Cell envelope biogenesis, outer membrane]
Probab=27.49 E-value=77 Score=29.49 Aligned_cols=58 Identities=12% Similarity=0.066 Sum_probs=37.2
Q ss_pred ceEEEEEeeC--CCCCccccchHHHHHHHHhCCCcEEecCCCeEEEEEEcccC----------CCcccccccC
Q 040282 101 KHLRIVVGTS--DEDSKKEAQKRMIKKLLKKESIEWTEDGNGQAILIQVDVID----------PKRLSFFRKK 161 (161)
Q Consensus 101 ~~L~VItG~G--~HS~g~~kiKpaV~klL~e~gi~~~e~~n~G~IlI~L~~~~----------~~~l~~~~~~ 161 (161)
..+++|.|-| ++|..-+.++-+-++.+=.+|-. +- +--++.|.++.-| -++|||+|++
T Consensus 42 ~~~Q~IrGFGg~~~~Aw~g~lsaa~l~t~Fgng~~--~l-g~si~Rv~I~~ndfsl~g~~d~w~kels~Ak~~ 111 (433)
T COG5520 42 AKHQVIRGFGGMNSSAWAGDLSAAQLETLFGNGAN--QL-GFSILRVPIDSNDFSLGGSADNWYKELSTAKSA 111 (433)
T ss_pred hhhceeecccccccchhhhhhHHHHHHHHhcCCcc--cc-CceEEEEEecccccccCCCcchhhhhcccchhh
Confidence 6789999999 88888777877766666555410 00 1123444554433 5789999863
No 59
>KOG3758 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.49 E-value=1.3e+02 Score=29.70 Aligned_cols=54 Identities=20% Similarity=0.212 Sum_probs=43.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhhCCCcceeecCCCCHHHHHHHHHHHHHhhcCCC
Q 040282 44 GHFFRQKASEADRKSAEKLVKTRNNEVMTLDWHSIEPKEVVCLLRVHLTSLSGIP 98 (161)
Q Consensus 44 Gk~~~~ka~ean~kAa~~IF~~rN~~~~~IDLHGLhVkEAi~iLk~~L~~l~~~~ 98 (161)
|-+..++|..+.+.|-+.||+=. ..+.+-||||..--|+-.+|+.-+..++.+|
T Consensus 185 g~eime~M~~~~E~a~erl~r~~-qs~e~~~l~~t~~~E~~~il~kA~~~L~~~p 238 (655)
T KOG3758|consen 185 GLEIMEKMALIQEGAYERLFRWS-QSSECRNLTGTDSQEVSPILRKAFVFLSSRP 238 (655)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh-hhHhhcCCccccchhhHHHHHHHHHHHhcCh
Confidence 56677899999999999999922 2337889999988899999888877776654
No 60
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=27.37 E-value=58 Score=23.64 Aligned_cols=30 Identities=17% Similarity=0.183 Sum_probs=22.2
Q ss_pred ccccc-hHHHHHHHHhCCCcEEecCCCe-EEEE
Q 040282 115 KKEAQ-KRMIKKLLKKESIEWTEDGNGQ-AILI 145 (161)
Q Consensus 115 g~~ki-KpaV~klL~e~gi~~~e~~n~G-~IlI 145 (161)
....+ ...|..+|++.|+.|.-. .+| .++|
T Consensus 51 ~Ve~id~~~i~~fC~~~gy~~~iv-~~g~~l~~ 82 (86)
T PF11360_consen 51 TVEEIDPEEIEEFCRSAGYEYEIV-PPGRDLLI 82 (86)
T ss_pred CeEEECHHHHHHHHHHCCceEEEE-CCCCCeeC
Confidence 33445 447999999999999988 566 6554
No 61
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=27.23 E-value=1.1e+02 Score=26.87 Aligned_cols=69 Identities=10% Similarity=0.136 Sum_probs=46.9
Q ss_pred CHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEE--ec----CCCeEEEEEEcccCC
Q 040282 79 EPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWT--ED----GNGQAILIQVDVIDP 152 (161)
Q Consensus 79 hVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~--e~----~n~G~IlI~L~~~~~ 152 (161)
.|+-|+++.++-+....+ +.+. . .|---..|-|.+-|++.|+.+. ++ +.+++++|+--|+.|
T Consensus 14 GV~rAi~~a~~~~~~~~~----~~vy-~-------lG~iVHN~~Vv~~L~~~Gv~~v~~~~~~~v~~~~~ViirAHGv~~ 81 (281)
T PRK12360 14 GVKRAIDTAYDEIEKNDG----KKIY-T-------LGPLIHNNQVVSDLEEKGVKTIEESEIDSLKEGDVVIIRSHGVSK 81 (281)
T ss_pred cHHHHHHHHHHHHHhcCC----CCeE-E-------ecCCcCCHHHHHHHHHCcCEEECcCchhhCCCCCEEEEeCCCCCH
Confidence 588999999886553322 1221 1 1222237899999999999987 33 246799999999988
Q ss_pred Ccccccc
Q 040282 153 KRLSFFR 159 (161)
Q Consensus 153 ~~l~~~~ 159 (161)
+..-.++
T Consensus 82 ~~~~~~~ 88 (281)
T PRK12360 82 KVYKDLK 88 (281)
T ss_pred HHHHHHH
Confidence 7665544
No 62
>TIGR03527 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis.
Probab=27.02 E-value=3.2e+02 Score=22.41 Aligned_cols=67 Identities=16% Similarity=0.175 Sum_probs=45.4
Q ss_pred eecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEecC-CCeEEEEEEcc
Q 040282 73 LDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTEDG-NGQAILIQVDV 149 (161)
Q Consensus 73 IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~~-n~G~IlI~L~~ 149 (161)
||+.|+.==.-+-..|+.|..+.. .+.|.|++--. .-+.-|.+||++.|++....+ ..|.+.|.+..
T Consensus 1 ID~rGl~CP~Pvi~tKkal~~l~~---g~~L~VlvD~~-------~a~~nV~~~~~~~G~~v~~~e~~~~~~~i~i~k 68 (194)
T TIGR03527 1 IDARGLACPQPVILTKKALDELGE---EGVLTVIVDNE-------AAKENVSKFATSLGYEVEVEEKEEGYWILIIKK 68 (194)
T ss_pred CCCCCCCCCHHHHHHHHHHHcCCC---CCEEEEEECCc-------cHHHHHHHHHHHcCCEEEEEEecCCEEEEEEEE
Confidence 577777766667778888877742 35788876321 123458899999999986543 56766666543
No 63
>COG3139 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.26 E-value=53 Score=24.40 Aligned_cols=49 Identities=22% Similarity=0.163 Sum_probs=35.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhh-CCCc--ceeecCCCCHHHHHHHHHHHHHh
Q 040282 44 GHFFRQKASEADRKSAEKLVKTR-NNEV--MTLDWHSIEPKEVVCLLRVHLTS 93 (161)
Q Consensus 44 Gk~~~~ka~ean~kAa~~IF~~r-N~~~--~~IDLHGLhVkEAi~iLk~~L~~ 93 (161)
|....+.-++.-.+|. ..++.+ |.+. ++||.+|++|--.-.-|+.++..
T Consensus 30 G~~LtqeQke~clQaV-mlwqarhN~~aqhmti~~~gq~v~ksk~elk~~f~~ 81 (90)
T COG3139 30 GVALTQEQKENCLQAV-MLWQARHNTEAQHMTIDTGGQMVMKSKQELKEDFGI 81 (90)
T ss_pred CCcCCHHHHHHHHHHH-HHHHHhcCChhhhhccccCCeeeecchHhhhhhhCc
Confidence 4445556666666665 677777 7654 99999999998877777777653
No 64
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=26.14 E-value=38 Score=23.31 Aligned_cols=14 Identities=0% Similarity=0.067 Sum_probs=10.2
Q ss_pred hHHHHHHHHhCCCc
Q 040282 120 KRMIKKLLKKESIE 133 (161)
Q Consensus 120 KpaV~klL~e~gi~ 133 (161)
-|.|.+||+++||=
T Consensus 29 ~~eV~~YC~~~GWI 42 (57)
T PF08727_consen 29 SPEVREYCEEQGWI 42 (57)
T ss_dssp -HHHHHHHHHHT--
T ss_pred CHHHHHHHHHCCcc
Confidence 46899999999873
No 65
>PF02410 Oligomerisation: Oligomerisation domain; InterPro: IPR004394 The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. Maize has two RNA polymerases in plastids, but the plastid-encoded one, similar to bacterial RNA polymerases, is missing in iojap mutants. The role of iojap in chloroplast development, and the role of its bacterial orthologs modeled here, is unclear [, ]. This entry contains the bacterial protein YbeB (P0AAT6 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2O5A_A 2ID1_B 3UPS_A.
Probab=25.67 E-value=1.5e+02 Score=21.47 Aligned_cols=45 Identities=16% Similarity=0.173 Sum_probs=28.0
Q ss_pred EEEeeCCCCCccccchHHHHHHH-HhCCCc--EEecC-CCeEEEEEEcc
Q 040282 105 IVVGTSDEDSKKEAQKRMIKKLL-KKESIE--WTEDG-NGQAILIQVDV 149 (161)
Q Consensus 105 VItG~G~HS~g~~kiKpaV~klL-~e~gi~--~~e~~-n~G~IlI~L~~ 149 (161)
.|+++|..+.-..++-..|.+.+ ++.+.. -.|.. .++-++|+..+
T Consensus 32 ~II~T~~S~rh~~aia~~v~~~~~k~~~~~~~~~eG~~~~~W~lvD~g~ 80 (100)
T PF02410_consen 32 FIIATGRSERHVRAIADEVEKALKKEYGERPLRIEGLDESDWVLVDYGD 80 (100)
T ss_dssp EEEEEESSHHHHHHHHHHHHHHH-HHTT----EEESTTTTSEEEEEESS
T ss_pred EEEEEcCCHHHHHHHHHHHHHHHHHHcCCcccccCCCCCCCEEEEcccE
Confidence 66666655444455677888888 555543 34432 77888888865
No 66
>PF11126 Phage_DsbA: Transcriptional regulator DsbA; InterPro: IPR020313 DsbA is a double stranded binding protein found in bacteriophage T4 which is involved in transcriptional regulation. DsbA, along with other viral proteins, interacts with the host RNA polymerase core enzyme enabling initiation of transcription. DsbA acts as an enhancer protein of late genes in vitro. The protein consists of mainly alpha helices [].
Probab=25.67 E-value=81 Score=22.47 Aligned_cols=34 Identities=15% Similarity=0.235 Sum_probs=27.3
Q ss_pred chHHH-HHHHHhHHHHHHHHHHHHHHHHHHHhhhCC
Q 040282 34 SSFLI-LLNLQGHFFRQKASEADRKSAEKLVKTRNN 68 (161)
Q Consensus 34 ~s~A~-~LSeqGk~~~~ka~ean~kAa~~IF~~rN~ 68 (161)
+.+|+ +|--.|+.|+++.+-++.++.++ |++.|.
T Consensus 23 k~~AK~ElGv~gk~Fnkl~~lyHk~~Re~-fE~e~e 57 (69)
T PF11126_consen 23 KDRAKDELGVDGKMFNKLLKLYHKQEREE-FEAENE 57 (69)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHhhHHH-HHHHHH
Confidence 56787 89999999999999999998755 555443
No 67
>TIGR01689 EcbF-BcbF capsule biosynthesis phosphatase. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology.
Probab=24.25 E-value=1.4e+02 Score=22.85 Aligned_cols=37 Identities=11% Similarity=0.032 Sum_probs=28.2
Q ss_pred ceEEEEEeeCCCCC-c-cccc----hHHHHHHHHhCCCcEEec
Q 040282 101 KHLRIVVGTSDEDS-K-KEAQ----KRMIKKLLKKESIEWTED 137 (161)
Q Consensus 101 ~~L~VItG~G~HS~-g-~~ki----KpaV~klL~e~gi~~~e~ 137 (161)
-.+.++||+...+. + .+++ -|...++|.++++.|.+-
T Consensus 41 ~~IiiaTGR~~~~~~~n~~~i~~~~~~~t~~wL~k~~ipYd~l 83 (126)
T TIGR01689 41 FEIVISSSRNMRTYEGNVGKINIHTLPIIILWLNQHNVPYDEI 83 (126)
T ss_pred CEEEEECCCCchhhhccccccchhhHHHHHHHHHHcCCCCceE
Confidence 46888899988873 3 3455 368999999999999664
No 68
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=24.18 E-value=2.3e+02 Score=18.97 Aligned_cols=65 Identities=14% Similarity=0.016 Sum_probs=41.5
Q ss_pred eecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEecC-CCeEEEEEE
Q 040282 73 LDWHSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTEDG-NGQAILIQV 147 (161)
Q Consensus 73 IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~~-n~G~IlI~L 147 (161)
||+-|+.==.=+-.++..|..+. +.+.|.|++--. .-..-|.++|++.|++..+.+ ..|.+.+.+
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~---~G~~l~V~~d~~-------~s~~ni~~~~~~~g~~v~~~~~~~~~~~~~i 67 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLK---PGEILEVISDCP-------QSINNIPIDARNHGYKVLAIEQSGPTIRYLI 67 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCC---CCCEEEEEecCc-------hHHHHHHHHHHHcCCEEEEEEecCCEEEEEE
Confidence 56666655555556677777664 246788876421 124568899999999986432 456666654
No 69
>TIGR03682 arCOG04112 arCOG04112 universal archaeal diphthamide biosynthesis domain protein. This family of proteins has been observed universally in archaeal genomes and contains a match to the TIGR00322 model for the diphthamide biosynthesis protein 2-related domain.
Probab=24.09 E-value=1.8e+02 Score=25.40 Aligned_cols=66 Identities=30% Similarity=0.408 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCcEEecCCCeEEEEEEcccCCCcc
Q 040282 81 KEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTEDGNGQAILIQVDVIDPKRL 155 (161)
Q Consensus 81 kEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~~n~G~IlI~L~~~~~~~l 155 (161)
.++.++|++|......-..-+..=||+|+=.- +|...+-..++++++++|.+. .+|-++.++|.+|
T Consensus 193 ~~~~~~l~~R~~~I~ka~~A~~vGIlvgTl~~-q~~~~~~~~l~~ll~~~gkk~--------y~i~~~~in~~kL 258 (308)
T TIGR03682 193 AEIDKFLRVRYARISKALDAKKFGILVSTKKG-QRRPELAEELKKLLEELGKEA--------LLILLDNISPDQL 258 (308)
T ss_pred hhHHHHHHHHHHHHHHHhhCCeEEEEEEccCc-CCCHHHHHHHHHHHHHcCCeE--------EEEEeCCCCHHHH
Confidence 35678888886654432223677888886321 222233456888899998865 4566777777766
No 70
>PF10150 RNase_E_G: Ribonuclease E/G family; InterPro: IPR019307 Ribonuclease E and Ribonuclease G are related enzymes that cleave a wide variety of RNAs []. RNA-binding protein AU-1 binds to RNA loop regions that are with AU-rich sequences [].; PDB: 2BX2_L 2VRT_D 2VMK_D 2C4R_L 1SMX_B 1SLJ_A 2C0B_L 1SN8_B.
Probab=24.01 E-value=3.9e+02 Score=22.83 Aligned_cols=50 Identities=16% Similarity=0.192 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHHHHHhh---hCCC-cceeecCCCCHHHHHHHHHHHHHhhc
Q 040282 46 FFRQKASEADRKSAEKLVKT---RNNE-VMTLDWHSIEPKEVVCLLRVHLTSLS 95 (161)
Q Consensus 46 ~~~~ka~ean~kAa~~IF~~---rN~~-~~~IDLHGLhVkEAi~iLk~~L~~l~ 95 (161)
...+.+-+.|.+||++|+++ ||-+ ...||+=+..-++.-.-|.+.|..+-
T Consensus 192 ~~~~~~~~~N~~Aa~ei~rqirLR~i~GiIviDfi~m~~~~~~~~l~~~~~~~~ 245 (271)
T PF10150_consen 192 NSEETALKTNLEAAKEIARQIRLRNIGGIIVIDFIDMKDKKDREKLLEALKEAL 245 (271)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHT--EEEEEE----SSHHHHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEEEecCCCCHHHHHHHHHHHHHHH
Confidence 35677889999999999995 6654 37777777766666666666666554
No 71
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=23.88 E-value=34 Score=26.53 Aligned_cols=11 Identities=36% Similarity=0.682 Sum_probs=9.8
Q ss_pred hhccCceeEEE
Q 040282 17 EVFSDHSFYVY 27 (161)
Q Consensus 17 ~~~~~~~~~~~ 27 (161)
||-.||.||||
T Consensus 71 ev~~eHPfFV~ 81 (116)
T smart00536 71 ECQVEHPFFVK 81 (116)
T ss_pred EEecCCCeEEc
Confidence 67789999998
No 72
>PRK13497 chemoreceptor glutamine deamidase CheD; Provisional
Probab=23.84 E-value=3.9e+02 Score=21.95 Aligned_cols=59 Identities=15% Similarity=0.121 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHHHHHhhcCCCCcceEEE-EEeeCCCCC---ccccch-HHHHHHHHhCCCcEEe
Q 040282 76 HSIEPKEVVCLLRVHLTSLSGIPTIKHLRI-VVGTSDEDS---KKEAQK-RMIKKLLKKESIEWTE 136 (161)
Q Consensus 76 HGLhVkEAi~iLk~~L~~l~~~~s~~~L~V-ItG~G~HS~---g~~kiK-paV~klL~e~gi~~~e 136 (161)
-+-|++.||+.|=+.|......++ .|++ |.|=++--. +.|.+. .++.++|+++||+-..
T Consensus 67 ~~rY~d~ai~~Li~~m~~~Ga~~~--~l~aKifGGA~m~~~~~~IG~rNi~~a~~~L~~~gI~i~a 130 (184)
T PRK13497 67 ATRYGVHLMELLINGLLKQGARRD--RLEAKIFGGAKTIATFSNVGEQNAAFAMQFLRDEGIPVVG 130 (184)
T ss_pred ccchHHHHHHHHHHHHHHcCCCHH--HEEEEEEeCchhccccccHHHHHHHHHHHHHHHcCCcEEE
Confidence 367999999999999999887664 5654 344333222 234342 4799999999998533
No 73
>PF07660 STN: Secretin and TonB N terminus short domain; InterPro: IPR011662 This is a conserved region found at the N-terminal region of bacterial proteins involved in either protein secretion or the uptake of selective substrates, including: Bundle-forming pilus protein B, an outer-membrane protein absolutely required for pilus biogenesis, and for enteropathogenic Escherichia coli localized adherence and autoaggregation []. PilQ, which is required for type IV pilus biogenesis and competence and is thought to function both as a pore for exit of the pilus and as a channel for entry of haem and antimicrobial agents and uptake of transforming DNA []. PupB, a specific receptor for the siderophores ferric pseudobactin BN8 and ferric pseudobactin BN7, iron chelating molecules that allow the organism to extract iron from the environment, especially under iron-restricted conditions []. TonB, which couples the electrochemical potential of the cytoplasmic membrane to the active transport of iron-siderophores and vitamin B12 across the outer membrane []. ; GO: 0019867 outer membrane; PDB: 2D1U_A 1ZZV_A 2W75_B 2O5P_A 2W77_A 2W16_A 2W6U_B 2W6T_A 2W76_B 2W78_B ....
Probab=23.50 E-value=83 Score=19.48 Aligned_cols=28 Identities=21% Similarity=0.432 Sum_probs=20.9
Q ss_pred ccchHHHHHHHHhCCCcEEecCCCeEEEEE
Q 040282 117 EAQKRMIKKLLKKESIEWTEDGNGQAILIQ 146 (161)
Q Consensus 117 ~kiKpaV~klL~e~gi~~~e~~n~G~IlI~ 146 (161)
..+..+...+|+..|+.|+.. .++|.|.
T Consensus 23 ~~~~~~L~~ll~~t~l~y~~~--~~~i~I~ 50 (52)
T PF07660_consen 23 MSLEEALDQLLKGTGLTYKIS--GNTIVIS 50 (52)
T ss_dssp E-HHHHHHHHTTTSTEEEEEE--TTEEEEE
T ss_pred cCHHHHHHHHHccCCcEEEEE--CCEEEEE
Confidence 345678999999999999985 5556553
No 74
>PRK12613 galactose-6-phosphate isomerase subunit LacA; Provisional
Probab=23.24 E-value=89 Score=24.75 Aligned_cols=31 Identities=26% Similarity=0.458 Sum_probs=23.3
Q ss_pred EEEEeeCCCCCccccchHHHHHHHHhCCCcEEec
Q 040282 104 RIVVGTSDEDSKKEAQKRMIKKLLKKESIEWTED 137 (161)
Q Consensus 104 ~VItG~G~HS~g~~kiKpaV~klL~e~gi~~~e~ 137 (161)
+|++|.++- .-.+|..|.++|++.|++..+-
T Consensus 2 kI~igsDha---G~~lK~~l~~~L~~~g~eV~D~ 32 (141)
T PRK12613 2 AIILGADAH---GNALKELIKSFLQEEGYDIIDV 32 (141)
T ss_pred EEEEEeCcc---hHHHHHHHHHHHHHCCCEEEEc
Confidence 466666543 2357999999999999988776
No 75
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=23.21 E-value=1.7e+02 Score=20.19 Aligned_cols=28 Identities=11% Similarity=0.039 Sum_probs=21.3
Q ss_pred ceeecCCCCHHHHHHHHHHHHHhhcCCC
Q 040282 71 MTLDWHSIEPKEVVCLLRVHLTSLSGIP 98 (161)
Q Consensus 71 ~~IDLHGLhVkEAi~iLk~~L~~l~~~~ 98 (161)
..|.+-|+.+.||...|+.+|...-..|
T Consensus 47 G~v~v~G~T~~e~~~~I~~~l~~~~~~p 74 (82)
T PF02563_consen 47 GPVKVAGLTLEEAEEEIKQRLQKYYRDP 74 (82)
T ss_dssp EEEE-TT--HHHHHHHHHHHHTTTSSS-
T ss_pred ceEEECCCCHHHHHHHHHHHHHHHhcCC
Confidence 7889999999999999999999865555
No 76
>COG1825 RplY Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis]
Probab=22.91 E-value=2.5e+02 Score=20.57 Aligned_cols=38 Identities=24% Similarity=0.299 Sum_probs=24.6
Q ss_pred HHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCC
Q 040282 89 VHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKES 131 (161)
Q Consensus 89 ~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~g 131 (161)
++|+.....|. ||+|.|......+--...+.+++.+.+
T Consensus 18 RrlR~~G~iPA-----viYG~g~~~v~i~l~~~~~~k~~~~~~ 55 (93)
T COG1825 18 RRLRRAGKIPA-----VVYGGGKEPVNIALDHHEFAKALRKLG 55 (93)
T ss_pred HhHHhcCCCCE-----EEECCCCCCceEEEcHHHHHHHHhhcc
Confidence 45555555565 999999988554333345777777776
No 77
>PLN03198 delta6-acyl-lipid desaturase; Provisional
Probab=22.63 E-value=44 Score=31.53 Aligned_cols=20 Identities=5% Similarity=0.109 Sum_probs=17.9
Q ss_pred cchHHHHHHHHhCCCcEEec
Q 040282 118 AQKRMIKKLLKKESIEWTED 137 (161)
Q Consensus 118 kiKpaV~klL~e~gi~~~e~ 137 (161)
++.|.|+++|+|.|++|++.
T Consensus 479 ~i~piVk~~C~k~GlpY~~~ 498 (526)
T PLN03198 479 KIAPQVEAFCIKHGLVYEDV 498 (526)
T ss_pred HHhHHHHHHHHHcCCCCCCC
Confidence 56789999999999999886
No 78
>PF08800 VirE_N: VirE N-terminal domain; InterPro: IPR014907 This domain is associated with the N terminus of Virulence E proteins. The function of the domain is unknown.
Probab=22.57 E-value=88 Score=23.96 Aligned_cols=85 Identities=22% Similarity=0.255 Sum_probs=42.7
Q ss_pred ceeecCCCCHHHHHHHHHHHHHhhcC------CCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCC----cEEecCCC
Q 040282 71 MTLDWHSIEPKEVVCLLRVHLTSLSG------IPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESI----EWTEDGNG 140 (161)
Q Consensus 71 ~~IDLHGLhVkEAi~iLk~~L~~l~~------~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi----~~~e~~n~ 140 (161)
..||.=++...| +.-+++.+...-. .||..-|++|+=........-.-+++-.+....+-+ ++.+. .
T Consensus 34 v~lDiD~l~~ee-~~~~r~~l~~~p~t~~~f~SpSG~GvKi~v~~~~~~~~~lp~~~~~~~~~h~~~y~~~~~~y~~--~ 110 (136)
T PF08800_consen 34 VVLDIDHLDPEE-AEELRQLLFEDPYTLAAFVSPSGRGVKIIVPFDYPDGSRLPQDEEEAELFHAHAYEAAVEYYQR--L 110 (136)
T ss_pred EEEEeCCCCHHH-HHHHHHHHhcCCcEEEEEEcCCCCeEEEEEEecCCCCccccchhHHHHHHHHHHHHHHHHHHhh--h
Confidence 899999999544 5566666665432 255566777764433222100001111111111111 11121 2
Q ss_pred eEEEEEEcccCCCccccc
Q 040282 141 QAILIQVDVIDPKRLSFF 158 (161)
Q Consensus 141 G~IlI~L~~~~~~~l~~~ 158 (161)
.-+-|+..+.|++|.+|.
T Consensus 111 ~~~~iD~s~kdi~R~cfl 128 (136)
T PF08800_consen 111 LGIEIDKSCKDISRACFL 128 (136)
T ss_pred cCCcccCcCCCcCccccc
Confidence 234677778888888874
No 79
>COG2403 Predicted GTPase [General function prediction only]
Probab=22.07 E-value=3.9e+02 Score=25.18 Aligned_cols=78 Identities=18% Similarity=0.275 Sum_probs=60.3
Q ss_pred HHHHHHHhhhCCCcceeecCCCCHHHHHHHHHHHHHhhcC----CC------CcceEEEEEeeCCCCCccccchHHHHHH
Q 040282 57 KSAEKLVKTRNNEVMTLDWHSIEPKEVVCLLRVHLTSLSG----IP------TIKHLRIVVGTSDEDSKKEAQKRMIKKL 126 (161)
Q Consensus 57 kAa~~IF~~rN~~~~~IDLHGLhVkEAi~iLk~~L~~l~~----~~------s~~~L~VItG~G~HS~g~~kiKpaV~kl 126 (161)
+.=+++.++...|.-.+||-.+...+-.+|...-|+.... .| +.++.--|||+|.. .|+.+.-+.|-++
T Consensus 72 ~~lek~ire~~VD~~VlaySDvs~e~v~~IaS~vLs~GA~f~~~gP~et~~~~ekPviaV~atrtg-~GKsaVS~~v~r~ 150 (449)
T COG2403 72 DDLEKIIREKDVDIVVLAYSDVSYEHVFRIASRVLSAGADFKELGPKETMLKLEKPVIAVTATRTG-VGKSAVSRYVARL 150 (449)
T ss_pred HHHHHHHHHcCCCeEEEEcccCCHHHHHHHHHHHHhCCceeEEeCccHHhhhhcCceEEEEEeccc-cchhHHHHHHHHH
Confidence 5567888999999889999999999999999998886531 01 23444567787765 6777788899999
Q ss_pred HHhCCCcEE
Q 040282 127 LKKESIEWT 135 (161)
Q Consensus 127 L~e~gi~~~ 135 (161)
|.+.||+-.
T Consensus 151 l~ergyrv~ 159 (449)
T COG2403 151 LRERGYRVC 159 (449)
T ss_pred HHHcCCceE
Confidence 999999743
No 80
>PRK13493 chemoreceptor glutamine deamidase CheD; Provisional
Probab=21.67 E-value=4e+02 Score=22.45 Aligned_cols=58 Identities=12% Similarity=0.032 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCC----ccccch-HHHHHHHHhCCCcEE
Q 040282 76 HSIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDS----KKEAQK-RMIKKLLKKESIEWT 135 (161)
Q Consensus 76 HGLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~----g~~kiK-paV~klL~e~gi~~~ 135 (161)
-|-|++.||+.|=+.|......+ +.|++-+==|-.-. ..|.+. .++.++|+++||+-.
T Consensus 94 ~~rY~d~Am~~Li~~m~~~Ga~~--~~l~aKifGGA~m~~~~~~IG~rNi~~a~~~L~~~gI~Iv 156 (213)
T PRK13493 94 SSRYGCYAMEVLINRLLSMGAER--ERLKFKLFGGAHLMGYQSLVGEKNVEFVLEYAKREKLNVV 156 (213)
T ss_pred ccccHHHHHHHHHHHHHHcCCCH--HHeEEEEEeCcccccccccHhHHHHHHHHHHHHHcCCcEE
Confidence 58899999999999999987765 36664332233222 234442 489999999999843
No 81
>PRK07193 fliF flagellar MS-ring protein; Reviewed
Probab=21.24 E-value=41 Score=32.06 Aligned_cols=37 Identities=19% Similarity=0.384 Sum_probs=28.3
Q ss_pred HHHHHHHHhCCCcEEecCCCeEEEEEEcccCCCcccc
Q 040282 121 RMIKKLLKKESIEWTEDGNGQAILIQVDVIDPKRLSF 157 (161)
Q Consensus 121 paV~klL~e~gi~~~e~~n~G~IlI~L~~~~~~~l~~ 157 (161)
-+|.+.|+++||.|.-++++|+|+|.=+..+.-|+..
T Consensus 66 ~~Iv~~L~~~gI~Y~l~~~g~~IlVp~~~v~~aRl~L 102 (552)
T PRK07193 66 SQVVEVLEAEGISYRIDPDSGQVLVPEDQLGKARMLL 102 (552)
T ss_pred HHHHHHHHHCCCCEEEcCCCCeEEecHHHHHHHHHHH
Confidence 3699999999999988768889998766554444433
No 82
>PHA02754 hypothetical protein; Provisional
Probab=21.13 E-value=1.5e+02 Score=20.75 Aligned_cols=32 Identities=22% Similarity=0.308 Sum_probs=23.5
Q ss_pred CHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCC
Q 040282 79 EPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDE 112 (161)
Q Consensus 79 hVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~H 112 (161)
..+|||+-|+.+|.... +- ...+++||-.|+.
T Consensus 15 ~Fke~MRelkD~LSe~G-iY-i~RIkai~~SGdk 46 (67)
T PHA02754 15 DFKEAMRELKDILSEAG-IY-IDRIKAITTSGDK 46 (67)
T ss_pred HHHHHHHHHHHHHhhCc-eE-EEEEEEEEecCCE
Confidence 36899999999998753 21 3677788877763
No 83
>PF09585 Lin0512_fam: Conserved hypothetical protein (Lin0512_fam); InterPro: IPR011719 This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N terminus.
Probab=20.94 E-value=50 Score=25.48 Aligned_cols=22 Identities=23% Similarity=0.256 Sum_probs=14.9
Q ss_pred ceeecCCCCHHHH-HHHHHHHHH
Q 040282 71 MTLDWHSIEPKEV-VCLLRVHLT 92 (161)
Q Consensus 71 ~~IDLHGLhVkEA-i~iLk~~L~ 92 (161)
+=.||||+.+..| .+-++.-|.
T Consensus 9 mG~DlhGqD~TkAA~RAv~DAI~ 31 (113)
T PF09585_consen 9 MGNDLHGQDYTKAAVRAVRDAIS 31 (113)
T ss_pred ccccccCCcHHHHHHHHHHHHHh
Confidence 4579999977554 556665554
No 84
>PF02817 E3_binding: e3 binding domain; InterPro: IPR004167 A small domain of the E2 subunit of 2-oxo-acid dehydrogenases that is responsible for the binding of the E3 subunit. Proteins containing this domain include the branched-chain alpha-keto acid dehydrogenase complex of bacteria, which catalyses the overall conversion of alpha-keto acids to acyl-CoA and carbon dioxide; and the E-3 binding protein of eukaryotic pyruvate dehydrogenase.; GO: 0016746 transferase activity, transferring acyl groups, 0008152 metabolic process; PDB: 1BBL_A 1W4H_A 1BAL_A 2WXC_A 2BTH_A 2BTG_A 2CYU_A 2EQ7_C 2EQ8_C 3RNM_E ....
Probab=20.90 E-value=58 Score=20.27 Aligned_cols=20 Identities=15% Similarity=0.177 Sum_probs=14.9
Q ss_pred cchHHHHHHHHhCCCcEEec
Q 040282 118 AQKRMIKKLLKKESIEWTED 137 (161)
Q Consensus 118 kiKpaV~klL~e~gi~~~e~ 137 (161)
..-|++.++.+|+|+....-
T Consensus 4 ~asP~ar~la~e~gidl~~v 23 (39)
T PF02817_consen 4 KASPAARKLAAELGIDLSQV 23 (39)
T ss_dssp CCSHHHHHHHHHTT--GGGS
T ss_pred ccCHHHHHHHHHcCCCcccc
Confidence 34699999999999988665
No 85
>TIGR00731 ctc_TL5 ribosomal protein L25, Ctc-form. The C-terminal domain of sll1824, an apparent L25 of Synechocystis PCC6803, matches the N-terminal domain of this family. Examples of L25 and Ctc are not separated by a UPGMA tree built on the region of shared homology.
Probab=20.49 E-value=2.3e+02 Score=22.74 Aligned_cols=38 Identities=24% Similarity=0.384 Sum_probs=25.0
Q ss_pred HHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCC
Q 040282 89 VHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKES 131 (161)
Q Consensus 89 ~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~g 131 (161)
++|+.....|. ||+|+|..+....--...+.+++.+.|
T Consensus 15 r~LR~~G~VPa-----VvYG~~~~~~~i~v~~~el~k~l~~~~ 52 (176)
T TIGR00731 15 RRIRKEGRIPA-----VVYGKGKENVNLELKSKEFIKYLRKGA 52 (176)
T ss_pred HHHHHCCCccE-----EEECCCCCCEEEEECHHHHHHHHhccC
Confidence 45555566676 999999765443333567888887654
No 86
>COG3002 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.47 E-value=1.9e+02 Score=29.10 Aligned_cols=61 Identities=18% Similarity=0.224 Sum_probs=44.2
Q ss_pred CCCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCcc---c--------------------cc--hHHHHHHHHhCC
Q 040282 77 SIEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKK---E--------------------AQ--KRMIKKLLKKES 131 (161)
Q Consensus 77 GLhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~---~--------------------ki--KpaV~klL~e~g 131 (161)
|..-+|-+.+..+-|+...=.-.+-+|-||+|-|.||++. + .+ .|.|.+-|.+.|
T Consensus 538 GFT~~Eq~~~a~qaLKmmgLte~fAp~Vvl~GHgSqS~NNPy~aaLdCGACgGaSg~fNArvla~l~N~peVRq~lke~G 617 (880)
T COG3002 538 GFTLDEQAQMAAQALKMMGLTEEFAPLVVLVGHGSQSQNNPYRAALDCGACGGASGGFNARVLAALCNDPEVRQALKEYG 617 (880)
T ss_pred CCchHHHHHHHHHHHHHhCchhhhCceEEEeccccccCCCchhhhcccccccCccccccHHHHHHHhCCHHHHHHHHhcC
Confidence 6666777777777777654333367899999999999532 1 11 578999999999
Q ss_pred CcEEec
Q 040282 132 IEWTED 137 (161)
Q Consensus 132 i~~~e~ 137 (161)
|.-.|+
T Consensus 618 I~Iped 623 (880)
T COG3002 618 ISIPED 623 (880)
T ss_pred ccCCcc
Confidence 986554
No 87
>PRK12800 fliF flagellar MS-ring protein; Reviewed
Probab=20.39 E-value=44 Score=32.04 Aligned_cols=35 Identities=26% Similarity=0.289 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCCcEEecCCCeEEEEEEcccCCCcc
Q 040282 121 RMIKKLLKKESIEWTEDGNGQAILIQVDVIDPKRL 155 (161)
Q Consensus 121 paV~klL~e~gi~~~e~~n~G~IlI~L~~~~~~~l 155 (161)
-+|.+.|+++||.|.-.+++|+|+|.=+..+.-|+
T Consensus 71 ~~Iv~~L~~~gI~Y~l~~~g~~I~Vp~~~v~~aRl 105 (574)
T PRK12800 71 AEAADLLRTAQIPFKIDQGTGAISVPQDRLYDARL 105 (574)
T ss_pred HHHHHHHHHCCCCEEEcCCCCeEEecHHHHHHHHH
Confidence 46999999999999988788899986555443343
No 88
>PF04153 NOT2_3_5: NOT2 / NOT3 / NOT5 family; InterPro: IPR007282 NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that negatively regulates the basal and activated transcription of many genes. This family includes NOT2, NOT3 and NOT5.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=20.37 E-value=82 Score=24.21 Aligned_cols=31 Identities=16% Similarity=0.319 Sum_probs=22.0
Q ss_pred cCceeEEEEEeeeCch---HHHHHHHHhHHHHHH
Q 040282 20 SDHSFYVYYSIIACSS---FLILLNLQGHFFRQK 50 (161)
Q Consensus 20 ~~~~~~~~~~~~~~~s---~A~~LSeqGk~~~~k 50 (161)
.|--||++|+-.|... .|++|-.+|-.+...
T Consensus 54 ~eTLFyiFY~~p~~~~Q~~AA~eL~~R~Wryhk~ 87 (134)
T PF04153_consen 54 EETLFYIFYYMPGDYQQLLAAKELYKRGWRYHKE 87 (134)
T ss_pred CceEEEEEeecCCcHHHHHHHHHHHHCCcEEecC
Confidence 3557999999988653 567777777665543
No 89
>COG2454 Uncharacterized conserved protein [Function unknown]
Probab=20.22 E-value=2.9e+02 Score=23.59 Aligned_cols=50 Identities=20% Similarity=0.189 Sum_probs=37.7
Q ss_pred CCHHHHHHHHHHHHHhhcCCCCcceEEEEEeeCCCCCccccchHHHHHHHHhCCCc
Q 040282 78 IEPKEVVCLLRVHLTSLSGIPTIKHLRIVVGTSDEDSKKEAQKRMIKKLLKKESIE 133 (161)
Q Consensus 78 LhVkEAi~iLk~~L~~l~~~~s~~~L~VItG~G~HS~g~~kiKpaV~klL~e~gi~ 133 (161)
-.+.+|++++-..|.... | +. ||+=-|.-+.+.|-++..|++.|++.+|+
T Consensus 110 E~t~~Al~lil~~lk~~~--~--k~--vi~L~d~~vs~SGel~~~i~~~mK~~~I~ 159 (211)
T COG2454 110 EKTDKALDLLLEFLKDVE--P--KS--VIFLFDAPVSKSGELAGRIEEKMKSLGIP 159 (211)
T ss_pred hHHHHHHHHHHHHHHHcC--C--ce--EEEEeCCCCCccHHHHHHHHHHHHhcCCC
Confidence 357889999988888764 2 23 55555655566777999999999999997
No 90
>TIGR03176 AllC allantoate amidohydrolase. This enzyme catalyzes the breakdown of allantoate, first to ureidoglycine by hydrolysis and then decarboxylation of one of the two equivalent ureido groups. Ureidoglycine then spontaneously exchanges ammonia for water resulting in ureidoglycolate. This enzyme is an alternative to allantoicase (3.5.3.4) which releases urea.
Probab=20.16 E-value=1.7e+02 Score=25.95 Aligned_cols=33 Identities=12% Similarity=0.059 Sum_probs=28.2
Q ss_pred hHHHHHHHHhCCCcEEecCCCeEEEEEEcccCCC
Q 040282 120 KRMIKKLLKKESIEWTEDGNGQAILIQVDVIDPK 153 (161)
Q Consensus 120 KpaV~klL~e~gi~~~e~~n~G~IlI~L~~~~~~ 153 (161)
+.-++++|++.|+.-+++ ..|-|..++.|.+|+
T Consensus 36 ~~~~~~~~~~~Gl~v~~D-~~gN~~~~~~g~~~~ 68 (406)
T TIGR03176 36 QQQFKKRMAESGLETRFD-DVGNLYGRLVGTEFP 68 (406)
T ss_pred HHHHHHHHHHcCCEEEEc-CCCcEEEEecCCCCC
Confidence 346899999999997777 789999999998874
No 91
>KOG2617 consensus Citrate synthase [Energy production and conversion]
Probab=20.16 E-value=76 Score=29.82 Aligned_cols=57 Identities=16% Similarity=0.225 Sum_probs=35.9
Q ss_pred ecCCCCHHHHHHHHHHHHHhhcCCCCcc-----------eEEEEEeeCCCCCcc-ccchHHHHHHHHhC
Q 040282 74 DWHSIEPKEVVCLLRVHLTSLSGIPTIK-----------HLRIVVGTSDEDSKK-EAQKRMIKKLLKKE 130 (161)
Q Consensus 74 DLHGLhVkEAi~iLk~~L~~l~~~~s~~-----------~L~VItG~G~HS~g~-~kiKpaV~klL~e~ 130 (161)
-|||+-..|.++.|..-...+...++.+ .=+||.|-|+----+ .-+-..+.+|-.|.
T Consensus 288 PLHGlAnqEvl~~L~~~~~Eig~~~s~e~ikeyiw~~ln~~rvvpGyGHavlr~tDPR~~~~~efA~k~ 356 (458)
T KOG2617|consen 288 PLHGLANQEVLRFLGKLIEEIGKDLSKENIKEYIWKTLNSGRVVPGYGHAVLRKTDPRYKVQREFALKH 356 (458)
T ss_pred ccccCchHHHHHHHHHhHHHhccccchhhhhHhhHHhhcccccccccccccccCCCchhhHHHHHHHhc
Confidence 4999999999999997777766443321 235888888653211 11222455666555
Done!