Query 011024
Match_columns 495
No_of_seqs 124 out of 238
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 07:14:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011024.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011024hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08590 DUF1771: Domain of un 99.6 2.4E-17 5.1E-22 132.6 1.0 65 333-399 1-65 (66)
2 smart00463 SMR Small MutS-rela 99.6 4E-15 8.6E-20 122.5 7.8 78 406-483 2-80 (80)
3 PF01713 Smr: Smr domain; Int 99.5 2E-14 4.4E-19 119.1 5.3 73 408-483 1-83 (83)
4 KOG2401 Predicted MutS-related 98.9 2E-09 4.4E-14 114.8 5.7 400 20-472 24-429 (448)
5 COG2840 Uncharacterized protei 98.1 8.5E-06 1.9E-10 78.4 8.1 81 402-484 93-180 (184)
6 PRK04946 hypothetical protein; 98.0 1.3E-05 2.9E-10 76.9 7.9 78 402-485 92-175 (181)
7 PRK00409 recombination and DNA 97.5 0.00017 3.6E-09 82.6 7.7 73 405-483 704-782 (782)
8 TIGR01069 mutS2 MutS2 family p 97.4 0.00027 5.9E-09 80.8 7.2 72 405-482 693-770 (771)
9 KOG2401 Predicted MutS-related 96.5 0.0061 1.3E-07 65.7 7.0 356 23-472 16-378 (448)
10 PF02845 CUE: CUE domain; Int 96.0 0.015 3.2E-07 42.9 4.9 40 159-201 3-42 (42)
11 smart00546 CUE Domain that may 95.0 0.066 1.4E-06 39.5 5.3 40 159-201 4-43 (43)
12 cd00194 UBA Ubiquitin Associat 94.9 0.056 1.2E-06 38.5 4.5 35 163-199 4-38 (38)
13 PF00627 UBA: UBA/TS-N domain; 90.0 0.33 7.1E-06 34.8 2.9 31 162-197 7-37 (37)
14 smart00165 UBA Ubiquitin assoc 89.8 0.39 8.5E-06 33.9 3.2 25 174-198 13-37 (37)
15 cd00194 UBA Ubiquitin Associat 83.8 1 2.3E-05 31.9 2.6 29 20-48 10-38 (38)
16 PF08938 HBS1_N: HBS1 N-termin 83.8 0.65 1.4E-05 38.9 1.7 39 165-204 36-74 (79)
17 PF03474 DMA: DMRTA motif; In 81.9 1.5 3.2E-05 32.8 2.7 26 173-198 14-39 (39)
18 PF00627 UBA: UBA/TS-N domain; 80.7 1.5 3.3E-05 31.3 2.5 25 22-46 13-37 (37)
19 smart00165 UBA Ubiquitin assoc 78.4 2 4.4E-05 30.2 2.5 28 20-47 10-37 (37)
20 COG1193 Mismatch repair ATPase 73.0 5.2 0.00011 46.5 5.3 72 405-482 676-753 (753)
21 PF14555 UBA_4: UBA-like domai 69.3 13 0.00029 27.4 5.0 38 158-200 2-39 (43)
22 PF14346 DUF4398: Domain of un 66.8 42 0.00092 28.9 8.5 42 343-384 40-81 (103)
23 PF02954 HTH_8: Bacterial regu 66.0 4.9 0.00011 29.5 2.1 31 174-205 5-35 (42)
24 cd00291 SirA_YedF_YeeD SirA, Y 64.3 36 0.00078 26.6 7.0 66 407-482 1-67 (69)
25 PF11848 DUF3368: Domain of un 63.5 9.3 0.0002 29.1 3.3 29 159-187 20-48 (48)
26 PF01963 TraB: TraB family; I 62.5 58 0.0013 31.7 9.5 91 341-468 165-255 (259)
27 PRK09591 celC cellobiose phosp 61.4 73 0.0016 28.4 9.0 53 341-396 13-65 (104)
28 PRK01905 DNA-binding protein F 60.8 13 0.00028 30.8 4.0 49 156-205 10-67 (77)
29 cd00215 PTS_IIA_lac PTS_IIA, P 57.9 44 0.00096 29.3 6.9 50 344-396 11-60 (97)
30 TIGR00823 EIIA-LAC phosphotran 56.4 48 0.001 29.2 6.9 44 343-386 12-55 (99)
31 PF04505 Dispanin: Interferon- 56.0 12 0.00027 31.6 3.1 27 353-379 42-68 (82)
32 cd03421 SirA_like_N SirA_like_ 55.3 57 0.0012 25.8 6.7 65 407-482 1-65 (67)
33 PF03357 Snf7: Snf7; InterPro 53.9 62 0.0013 29.5 7.7 55 334-388 10-64 (171)
34 PF01206 TusA: Sulfurtransfera 53.1 62 0.0013 25.6 6.6 66 407-482 2-68 (70)
35 smart00685 DM14 Repeats in fly 51.1 63 0.0014 26.2 6.2 37 348-384 8-44 (59)
36 PF13763 DUF4167: Domain of un 50.9 67 0.0015 27.6 6.7 39 348-386 39-77 (80)
37 PRK10454 PTS system N,N'-diace 49.0 69 0.0015 29.1 6.9 53 341-396 24-76 (115)
38 PF02255 PTS_IIA: PTS system, 47.7 87 0.0019 27.3 7.1 49 345-396 11-59 (96)
39 COG2023 RPR2 RNase P subunit R 45.8 66 0.0014 29.0 6.1 42 340-382 6-47 (105)
40 PF02845 CUE: CUE domain; Int 41.8 19 0.00042 26.3 1.9 27 23-49 15-41 (42)
41 PF07743 HSCB_C: HSCB C-termin 41.7 1.9E+02 0.0041 23.5 8.5 51 335-385 27-77 (78)
42 cd03420 SirA_RHOD_Pry_redox Si 41.2 77 0.0017 25.5 5.5 66 407-482 1-67 (69)
43 COG1447 CelC Phosphotransferas 40.4 84 0.0018 28.3 6.0 39 345-384 17-55 (105)
44 PF02403 Seryl_tRNA_N: Seryl-t 40.0 1.3E+02 0.0029 25.8 7.2 61 328-390 32-92 (108)
45 PLN03218 maturation of RBCL 1; 39.7 46 0.001 40.4 5.6 76 405-480 921-1010(1060)
46 PF06972 DUF1296: Protein of u 38.4 41 0.00088 27.5 3.3 28 174-201 19-46 (60)
47 PF06972 DUF1296: Protein of u 37.9 29 0.00063 28.3 2.4 29 20-49 17-45 (60)
48 PF10006 DUF2249: Uncharacteri 37.2 1.7E+02 0.0036 23.4 6.8 64 407-482 1-67 (69)
49 PF02861 Clp_N: Clp amino term 37.0 42 0.00092 24.7 3.1 39 157-199 12-50 (53)
50 cd03423 SirA SirA (also known 34.5 1.3E+02 0.0029 24.0 5.9 65 408-482 2-67 (69)
51 PF02954 HTH_8: Bacterial regu 34.5 28 0.00061 25.5 1.8 22 26-47 8-29 (42)
52 PF14164 YqzH: YqzH-like prote 34.2 21 0.00045 29.5 1.1 13 179-191 10-22 (64)
53 PRK03954 ribonuclease P protei 32.2 1.5E+02 0.0032 27.4 6.3 37 346-383 20-56 (121)
54 TIGR01038 L22_arch ribosomal p 31.8 86 0.0019 29.7 5.0 38 410-450 33-70 (150)
55 PRK01773 hscB co-chaperone Hsc 31.2 2.3E+02 0.0049 27.3 7.8 54 333-386 112-165 (173)
56 cd00248 Mth938-like Mth938-lik 30.8 62 0.0014 28.6 3.6 31 439-472 55-85 (109)
57 PRK11018 hypothetical protein; 27.3 3.6E+02 0.0078 22.3 8.0 68 405-482 8-76 (78)
58 cd05125 Mth938_2P1-like Mth938 27.0 75 0.0016 28.6 3.5 51 418-472 37-87 (114)
59 PF06413 Neugrin: Neugrin; In 26.5 32 0.00068 34.6 1.1 29 157-185 24-52 (225)
60 TIGR02977 phageshock_pspA phag 26.4 4.2E+02 0.0091 26.0 9.0 50 334-383 54-103 (219)
61 PF09644 Mg296: Mg296 protein; 26.1 18 0.0004 32.7 -0.5 25 158-182 47-71 (121)
62 TIGR00714 hscB Fe-S protein as 25.8 3.8E+02 0.0083 25.2 8.2 53 334-386 99-151 (157)
63 cd05560 Xcc1710_like Xcc1710_l 24.9 94 0.002 27.5 3.7 31 439-472 55-85 (109)
64 PRK00430 fis global DNA-bindin 24.2 1.1E+02 0.0024 26.6 4.0 48 157-205 29-85 (95)
65 PF04012 PspA_IM30: PspA/IM30 23.7 6.5E+02 0.014 24.3 9.6 53 332-384 51-103 (221)
66 COG1842 PspA Phage shock prote 23.0 5.6E+02 0.012 25.8 9.2 47 339-385 59-105 (225)
67 cd03422 YedF YedF is a bacteri 22.9 3.9E+02 0.0084 21.4 6.6 65 408-482 2-67 (69)
68 PRK01356 hscB co-chaperone Hsc 22.1 4.9E+02 0.011 24.8 8.2 53 335-387 109-161 (166)
69 COG2178 Predicted RNA-binding 22.1 4.7E+02 0.01 26.3 8.2 51 332-382 13-63 (204)
70 PF04032 Rpr2: RNAse P Rpr2/Rp 21.9 1.2E+02 0.0027 24.7 3.7 33 347-379 2-34 (85)
71 KOG2617 Citrate synthase [Ener 21.8 64 0.0014 35.4 2.4 58 408-465 287-356 (458)
72 PRK12402 replication factor C 21.7 1.8E+02 0.0038 29.3 5.5 46 154-199 183-229 (337)
73 PF01402 RHH_1: Ribbon-helix-h 21.5 1.1E+02 0.0024 21.4 2.9 31 330-360 7-37 (39)
74 PF04430 DUF498: Protein of un 21.4 1.1E+02 0.0024 26.8 3.5 31 439-472 56-86 (110)
75 PF12854 PPR_1: PPR repeat 21.0 78 0.0017 22.0 2.0 27 23-50 8-34 (34)
76 PRK03578 hscB co-chaperone Hsc 21.0 5.3E+02 0.011 24.8 8.2 55 333-387 115-170 (176)
77 PRK00299 sulfur transfer prote 20.8 3.6E+02 0.0077 22.5 6.2 69 405-483 9-78 (81)
78 PF11626 Rap1_C: TRF2-interact 20.1 1.1E+02 0.0024 25.8 3.1 34 171-204 6-39 (87)
79 PF13986 DUF4224: Domain of un 20.0 1.5E+02 0.0032 22.8 3.4 26 454-480 16-41 (47)
80 PF14863 Alkyl_sulf_dimr: Alky 20.0 4.2E+02 0.0092 24.7 7.1 55 337-391 56-116 (141)
No 1
>PF08590 DUF1771: Domain of unknown function (DUF1771); InterPro: IPR013899 This domain is almost always found adjacent to IPR002625 from INTERPRO. ; PDB: 2VKC_A.
Probab=99.65 E-value=2.4e-17 Score=132.60 Aligned_cols=65 Identities=32% Similarity=0.502 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 011024 333 SFQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETSGRN 399 (495)
Q Consensus 333 ~Y~~~R~~A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~~AA~~If~~r~~N 399 (495)
+|..+|.+|.+|++.|++||++|++||.+||++.|++||++||.|.++|+++|.+||++||..| |
T Consensus 1 ~Y~~~R~~A~~~~~~r~~~~~~A~~Ay~~Gd~~~A~~ls~~gk~~~~~~~~~n~~AA~~I~~~~--N 65 (66)
T PF08590_consen 1 DYEKLRAEADEHARKRNECFQKAAEAYRRGDKAAAKELSEEGKQHNEKMKEANRQAAEAIFEER--N 65 (66)
T ss_dssp --------------------------------------------------SHHHHHHHHHHHHH--H
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--c
Confidence 5999999999999999999999999999999999999999999999999999999999999999 7
No 2
>smart00463 SMR Small MutS-related domain.
Probab=99.58 E-value=4e-15 Score=122.47 Aligned_cols=78 Identities=27% Similarity=0.344 Sum_probs=68.4
Q ss_pred CeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCC-CCCcchHHHHHHHHHcCCceEeeCCCeEEEEEeC
Q 011024 406 LLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDT-TKGGRRRRVMKLLEEESIEWTEEGNAGTILIPLD 483 (495)
Q Consensus 406 ~tIDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~-g~~k~kpAV~klL~eegi~~~e~~n~G~IlI~L~ 483 (495)
++|||||++|.||+.+|+..|..+...+....++||||+|+||. |...++++|.++|...+|.|.++.|.|+++|.|.
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 68999999999999999999998875432268999999999998 4567889999999999999987569999999874
No 3
>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=99.50 E-value=2e-14 Score=119.05 Aligned_cols=73 Identities=29% Similarity=0.449 Sum_probs=58.4
Q ss_pred eecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCCceEe----------eCCCeE
Q 011024 408 LDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTE----------EGNAGT 477 (495)
Q Consensus 408 IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi~~~e----------~~n~G~ 477 (495)
|||||++++||++.|+..|..+... ....++||||+|+||.++. ++++|.++|++ ++.|.+ ..|.|+
T Consensus 1 iDLHG~~~~eA~~~l~~~l~~~~~~-~~~~~~II~G~G~hS~~g~-Lk~~V~~~L~~-~~~~~~v~~~~~~~~~~g~~G~ 77 (83)
T PF01713_consen 1 IDLHGLTVEEALRALEEFLDEARQR-GIRELRIITGKGNHSKGGV-LKRAVRRWLEE-GYQYEEVLAYRDAEPEDGNSGA 77 (83)
T ss_dssp EE-TTS-HHHHHHHHHHHHHHHHHT-THSEEEEE--STCTCCTSH-HHHHHHHHHHH-THCCTTEEEEEE--CCCTGGGE
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHHc-CCCEEEEEeccCCCCCCCc-HHHHHHHHHHh-hhccchhheeeecCCCCCCCeE
Confidence 8999999999999999999987644 3489999999999999886 99999999988 766543 129999
Q ss_pred EEEEeC
Q 011024 478 ILIPLD 483 (495)
Q Consensus 478 IlI~L~ 483 (495)
++|.|.
T Consensus 78 ~~V~lk 83 (83)
T PF01713_consen 78 TIVYLK 83 (83)
T ss_dssp EEEEE-
T ss_pred EEEEeC
Confidence 999873
No 4
>KOG2401 consensus Predicted MutS-related protein involved in mismatch repair [Replication, recombination and repair]
Probab=98.87 E-value=2e-09 Score=114.85 Aligned_cols=400 Identities=13% Similarity=0.047 Sum_probs=213.4
Q ss_pred CCccCHHHHHHHHHHhCCCchhhhhhhhcccCCCCCcccCCCCCccCCCCCCCCCCCCccccccccCCCCCCCCCcceec
Q 011024 20 GSVFTMQEIALACRNAGRNPDLAGESLCDKQANASTSSIHPSTGEARGKESSKSSNSNISEKSFYANGKSKPPKTKWHPV 99 (495)
Q Consensus 20 gs~fSl~~ia~Ay~~A~~d~~~A~eiL~~~~~~~sts~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~~~k~~k~k~~~v 99 (495)
++.|.+.++..|+++++..+++...++.+++..++...-.-.+.+.+ .+++......++..... ..+....+....
T Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~-~~s~~~~~~~~~~~~~~---~~~~~~~~~~~~ 99 (448)
T KOG2401|consen 24 SFSFKLVDLKAASEESSDEVDLGPPELSEMATSTSSADRLQYTIELL-EPSPSSVSFESLRARAS---DENVDRGNQERI 99 (448)
T ss_pred hhhhhhHhhhhcccccccccccCCCcchhhccccchhhhhccccccc-CCCcccccccccccchh---hhccccHHHHhh
Confidence 56688888999999999999988888888877553222222333322 11111111111111111 011122333444
Q ss_pred ccccccccccccccccCCCCCCCcccCCCCcCCCCCCCccccccCCC-CCCCCCCccchhHHHHHHHHHhcCccccCHHH
Q 011024 100 SGGTVSSFLGKDYVKPAQPTNGTGLASKPLKLDPKEFPMSALWGEET-KPKQSKGDHLQKEMEDFLFKLLGEGFQLSRDV 178 (495)
Q Consensus 100 s~GtVSsviGK~y~r~~~~~~~~~~~~kp~k~~~k~~~~~~~w~~~~-~~~~~~~~~~~~d~E~FL~~MLG~gf~L~~~v 178 (495)
.-.....+.|+.+++............+++..+.+.+|....|.++. -++.+.........+++|+.|..+++.-+--.
T Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~n~~ 179 (448)
T KOG2401|consen 100 LDRSRNQVAGKLKVSFVEKKLNEEEPQKEINPDGRILPEDPSFEESFRVENGFDPGEAIAFKIEDLPQKQVEGEDVDNCK 179 (448)
T ss_pred cccccccccccccccccccccCccccccccCCcccccccccchHHHHHHhccCccchhhhcchhhhccccccccccccce
Confidence 55678889999999999888888888888888888777766654333 33333333333344444444444444333333
Q ss_pred HHHHHHhcCCcHHHHHHHHHcccccccccccccccccccccccccCCcCcchhHhhhhhhccCCCCCcCCCCCCcccccC
Q 011024 179 IREVLDSCGYDMQKSMSKLIDHSAETLGEKTKFLGKSSEKCMDICSTFGGSQRERKLQQLNSSGGRAKEDPNTNKGELLK 258 (495)
Q Consensus 179 Ir~VL~~cGyDv~ks~d~LLd~s~~~~~k~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~ 258 (495)
|. ...+|.+|..++..-.++-+.+.... ...... +... + .+........
T Consensus 180 ~~-~~~~~~~d~~~~~~~~~~~~~~~~~~----~~~~~~---------~~~~-------~--~~~~~~~~~~-------- 228 (448)
T KOG2401|consen 180 VK-NQITNSSDSKMATEPGLNDSLKKAYE----NVDSSE---------ESVE-------L--LRKEGFSVDV-------- 228 (448)
T ss_pred ee-ccccccccccccccccccchhhcccc----ccCcch---------hhhh-------h--hccCCCCccC--------
Confidence 33 33444444444333333333222110 000010 0000 0 0000000000
Q ss_pred CCcchhhhHHHHHHHhccCCCCCCcchhhH-HHhhhccccCCccccCCCCCCcccccccccccccccCC---CccchhHH
Q 011024 259 HPKDRNELQKEVFAALFSAPKKSDEFPEIM-VKTKRRSKALGKVVSGPPEDLVPEYKANVVHLQQDNQN---NNVEEDSF 334 (495)
Q Consensus 259 ~~~~~~~l~~~vle~lF~~~e~~~~~p~~~-~~~~~~~~~~g~~v~~p~~d~~~~~~~~~~~s~q~n~~---~~~~d~~Y 334 (495)
.......-...+++..+..++.....+.+. -...+++-..+++.+++.++.....- ......++-. ..+....|
T Consensus 229 ~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~~~d~~~~~~~~~~~~~~~ 306 (448)
T KOG2401|consen 229 PSNAEKNSAKRLEELQKSQPEEDKAKKLRDQLYKSKRPAGSGKCLRKRHELSDKPRG--VLQAEDDYNADELSDEFGNKE 306 (448)
T ss_pred cchhhcccccchhhcchhhhccchhhhHHHhhhhhcccccccchhhhhhhhhhhhhh--hhhcccccchhhhhhhhhhhh
Confidence 000111112233333333333333332222 12233333333455544433322211 0011111100 12233334
Q ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCeeecCCC
Q 011024 335 QHLRTAVMEYRG-TMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETSGRNRDTKNDLLLDLHDH 413 (495)
Q Consensus 335 ~~~R~~A~~h~~-~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~~AA~~If~~r~~N~~~~~~~tIDLHGL 413 (495)
......+++..+ .+..++++|+.++..+....|.++.-.+......+......+-+.++... |.......+.++|+.
T Consensus 307 s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~a~~~~~~--~~~~~r~~~~~~~~~ 384 (448)
T KOG2401|consen 307 SIKSEREIDNQRLYKKAAEQKAQPEIEDAINLQASELKPKVSLAVKGSYAVAKLKPATQWKLD--NEEIERRSEVGEHGE 384 (448)
T ss_pred hhhhhHHhhhhhHHHHHHHhhhhhhhhhhhhhhhhhhchhhhhcccccchhhhcchHHHHHHh--hhhhhcccccccchh
Confidence 444555555555 77889999999999999999999999988777666666555555566666 656666788999999
Q ss_pred CHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCCceEee
Q 011024 414 GAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE 472 (495)
Q Consensus 414 hVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi~~~e~ 472 (495)
+|.++...++ +.|++|+|.||.+...+.+++.+.++..++.+...
T Consensus 385 ~i~~~~~~~~--------------~qv~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~ 429 (448)
T KOG2401|consen 385 KISELSRRLK--------------LQVLFGRGIHSRGEARLPRAEKRSYEDPPQGFVEE 429 (448)
T ss_pred hhHhHhhhcc--------------ccccccccccCccchhhhhhhhhhccCCccceeee
Confidence 9998776543 44889999999998888888888788888765443
No 5
>COG2840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.11 E-value=8.5e-06 Score=78.37 Aligned_cols=81 Identities=16% Similarity=0.202 Sum_probs=64.7
Q ss_pred CCCCCeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCC-cchHHHHHHHHHcCC--ceEeeC----C
Q 011024 402 TKNDLLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKG-GRRRRVMKLLEEESI--EWTEEG----N 474 (495)
Q Consensus 402 ~~~~~tIDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~-k~kpAV~klL~eegi--~~~e~~----n 474 (495)
...+..|||||+.++||-..|-..|..+... ....+.||+|+|. |.|+. -++++|-.+|.++-. .|++.. .
T Consensus 93 ~~~e~~LDLHG~tq~eAr~~L~~Fi~~a~~~-~~rcv~VihGkG~-s~g~~~vLK~~Vp~WL~qhp~V~a~~~a~~~hGG 170 (184)
T COG2840 93 YPPEARLDLHGLTQEEARQELGAFIARARAE-GLRCVLVIHGKGR-SKGSKPVLKSQVPRWLTQHPDVLAFHQAPRRHGG 170 (184)
T ss_pred CCcceeeeccCCCHHHHHHHHHHHHHHHHHh-CCcEEEEEeCCCc-CCCCchhHHHHHHHHHHhChHHHhhcccchhcCC
Confidence 3457899999999999999999999988643 4578999999999 99855 468899999999533 244432 6
Q ss_pred CeEEEEEeCC
Q 011024 475 AGTILIPLDK 484 (495)
Q Consensus 475 ~G~IlI~L~g 484 (495)
.|.|+|.|.-
T Consensus 171 ~GAlyVlL~~ 180 (184)
T COG2840 171 DGALYVLLRR 180 (184)
T ss_pred ceEEEEEEec
Confidence 7899998864
No 6
>PRK04946 hypothetical protein; Provisional
Probab=98.04 E-value=1.3e-05 Score=76.91 Aligned_cols=78 Identities=14% Similarity=0.165 Sum_probs=62.8
Q ss_pred CCCCCeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCC--ceEee----CCC
Q 011024 402 TKNDLLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESI--EWTEE----GNA 475 (495)
Q Consensus 402 ~~~~~tIDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi--~~~e~----~n~ 475 (495)
...+.+|||||+.++||...|...|..+.. .....+.||.|+|. +.++.+|..+|.+.-. .|+.. .+.
T Consensus 92 ~~~~~~LDLhG~~~eeA~~~L~~fl~~a~~-~g~r~v~IIHGkG~-----gvLk~~V~~wL~q~~~V~af~~A~~~~GG~ 165 (181)
T PRK04946 92 YSPELFLDLHGLTQLQAKQELGALIAACRK-EHVFCACVMHGHGK-----HILKQQTPLWLAQHPDVMAFHQAPKEWGGD 165 (181)
T ss_pred CCCceEEECCCCCHHHHHHHHHHHHHHHHH-cCCCEEEEEcCCCH-----hHHHHHHHHHHcCCchhheeeccCcccCCc
Confidence 334799999999999999999999988754 34578999999996 4678899999988755 36542 278
Q ss_pred eEEEEEeCCC
Q 011024 476 GTILIPLDKV 485 (495)
Q Consensus 476 G~IlI~L~g~ 485 (495)
|.++|.|...
T Consensus 166 GA~~VlLk~~ 175 (181)
T PRK04946 166 AALLVLIEIE 175 (181)
T ss_pred eEEEEEEecC
Confidence 9999999764
No 7
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=97.54 E-value=0.00017 Score=82.63 Aligned_cols=73 Identities=21% Similarity=0.238 Sum_probs=59.7
Q ss_pred CCeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCC--ceEeeC----CCeEE
Q 011024 405 DLLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESI--EWTEEG----NAGTI 478 (495)
Q Consensus 405 ~~tIDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi--~~~e~~----n~G~I 478 (495)
..+|||||+.|+||+..|+..|..+... +...++||.|+|. +.++.+|.+||+++-+ .|+... +.|+.
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 SLELDLRGMRYEEALERLDKYLDDALLA-GYGEVLIIHGKGT-----GKLRKGVQEFLKKHPSVKSFRDAPPNEGGFGVT 777 (782)
T ss_pred CceEECCCCCHHHHHHHHHHHHHHHHHc-CCCEEEEEcCCCh-----hHHHHHHHHHHcCCCceeeeeecCcccCCCeEE
Confidence 5799999999999999999999876532 4588999999985 4789999999998865 355432 78999
Q ss_pred EEEeC
Q 011024 479 LIPLD 483 (495)
Q Consensus 479 lI~L~ 483 (495)
+|.|.
T Consensus 778 ~V~lk 782 (782)
T PRK00409 778 IVELK 782 (782)
T ss_pred EEEEC
Confidence 99873
No 8
>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=97.41 E-value=0.00027 Score=80.82 Aligned_cols=72 Identities=24% Similarity=0.357 Sum_probs=58.8
Q ss_pred CCeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCC--ceEee----CCCeEE
Q 011024 405 DLLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESI--EWTEE----GNAGTI 478 (495)
Q Consensus 405 ~~tIDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi--~~~e~----~n~G~I 478 (495)
..+|||||+.++||++.|...|..+.- .+...++||.|+|. +.++++|..||++.-+ .|+.. .+.|+.
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 SLTLDLRGQRSEEALDRLEKFLNDALL-AGYEVVLIIHGKGS-----GKLRKGVQELLKNHPKVKSFRDAPPNDGGSGVT 766 (771)
T ss_pred CceEECCCCCHHHHHHHHHHHHHHHHH-CCCCEEEEEcCCCh-----hHHHHHHHHHhcCCcceeeecccCcccCCceEE
Confidence 569999999999999999999987643 24578999999995 4689999999999865 35432 278899
Q ss_pred EEEe
Q 011024 479 LIPL 482 (495)
Q Consensus 479 lI~L 482 (495)
+|.|
T Consensus 767 ~V~l 770 (771)
T TIGR01069 767 IVYL 770 (771)
T ss_pred EEEE
Confidence 9987
No 9
>KOG2401 consensus Predicted MutS-related protein involved in mismatch repair [Replication, recombination and repair]
Probab=96.46 E-value=0.0061 Score=65.69 Aligned_cols=356 Identities=13% Similarity=0.032 Sum_probs=212.9
Q ss_pred cCHHHHHHHHHHhCCCchhhhhhhhcccCCCCCcccCCCCCcc------CCCCCCCCCCCCccccccccCCCCCCCCCcc
Q 011024 23 FTMQEIALACRNAGRNPDLAGESLCDKQANASTSSIHPSTGEA------RGKESSKSSNSNISEKSFYANGKSKPPKTKW 96 (495)
Q Consensus 23 fSl~~ia~Ay~~A~~d~~~A~eiL~~~~~~~sts~~~~s~~~~------~~~~~~~~~~~~~~e~~~~~~~~~k~~k~k~ 96 (495)
.++.-.+..|...+.+.+.|.+.+...-+...+-.++....++ .+....+.++..++. . ....+...
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~s~~~~~~---~-~~~~~~~~--- 88 (448)
T KOG2401|consen 16 LTLSLAAFSFSFKLVDLKAASEESSDEVDLGPPELSEMATSTSSADRLQYTIELLEPSPSSVSF---E-SLRARASD--- 88 (448)
T ss_pred chhccchhhhhhhhHhhhhcccccccccccCCCcchhhccccchhhhhcccccccCCCcccccc---c-ccccchhh---
Confidence 4566678899999999999999998887776555554333322 101111111111100 0 00011100
Q ss_pred eecccccccccccccccccCCCCCCCcccCCCCcCCCCCCCccccccCCCCCCCCCCccchhHHHHHHHHHhcCccccCH
Q 011024 97 HPVSGGTVSSFLGKDYVKPAQPTNGTGLASKPLKLDPKEFPMSALWGEETKPKQSKGDHLQKEMEDFLFKLLGEGFQLSR 176 (495)
Q Consensus 97 ~~vs~GtVSsviGK~y~r~~~~~~~~~~~~kp~k~~~k~~~~~~~w~~~~~~~~~~~~~~~~d~E~FL~~MLG~gf~L~~ 176 (495)
..+-.|+ --.+++.+..+....-. ....+.+++. ++|+.. |. -..+......-.++++-.+++......+
T Consensus 89 ~~~~~~~-~~~~~~~~~~~~~~~~~--~~~~~~~~~~-~~~~~~-~~-----~~~~~~~~~~~~~e~~~~~~~f~~~~~~ 158 (448)
T KOG2401|consen 89 ENVDRGN-QERILDRSRNQVAGKLK--VSFVEKKLNE-EEPQKE-IN-----PDGRILPEDPSFEESFRVENGFDPGEAI 158 (448)
T ss_pred hccccHH-HHhhccccccccccccc--ccccccccCc-cccccc-cC-----CcccccccccchHHHHHHhccCccchhh
Confidence 0011121 12345555544432211 1223333331 122222 11 1122333466778888889999999999
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHcccccccccccccccccccccccccCCcCcchhHhhhhhhccCCCCCcCCCCCCcccc
Q 011024 177 DVIREVLDSCGYDMQKSMSKLIDHSAETLGEKTKFLGKSSEKCMDICSTFGGSQRERKLQQLNSSGGRAKEDPNTNKGEL 256 (495)
Q Consensus 177 ~vIr~VL~~cGyDv~ks~d~LLd~s~~~~~k~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~ 256 (495)
..+.+.|.+|.+...-+.....+...+ ..- +.+.......+..
T Consensus 159 ~~~~~~~~~~~~~~~~~~n~~~~~~~~-~~~------------------------------------d~~~~~~~~~~~~ 201 (448)
T KOG2401|consen 159 AFKIEDLPQKQVEGEDVDNCKVKNQIT-NSS------------------------------------DSKMATEPGLNDS 201 (448)
T ss_pred hcchhhhccccccccccccceeecccc-ccc------------------------------------cccccccccccch
Confidence 999999999998776655544441111 000 0000000000111
Q ss_pred cCCCcchhhhHHHHHHHhccCCCCCCcchhhHHHhhhccccCCccccCCCCCCcccccccccccccccCCCccchhHHHH
Q 011024 257 LKHPKDRNELQKEVFAALFSAPKKSDEFPEIMVKTKRRSKALGKVVSGPPEDLVPEYKANVVHLQQDNQNNNVEEDSFQH 336 (495)
Q Consensus 257 ~~~~~~~~~l~~~vle~lF~~~e~~~~~p~~~~~~~~~~~~~g~~v~~p~~d~~~~~~~~~~~s~q~n~~~~~~d~~Y~~ 336 (495)
......-..++.+.++.+|+. +.++-.|. .+-.....-..+|+.
T Consensus 202 ~~~~~~~~~~~~~~~~~~~~~---------------------~~~~~~~~---------------~~~~~~~~~~~~~~~ 245 (448)
T KOG2401|consen 202 LKKAYENVDSSEESVELLRKE---------------------GFSVDVPS---------------NAEKNSAKRLEELQK 245 (448)
T ss_pred hhccccccCcchhhhhhhccC---------------------CCCccCcc---------------hhhcccccchhhcch
Confidence 111111123344555555544 11111111 111112445568888
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCeeecCCCCHH
Q 011024 337 LRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETSGRNRDTKNDLLLDLHDHGAK 416 (495)
Q Consensus 337 ~R~~A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~~AA~~If~~r~~N~~~~~~~tIDLHGLhVk 416 (495)
.+........++...|..+.-|+..+....++.++.+.+......+.++.++....|... +.. .....+|+|+++++
T Consensus 246 ~~~~~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~--~s~-~~~~~~~~~~~~~~ 322 (448)
T KOG2401|consen 246 SQPEEDKAKKLRDQLYKSKRPAGSGKCLRKRHELSDKPRGVLQAEDDYNADELSDEFGNK--ESI-KSEREIDNQRLYKK 322 (448)
T ss_pred hhhccchhhhHHHhhhhhcccccccchhhhhhhhhhhhhhhhhcccccchhhhhhhhhhh--hhh-hhhHHhhhhhHHHH
Confidence 888888899999999999999999999999999999999999999999999999999877 533 34688999999999
Q ss_pred HHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCC-CCcchHHHHHHHHHcCCceEee
Q 011024 417 EAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTT-KGGRRRRVMKLLEEESIEWTEE 472 (495)
Q Consensus 417 EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g-~~k~kpAV~klL~eegi~~~e~ 472 (495)
.|...+...+...... ...++.++.+.++|... ..++++++...+..+.+.-...
T Consensus 323 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~v~~~~~a~~~~~~~~~~~r~~~ 378 (448)
T KOG2401|consen 323 AAEQKAQPEIEDAINL-QASELKPKVSLAVKGSYAVAKLKPATQWKLDNEEIERRSE 378 (448)
T ss_pred HHHhhhhhhhhhhhhh-hhhhhchhhhhcccccchhhhcchHHHHHHhhhhhhcccc
Confidence 9999998887665433 23788999999999974 4568999999999988764443
No 10
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=96.00 E-value=0.015 Score=42.91 Aligned_cols=40 Identities=30% Similarity=0.471 Sum_probs=33.3
Q ss_pred HHHHHHHHHhcCccccCHHHHHHHHHhcCCcHHHHHHHHHccc
Q 011024 159 EMEDFLFKLLGEGFQLSRDVIREVLDSCGYDMQKSMSKLIDHS 201 (495)
Q Consensus 159 d~E~FL~~MLG~gf~L~~~vIr~VL~~cGyDv~ks~d~LLd~s 201 (495)
++-+.|..|+- +++.++|+.||.+|++||+.+++.||+++
T Consensus 3 ~~v~~L~~mFP---~~~~~~I~~~L~~~~~~ve~ai~~LL~~~ 42 (42)
T PF02845_consen 3 EMVQQLQEMFP---DLDREVIEAVLQANNGDVEAAIDALLEMS 42 (42)
T ss_dssp HHHHHHHHHSS---SS-HHHHHHHHHHTTTTHHHHHHHHHHHH
T ss_pred HHHHHHHHHCC---CCCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence 44466777765 69999999999999999999999999874
No 11
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=94.95 E-value=0.066 Score=39.49 Aligned_cols=40 Identities=23% Similarity=0.382 Sum_probs=33.4
Q ss_pred HHHHHHHHHhcCccccCHHHHHHHHHhcCCcHHHHHHHHHccc
Q 011024 159 EMEDFLFKLLGEGFQLSRDVIREVLDSCGYDMQKSMSKLIDHS 201 (495)
Q Consensus 159 d~E~FL~~MLG~gf~L~~~vIr~VL~~cGyDv~ks~d~LLd~s 201 (495)
++-+.|..|+- +|+..+|+.+|-.|++||+.+++.||..+
T Consensus 4 ~~v~~L~~mFP---~l~~~~I~~~L~~~~g~ve~~i~~LL~~~ 43 (43)
T smart00546 4 EALHDLKDMFP---NLDEEVIKAVLEANNGNVEATINNLLEGS 43 (43)
T ss_pred HHHHHHHHHCC---CCCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence 45556666633 79999999999999999999999999764
No 12
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=94.87 E-value=0.056 Score=38.45 Aligned_cols=35 Identities=26% Similarity=0.462 Sum_probs=28.6
Q ss_pred HHHHHhcCccccCHHHHHHHHHhcCCcHHHHHHHHHc
Q 011024 163 FLFKLLGEGFQLSRDVIREVLDSCGYDMQKSMSKLID 199 (495)
Q Consensus 163 FL~~MLG~gf~L~~~vIr~VL~~cGyDv~ks~d~LLd 199 (495)
-+..|..-||. +..++++|..|++|+++|++.|++
T Consensus 4 ~v~~L~~mGf~--~~~~~~AL~~~~~d~~~A~~~L~~ 38 (38)
T cd00194 4 KLEQLLEMGFS--REEARKALRATNNNVERAVEWLLE 38 (38)
T ss_pred HHHHHHHcCCC--HHHHHHHHHHhCCCHHHHHHHHhC
Confidence 34445555766 999999999999999999999974
No 13
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=89.99 E-value=0.33 Score=34.76 Aligned_cols=31 Identities=32% Similarity=0.665 Sum_probs=25.3
Q ss_pred HHHHHHhcCccccCHHHHHHHHHhcCCcHHHHHHHH
Q 011024 162 DFLFKLLGEGFQLSRDVIREVLDSCGYDMQKSMSKL 197 (495)
Q Consensus 162 ~FL~~MLG~gf~L~~~vIr~VL~~cGyDv~ks~d~L 197 (495)
+=|..| || +...+++.|-.|++||++|++.|
T Consensus 7 ~~L~~m---Gf--~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 7 QQLMEM---GF--SREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHH---TS---HHHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHc---CC--CHHHHHHHHHHcCCCHHHHHHhC
Confidence 447777 55 56699999999999999999976
No 14
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=89.82 E-value=0.39 Score=33.92 Aligned_cols=25 Identities=16% Similarity=0.311 Sum_probs=22.3
Q ss_pred cCHHHHHHHHHhcCCcHHHHHHHHH
Q 011024 174 LSRDVIREVLDSCGYDMQKSMSKLI 198 (495)
Q Consensus 174 L~~~vIr~VL~~cGyDv~ks~d~LL 198 (495)
.+...++.+|-.|++|+++|++-|+
T Consensus 13 f~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 13 FSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 4566999999999999999999885
No 15
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=83.81 E-value=1 Score=31.86 Aligned_cols=29 Identities=28% Similarity=0.195 Sum_probs=26.0
Q ss_pred CCccCHHHHHHHHHHhCCCchhhhhhhhc
Q 011024 20 GSVFTMQEIALACRNAGRNPDLAGESLCD 48 (495)
Q Consensus 20 gs~fSl~~ia~Ay~~A~~d~~~A~eiL~~ 48 (495)
.-+|+-+++..|+...++|++.|++.|.+
T Consensus 10 ~mGf~~~~~~~AL~~~~~d~~~A~~~L~~ 38 (38)
T cd00194 10 EMGFSREEARKALRATNNNVERAVEWLLE 38 (38)
T ss_pred HcCCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence 45699999999999999999999999863
No 16
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=83.81 E-value=0.65 Score=38.85 Aligned_cols=39 Identities=21% Similarity=0.344 Sum_probs=31.1
Q ss_pred HHHhcCccccCHHHHHHHHHhcCCcHHHHHHHHHcccccc
Q 011024 165 FKLLGEGFQLSRDVIREVLDSCGYDMQKSMSKLIDHSAET 204 (495)
Q Consensus 165 ~~MLG~gf~L~~~vIr~VL~~cGyDv~ks~d~LLd~s~~~ 204 (495)
-.-||+... +-..|+++|=.|.|||+||++.||.-....
T Consensus 36 r~~Lg~~~~-~e~~i~eal~~~~fDvekAl~~Ll~~~~~~ 74 (79)
T PF08938_consen 36 REVLGDYVP-PEEQIKEALWHYYFDVEKALDYLLSKFKKK 74 (79)
T ss_dssp HHHCCCCC---CCHHHHHHHHTTT-CCHHHHHHHHCCHSS
T ss_pred HHHHcccCC-CHHHHHHHHHHHcCCHHHHHHHHHHhccCC
Confidence 456899887 889999999999999999999999876543
No 17
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=81.87 E-value=1.5 Score=32.77 Aligned_cols=26 Identities=19% Similarity=0.524 Sum_probs=23.2
Q ss_pred ccCHHHHHHHHHhcCCcHHHHHHHHH
Q 011024 173 QLSRDVIREVLDSCGYDMQKSMSKLI 198 (495)
Q Consensus 173 ~L~~~vIr~VL~~cGyDv~ks~d~LL 198 (495)
+-.+.++.-||..|+.||=+|||.+|
T Consensus 14 ~~kr~~Le~iL~~C~GDvv~AIE~~l 39 (39)
T PF03474_consen 14 HQKRSVLELILQRCNGDVVQAIEQFL 39 (39)
T ss_pred CCChHHHHHHHHHcCCcHHHHHHHhC
Confidence 45688999999999999999999875
No 18
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=80.69 E-value=1.5 Score=31.30 Aligned_cols=25 Identities=24% Similarity=0.174 Sum_probs=22.7
Q ss_pred ccCHHHHHHHHHHhCCCchhhhhhh
Q 011024 22 VFTMQEIALACRNAGRNPDLAGESL 46 (495)
Q Consensus 22 ~fSl~~ia~Ay~~A~~d~~~A~eiL 46 (495)
+|+-+++-.|+...++|++.|.++|
T Consensus 13 Gf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 13 GFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 5999999999999999999999987
No 19
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=78.45 E-value=2 Score=30.22 Aligned_cols=28 Identities=32% Similarity=0.230 Sum_probs=25.4
Q ss_pred CCccCHHHHHHHHHHhCCCchhhhhhhh
Q 011024 20 GSVFTMQEIALACRNAGRNPDLAGESLC 47 (495)
Q Consensus 20 gs~fSl~~ia~Ay~~A~~d~~~A~eiL~ 47 (495)
.-+|+-+++..|+...++|++.|.+.|.
T Consensus 10 ~mGf~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 10 EMGFSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred HcCCCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 4569999999999999999999999873
No 20
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=73.04 E-value=5.2 Score=46.53 Aligned_cols=72 Identities=19% Similarity=0.277 Sum_probs=52.9
Q ss_pred CCeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCCc--eEee----CCCeEE
Q 011024 405 DLLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIE--WTEE----GNAGTI 478 (495)
Q Consensus 405 ~~tIDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi~--~~e~----~n~G~I 478 (495)
..+|||+|.-+.||+..|...+..+-- ..+..+.||=|.| -++++..|.++|+++--. |+.. ...|+=
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 SNRLDLRGERSEEALDELDKSIDEAIL-EGYEKVSIIHGKG-----TGKLREGVQEYLKKHKKVKSFRDAPPNEGGSGVT 749 (753)
T ss_pred cccccccccccHHHHHHHHhhhHHHHH-cCCcceeEEeeee-----chHHHHHHHHHHHhCCCccCcCCCCcCCCCCCee
Confidence 369999999999999999999986532 2456788986655 456888999999998542 3332 156666
Q ss_pred EEEe
Q 011024 479 LIPL 482 (495)
Q Consensus 479 lI~L 482 (495)
+|.|
T Consensus 750 iv~l 753 (753)
T COG1193 750 IVEL 753 (753)
T ss_pred EEeC
Confidence 6654
No 21
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=69.32 E-value=13 Score=27.39 Aligned_cols=38 Identities=18% Similarity=0.506 Sum_probs=29.4
Q ss_pred hHHHHHHHHHhcCccccCHHHHHHHHHhcCCcHHHHHHHHHcc
Q 011024 158 KEMEDFLFKLLGEGFQLSRDVIREVLDSCGYDMQKSMSKLIDH 200 (495)
Q Consensus 158 ~d~E~FL~~MLG~gf~L~~~vIr~VL~~cGyDv~ks~d~LLd~ 200 (495)
+.+++|. +..| .+.++-+..|..|++|++.|++.-++-
T Consensus 2 e~i~~F~-~iTg----~~~~~A~~~L~~~~wdle~Av~~y~~~ 39 (43)
T PF14555_consen 2 EKIAQFM-SITG----ADEDVAIQYLEANNWDLEAAVNAYFDD 39 (43)
T ss_dssp HHHHHHH-HHH-----SSHHHHHHHHHHTTT-HHHHHHHHHHS
T ss_pred HHHHHHH-HHHC----cCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence 4567776 4444 388999999999999999999988764
No 22
>PF14346 DUF4398: Domain of unknown function (DUF4398)
Probab=66.82 E-value=42 Score=28.85 Aligned_cols=42 Identities=26% Similarity=0.162 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHH
Q 011024 343 EYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREA 384 (495)
Q Consensus 343 ~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrea 384 (495)
.++..-.+.+.+|..+|..|+...|..|..+++.+.+++...
T Consensus 40 ~el~~A~~~L~~A~~a~~~~~y~~A~~~A~~A~~~A~~A~~~ 81 (103)
T PF14346_consen 40 VELKEAREKLQRAKAALDDGDYERARRLAEQAQADAELAEAK 81 (103)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 366677788899999999999999999999999987777654
No 23
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=65.97 E-value=4.9 Score=29.55 Aligned_cols=31 Identities=32% Similarity=0.638 Sum_probs=22.1
Q ss_pred cCHHHHHHHHHhcCCcHHHHHHHHHccccccc
Q 011024 174 LSRDVIREVLDSCGYDMQKSMSKLIDHSAETL 205 (495)
Q Consensus 174 L~~~vIr~VL~~cGyDv~ks~d~LLd~s~~~~ 205 (495)
+...+|+++|..||+++.++-. +|.++-.++
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~-~Lgisr~tL 35 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAAR-LLGISRRTL 35 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHH-HHTS-HHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHH-HHCCCHHHH
Confidence 3468999999999999988765 456655543
No 24
>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=64.32 E-value=36 Score=26.62 Aligned_cols=66 Identities=21% Similarity=0.163 Sum_probs=46.6
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCCceEeeC-CCeEEEEEe
Q 011024 407 LLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEEG-NAGTILIPL 482 (495)
Q Consensus 407 tIDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi~~~e~~-n~G~IlI~L 482 (495)
+||+.|+--=.-+-.++..|..+. ....|.||+.... -..-|.++|++.|+.|.... ..|.+.|.+
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 489999888888888888888754 3377888865322 23458999999999986432 445666554
No 25
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=63.49 E-value=9.3 Score=29.09 Aligned_cols=29 Identities=34% Similarity=0.627 Sum_probs=28.0
Q ss_pred HHHHHHHHHhcCccccCHHHHHHHHHhcC
Q 011024 159 EMEDFLFKLLGEGFQLSRDVIREVLDSCG 187 (495)
Q Consensus 159 d~E~FL~~MLG~gf~L~~~vIr~VL~~cG 187 (495)
+++.+|..|.--||=||..+++++|..+|
T Consensus 20 ~~~~~l~~l~~~g~~is~~l~~~~L~~~g 48 (48)
T PF11848_consen 20 EVKPLLDRLQQAGFRISPKLIEEILRRAG 48 (48)
T ss_pred hHHHHHHHHHHcCcccCHHHHHHHHHHcC
Confidence 89999999999999999999999999887
No 26
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=62.54 E-value=58 Score=31.66 Aligned_cols=91 Identities=14% Similarity=0.157 Sum_probs=56.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCeeecCCCCHHHHHH
Q 011024 341 VMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETSGRNRDTKNDLLLDLHDHGAKEAIR 420 (495)
Q Consensus 341 A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~~AA~~If~~r~~N~~~~~~~tIDLHGLhVkEAi~ 420 (495)
.........+.+.+-.+||..||-..-..+..+.. ......+.++..| |..
T Consensus 165 ~l~~~~~~~~~~~~~~~~~~~gd~~~l~~~~~~~~--------~~p~~~~~ll~~R--N~~------------------- 215 (259)
T PF01963_consen 165 TLDDIEDGEKMLEQLIEAWKNGDLDALMELMKEDE--------SFPELYEVLLDER--NRR------------------- 215 (259)
T ss_pred HHhccccchHHHHHHHHHHHccCHHHHHHHHHhcc--------cCHHHHHHHHHHH--hHH-------------------
Confidence 33445667888999999999999754333311111 4444556788888 633
Q ss_pred HHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCCc
Q 011024 421 LLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIE 468 (495)
Q Consensus 421 iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi~ 468 (495)
+++.-...+.. + ....|+||.||----. -|..+|++.||+
T Consensus 216 ~~~~i~~~l~~-~--~~~fvvVGa~HL~G~~-----gvl~lLr~~Gy~ 255 (259)
T PF01963_consen 216 WAEKIEELLKE-G--GTVFVVVGAGHLPGED-----GVLDLLRKKGYT 255 (259)
T ss_pred HHHHHHHHHhc-C--CCEEEEEcchhccchh-----hHHHHHHhCCce
Confidence 11111122222 1 4688999999985421 288999999964
No 27
>PRK09591 celC cellobiose phosphotransferase system IIA component; Reviewed
Probab=61.41 E-value=73 Score=28.37 Aligned_cols=53 Identities=23% Similarity=0.227 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011024 341 VMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETS 396 (495)
Q Consensus 341 A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~~AA~~If~~r 396 (495)
-.-|+-.-+.+|-+|-++.+.||.+.|..+..+|+.....+.+++ .+.|-.+-
T Consensus 13 II~~aG~Ars~~~eAl~~ak~gdf~~A~~~l~eA~~~l~~AH~~q---t~liq~Ea 65 (104)
T PRK09591 13 IILHSGNARTEVHEAFAAMREGNFDLAEQKLNQSNEELLEAHHAQ---TKLLQEYA 65 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHh
Confidence 344555556677779999999999999999999998877777666 34454443
No 28
>PRK01905 DNA-binding protein Fis; Provisional
Probab=60.84 E-value=13 Score=30.81 Aligned_cols=49 Identities=12% Similarity=0.317 Sum_probs=38.3
Q ss_pred chhHHHHHHHHHhcCc---------cccCHHHHHHHHHhcCCcHHHHHHHHHccccccc
Q 011024 156 LQKEMEDFLFKLLGEG---------FQLSRDVIREVLDSCGYDMQKSMSKLIDHSAETL 205 (495)
Q Consensus 156 ~~~d~E~FL~~MLG~g---------f~L~~~vIr~VL~~cGyDv~ks~d~LLd~s~~~~ 205 (495)
.++.++.||-.++|.+ -++.+..|+++|..||.++.++- .+|.++..++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~E~~~i~~aL~~~~gn~s~aA-r~LGIsrstL 67 (77)
T PRK01905 10 IRDSLDQYFRDLDGSNPHDVYDMVLSCVEKPLLEVVMEQAGGNQSLAA-EYLGINRNTL 67 (77)
T ss_pred HHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHHHHHHcCCCHHHHH-HHHCCCHHHH
Confidence 3778999999998855 23567789999999999999885 5667766653
No 29
>cd00215 PTS_IIA_lac PTS_IIA, PTS system, lactose/cellobiose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. This family of proteins normally function as a homotrimer, stabilized by a centrally located metal ion. Separation into subunits is thought to occur after phosphorylation.
Probab=57.95 E-value=44 Score=29.33 Aligned_cols=50 Identities=26% Similarity=0.335 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011024 344 YRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETS 396 (495)
Q Consensus 344 h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~~AA~~If~~r 396 (495)
|+-.-+.||-+|-++.+.||.+.|..+..+|.....++.+.+- +.|-.+-
T Consensus 11 ~aG~Ars~~~eAl~~a~~g~fe~A~~~l~ea~~~l~~AH~~qt---~liq~ea 60 (97)
T cd00215 11 HAGNARSKALEALKAAKEGDFAEAEELLEEANDSLNEAHHAQT---KLLQQEA 60 (97)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHh
Confidence 3444456677799999999999999999999988877777763 4554444
No 30
>TIGR00823 EIIA-LAC phosphotransferase system enzyme II, lactose-specific, factor III. operon. While the Lac permeases consist of two polypeptide chains (IIA and IICB), the Chb permease of E. coli consists of three (IIA, IIB and IIC). In B. subtilis, a PTS permease similar to the Chb permease of E. coli is believed to transport lichenan (a b-1,3;1,4 glucan) degradation products, oligosaccharides of 2-4 glucose units. This model is specific for the IIA subunit of the Lac PTS family.
Probab=56.36 E-value=48 Score=29.22 Aligned_cols=44 Identities=27% Similarity=0.384 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHH
Q 011024 343 EYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADE 386 (495)
Q Consensus 343 ~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~ 386 (495)
-++-.-+.||-+|-++.+.||.+.|..+.++|+.....+.+.+-
T Consensus 12 ~~aG~Ars~~~eAl~~a~~gdfe~A~~~l~eA~~~l~~AH~~qt 55 (99)
T TIGR00823 12 AYAGDARSKALEALKAAKAGDFAKARALVEQAGMCLNEAHLAQT 55 (99)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444556677799999999999999999999998887777763
No 31
>PF04505 Dispanin: Interferon-induced transmembrane protein; InterPro: IPR007593 This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression [].; GO: 0009607 response to biotic stimulus, 0016021 integral to membrane
Probab=55.99 E-value=12 Score=31.62 Aligned_cols=27 Identities=19% Similarity=0.178 Sum_probs=24.2
Q ss_pred HHHHHHHHcCChHHHHHHHHHHHHHHH
Q 011024 353 KAAIDAFAQGDHVQAEKLLEQGKFFYE 379 (495)
Q Consensus 353 ~kAa~AY~kGd~a~A~~LSeqGk~~~~ 379 (495)
.++..+|++||.+.|.+.|.++|.+.-
T Consensus 42 ~kv~~~~~~Gd~~~A~~aS~~Ak~~~~ 68 (82)
T PF04505_consen 42 SKVRSRYAAGDYEGARRASRKAKKWSI 68 (82)
T ss_pred hhhHHHHHCCCHHHHHHHHHHhHHHHH
Confidence 578999999999999999999998764
No 32
>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=55.32 E-value=57 Score=25.75 Aligned_cols=65 Identities=17% Similarity=0.236 Sum_probs=44.5
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCCceEeeCCCeEEEEEe
Q 011024 407 LLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEEGNAGTILIPL 482 (495)
Q Consensus 407 tIDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi~~~e~~n~G~IlI~L 482 (495)
+||+-|+.==+-+-.++..| .+. ....|.||+-. .+ -..-|..+|++.|+.+......|.+.|.+
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-ELE---AGGEIEVLVDN-EV------AKENVSRFAESRGYEVSVEEKGGEFEITI 65 (67)
T ss_pred CcccCCCCCCHHHHHHHHHH-hcC---CCCEEEEEEcC-hh------HHHHHHHHHHHcCCEEEEEecCCEEEEEE
Confidence 48899998878888888888 543 22578887532 11 23358999999999986443555666655
No 33
>PF03357 Snf7: Snf7; InterPro: IPR005024 This is a family of eukaryotic proteins which are variously described as either hypothetical protein, developmental protein or related to yeast SNF7. The family contains human CHMP1. CHMP1 (CHromatin Modifying Protein; CHarged Multivesicular body Protein), is encoded by an alternative open reading frame in the PRSM1 gene [] and is conserved in both complex and simple eukaryotes. CHMP1 contains a predicted bipartite nuclear localisation signal and distributes as distinct forms to the cytoplasm and the nuclear matrix in all cell lines tested. Human CHMP1 is strongly implicated in multivesicular body formation. A multivesicular body is a vesicle-filled endosome that targets proteins to the interior of lysosomes. Immunocytochemistry and biochemical fractionation localise CHMP1 to early endosomes and CHMP1 physically interacts with SKD1/VPS4, a highly conserved protein directly linked to multivesicular body sorting in yeast. Similar to the action of a mutant SKD1 protein, over expression of a fusion derivative of human CHMP1 dilates endosomal compartments and disrupts the normal distribution of several endosomal markers. Genetic studies in Saccharomyces cerevisiae (Baker's yeast) further support a conserved role of CHMP1 in vesicle trafficking. Deletion of CHM1, the budding yeast homologue of CHMP1, results in defective sorting of carboxypeptidases S and Y and produces abnormal, multi-lamellar prevacuolar compartments. This phenotype classifies CHM1 as a member of the class E vacuolar protein sorting genes []. ; GO: 0015031 protein transport; PDB: 2V6X_B 2W2U_D 2GD5_D 3FRT_B 3FRV_A 4ABM_D 3EAB_H 3HTU_D.
Probab=53.92 E-value=62 Score=29.49 Aligned_cols=55 Identities=16% Similarity=0.212 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHH
Q 011024 334 FQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEES 388 (495)
Q Consensus 334 Y~~~R~~A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~~A 388 (495)
...+.+.+...-..-.++..+|..|.++|++..|+.|..+-+.+.+....+....
T Consensus 10 ~~~L~~~~~~le~~i~~~~~~~k~~~~~~~~~~A~~~lk~~k~~~k~~~~~~~~~ 64 (171)
T PF03357_consen 10 IRRLEKQIKRLEKKIKKLEKKAKKAIKKGNKERAKIYLKRKKRLEKQLEKLLNQL 64 (171)
T ss_dssp HHHHHHHHHHHHHHHHHCHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456777778888888999999999999999999999999988877766655433
No 34
>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=53.14 E-value=62 Score=25.59 Aligned_cols=66 Identities=21% Similarity=0.198 Sum_probs=46.5
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCCceEee-CCCeEEEEEe
Q 011024 407 LLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE-GNAGTILIPL 482 (495)
Q Consensus 407 tIDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi~~~e~-~n~G~IlI~L 482 (495)
+||+-|+.==.-+-.++..|..+.. ...|.||+-.. .-..-|..+|++.|+.+.+. ...|.+.|.|
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~---G~~l~v~~d~~-------~~~~di~~~~~~~g~~~~~~~~~~~~~~i~I 68 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPP---GEVLEVLVDDP-------AAVEDIPRWCEENGYEVVEVEEEGGEYRILI 68 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGT---T-EEEEEESST-------THHHHHHHHHHHHTEEEEEEEESSSSEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCC---CCEEEEEECCc-------cHHHHHHHHHHHCCCEEEEEEEeCCEEEEEE
Confidence 6899998888888888888887743 37898887432 12356999999999986543 2667666654
No 35
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=51.12 E-value=63 Score=26.22 Aligned_cols=37 Identities=30% Similarity=0.402 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHH
Q 011024 348 MKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREA 384 (495)
Q Consensus 348 Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrea 384 (495)
+.+|=+.|.+|-+.||.+.|+.+....|.|....+.+
T Consensus 8 ~~~yk~Aa~~AK~~gd~~kAr~~~R~~K~~~~~I~~~ 44 (59)
T smart00685 8 QEQYKQAALQAKRAGDEEKARRHLRIAKQFDDAIKAA 44 (59)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHhhHHHHHHHH
Confidence 3445566778999999998888888888877666544
No 36
>PF13763 DUF4167: Domain of unknown function (DUF4167)
Probab=50.95 E-value=67 Score=27.63 Aligned_cols=39 Identities=28% Similarity=0.480 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHH
Q 011024 348 MKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADE 386 (495)
Q Consensus 348 Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~ 386 (495)
-.+|-+-|.+|-..||.-.|..|.+-+-+|.+++.++..
T Consensus 39 ~EKY~~LArDA~ssGDrV~aEny~QHAeHY~Ril~~~~~ 77 (80)
T PF13763_consen 39 IEKYNQLARDAQSSGDRVLAENYLQHAEHYFRILAAAQA 77 (80)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345666799999999999999999999999998887654
No 37
>PRK10454 PTS system N,N'-diacetylchitobiose-specific transporter subunit IIA; Provisional
Probab=48.99 E-value=69 Score=29.10 Aligned_cols=53 Identities=21% Similarity=0.298 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011024 341 VMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETS 396 (495)
Q Consensus 341 A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~~AA~~If~~r 396 (495)
-.-|+-.-+.||-+|-++.+.||.+.|..|.++|+.....+.+++ .+-|-.+-
T Consensus 24 II~~aG~ArS~~~eAl~~Ak~gdfe~A~~~l~eA~e~l~~AH~~q---t~Liq~Ea 76 (115)
T PRK10454 24 LIINSGQARSLAYAALKQAKQGDFAAAKAMMDQSRMALNEAHLVQ---TKLIEGDQ 76 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHh
Confidence 344455555666679999999999999999999999877777666 45555444
No 38
>PF02255 PTS_IIA: PTS system, Lactose/Cellobiose specific IIA subunit; InterPro: IPR003188 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC []. These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose [, , , ]. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIA PTS system enzymes. This family of proteins normally function as a homotrimer, stabilised by a centrally located metal ion []. Separation into subunits is thought to occur after phosphorylation.; GO: 0005351 sugar:hydrogen symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane; PDB: 3L8R_D 2E2A_B 1E2A_C 3K1S_C 2LRK_C 2LRL_A 2WY2_A 1WCR_A 2WWV_C.
Probab=47.66 E-value=87 Score=27.35 Aligned_cols=49 Identities=22% Similarity=0.295 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 011024 345 RGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETS 396 (495)
Q Consensus 345 ~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~~AA~~If~~r 396 (495)
+-.-+.+|-+|-++.+.||.+.|..+..+|+....++.+.+- +.|-.+-
T Consensus 11 aG~Ars~~~eAl~~a~~~~fe~A~~~l~~a~~~l~~AH~~qt---~llq~ea 59 (96)
T PF02255_consen 11 AGDARSLAMEALKAAREGDFEEAEELLKEADEELLKAHKIQT---ELLQQEA 59 (96)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHH---HHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHh
Confidence 334445666799999999999999999999988777776654 4444444
No 39
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=45.85 E-value=66 Score=29.02 Aligned_cols=42 Identities=14% Similarity=0.070 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHH
Q 011024 340 AVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAR 382 (495)
Q Consensus 340 ~A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmr 382 (495)
..+.+....+.+|+-|..+|..| .++|..|.+.++...++++
T Consensus 6 ~~kia~eRi~~L~~lA~~~~~~~-~~laRrYv~la~~Is~K~r 47 (105)
T COG2023 6 MKKIAAERIDYLYSLAEETFRTG-PDLARRYVKLARRISMKYR 47 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcC-cHHHHHHHHHHHHHHHhhc
Confidence 34556666788999999999999 6777777776666555544
No 40
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=41.76 E-value=19 Score=26.30 Aligned_cols=27 Identities=11% Similarity=0.116 Sum_probs=24.0
Q ss_pred cCHHHHHHHHHHhCCCchhhhhhhhcc
Q 011024 23 FTMQEIALACRNAGRNPDLAGESLCDK 49 (495)
Q Consensus 23 fSl~~ia~Ay~~A~~d~~~A~eiL~~~ 49 (495)
++.+.|..++.+.+||++.|-+.|..+
T Consensus 15 ~~~~~I~~~L~~~~~~ve~ai~~LL~~ 41 (42)
T PF02845_consen 15 LDREVIEAVLQANNGDVEAAIDALLEM 41 (42)
T ss_dssp S-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 788999999999999999999998765
No 41
>PF07743 HSCB_C: HSCB C-terminal oligomerisation domain; InterPro: IPR009073 This entry represents the C-terminal oligomerisation domain found in HscB (heat shock cognate protein B), which is also known as HSC20 (20K heat shock cognate protein). HscB acts as a co-chaperone to regulate the ATPase activity and peptide-binding specificity of the molecular chaperone HscA, also known as HSC66 (HSP70 class). HscB proteins contain two domains, an N-terminal J-domain, which is involved in interactions with HscA, connected by a short loop to the C-terminal oligomerisation domain; the two domains make contact through a hydrophobic interface. The core of the oligomerisation domain is thought to bind and target proteins to HscA and consists of an open, three-helical bundle []. HscB, along with HscA, has been shown to play a role in the biogenesis of iron-sulphur proteins.; GO: 0006457 protein folding; PDB: 1FPO_C 3BVO_B 3HHO_A 3UO2_B 3UO3_B.
Probab=41.66 E-value=1.9e+02 Score=23.49 Aligned_cols=51 Identities=24% Similarity=0.272 Sum_probs=45.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHH
Q 011024 335 QHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREAD 385 (495)
Q Consensus 335 ~~~R~~A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean 385 (495)
..+.....+.....++|.++-..+|..+|...|..+..+=+++.+..++..
T Consensus 27 ~~L~~l~~~~~~~~~~~~~~l~~~f~~~d~~~A~~~~~kLky~~kl~~~ik 77 (78)
T PF07743_consen 27 AELEELKKEIEERIKELIKELAEAFDAKDWEEAKEALRKLKYLQKLLEEIK 77 (78)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHHHHHHHHhc
Confidence 678888888889999999999999999999999999999999988877654
No 42
>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=41.24 E-value=77 Score=25.50 Aligned_cols=66 Identities=14% Similarity=0.028 Sum_probs=46.8
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCCceEee-CCCeEEEEEe
Q 011024 407 LLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE-GNAGTILIPL 482 (495)
Q Consensus 407 tIDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi~~~e~-~n~G~IlI~L 482 (495)
+||+.|+.==.-+-.++..|..+.. ...|.||+... . -..-|..|+++.|+.+... ...|.+.|.+
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 4788888877777778888877642 36788887622 1 2345889999999998642 2577777765
No 43
>COG1447 CelC Phosphotransferase system cellobiose-specific component IIA [Carbohydrate transport and metabolism]
Probab=40.38 E-value=84 Score=28.32 Aligned_cols=39 Identities=21% Similarity=0.279 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHH
Q 011024 345 RGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREA 384 (495)
Q Consensus 345 ~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrea 384 (495)
++.|..+| +|-++.+.|+.+.|..+.++|+..-..+..+
T Consensus 17 G~ArS~~~-eAl~~Ak~g~f~~A~~~i~eA~~~l~eAH~~ 55 (105)
T COG1447 17 GNARSKAY-EALKAAKEGDFEEAEELIQEANDALNEAHHV 55 (105)
T ss_pred ccHhHHHH-HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555 5999999999999999999998755544443
No 44
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=40.01 E-value=1.3e+02 Score=25.84 Aligned_cols=61 Identities=21% Similarity=0.190 Sum_probs=49.4
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 011024 328 NVEEDSFQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNK 390 (495)
Q Consensus 328 ~~~d~~Y~~~R~~A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~~AA~ 390 (495)
-..+..|..+..+.......||++.++=..+...| +.+..|.++++.....+..+..+...
T Consensus 32 ~~ld~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~--~~~~~l~~e~~~lk~~i~~le~~~~~ 92 (108)
T PF02403_consen 32 IELDQERRELQQELEELRAERNELSKEIGKLKKAG--EDAEELKAEVKELKEEIKELEEQLKE 92 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTT--CCTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhCc--ccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35567888888899999999999999999999988 56677888888888888777655443
No 45
>PLN03218 maturation of RBCL 1; Provisional
Probab=39.74 E-value=46 Score=40.40 Aligned_cols=76 Identities=14% Similarity=0.214 Sum_probs=52.0
Q ss_pred CCeeecCCCCHHHHHHHHHHHHHhh-------cCCCCcce------EEEEEecCCCCCCCC-cchHHHHHHHHHcCCceE
Q 011024 405 DLLLDLHDHGAKEAIRLLKCHLSSL-------SGIPTIKY------LKVILEMNDEDTTKG-GRRRRVMKLLEEESIEWT 470 (495)
Q Consensus 405 ~~tIDLHGLhVkEAi~iLk~~L~~l-------~~~~s~~~------LrVItG~G~HS~g~~-k~kpAV~klL~eegi~~~ 470 (495)
.+.||+|.|-|--|.-.|-..|..+ ...|...- =.+.||.|.|+..-. ++..+|..+|++-++.|.
T Consensus 921 ~~~~d~~~~~~~aa~~~l~~wl~~~~~~~~~g~~lp~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~l~~l~~~~~ 1000 (1060)
T PLN03218 921 PIVIDAEELPVFAAEVYLLTILKGLKHRLAAGAKLPNVTILLPTEKKEIYTPKGEKTINLAGRVGQAVAALLRRLGLPYQ 1000 (1060)
T ss_pred ceEEEcccCcchhHHHHHHHHHHHHHHHHhccCcCCcceeeeccccceeeccCCchhHHHHHHHHHHHHHHHHHhCCCCC
Confidence 5899999999999977766555433 33443111 125566666644432 355699999999999999
Q ss_pred eeCCCeEEEE
Q 011024 471 EEGNAGTILI 480 (495)
Q Consensus 471 e~~n~G~IlI 480 (495)
+....|.|.+
T Consensus 1001 ~~~~~g~~~~ 1010 (1060)
T PLN03218 1001 GSESHGKLRI 1010 (1060)
T ss_pred CCCCCCeEEe
Confidence 8765598887
No 46
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=38.44 E-value=41 Score=27.50 Aligned_cols=28 Identities=21% Similarity=0.483 Sum_probs=24.4
Q ss_pred cCHHHHHHHHHhcCCcHHHHHHHHHccc
Q 011024 174 LSRDVIREVLDSCGYDMQKSMSKLIDHS 201 (495)
Q Consensus 174 L~~~vIr~VL~~cGyDv~ks~d~LLd~s 201 (495)
-+-+-|-.+|.-|+.|...+..+||++-
T Consensus 19 hse~eIya~L~ecnMDpnea~qrLL~qD 46 (60)
T PF06972_consen 19 HSEEEIYAMLKECNMDPNEAVQRLLSQD 46 (60)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHHHhcC
Confidence 4566788899999999999999999863
No 47
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=37.91 E-value=29 Score=28.29 Aligned_cols=29 Identities=21% Similarity=0.311 Sum_probs=26.4
Q ss_pred CCccCHHHHHHHHHHhCCCchhhhhhhhcc
Q 011024 20 GSVFTMQEIALACRNAGRNPDLAGESLCDK 49 (495)
Q Consensus 20 gs~fSl~~ia~Ay~~A~~d~~~A~eiL~~~ 49 (495)
|+ .|=+||-+.+++.|-|+|.|++=|...
T Consensus 17 ~~-hse~eIya~L~ecnMDpnea~qrLL~q 45 (60)
T PF06972_consen 17 GC-HSEEEIYAMLKECNMDPNEAVQRLLSQ 45 (60)
T ss_pred cC-CCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence 77 899999999999999999999988754
No 48
>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=37.24 E-value=1.7e+02 Score=23.43 Aligned_cols=64 Identities=23% Similarity=0.331 Sum_probs=44.2
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHc-CC-ceEe-eCCCeEEEEEe
Q 011024 407 LLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEE-SI-EWTE-EGNAGTILIPL 482 (495)
Q Consensus 407 tIDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~ee-gi-~~~e-~~n~G~IlI~L 482 (495)
+||+.|+-..+....+-..+..+.. ...|.||. .|- . . -+...|+.. |+ .|.. ...+|...|++
T Consensus 1 ~LDvR~l~~~~p~~~il~~~~~L~~---Ge~l~lv~---d~~--P---~-pL~~~l~~~~g~~~~~~~~~~~~~w~v~i 67 (69)
T PF10006_consen 1 VLDVRGLPPPEPHERILEALDELPP---GETLELVN---DHD--P---R-PLYPQLEERRGFFSWEYEEQGPGEWRVRI 67 (69)
T ss_pred CEECCCCCCcChHHHHHHHHHcCCC---CCEEEEEe---CCC--C---H-HHHHHHHHhCCCceEEEEEcCCCEEEEEE
Confidence 5899999888888888888887753 36677764 221 1 2 355666666 88 8864 34777777766
No 49
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=36.95 E-value=42 Score=24.65 Aligned_cols=39 Identities=18% Similarity=0.272 Sum_probs=30.7
Q ss_pred hhHHHHHHHHHhcCccccCHHHHHHHHHhcCCcHHHHHHHHHc
Q 011024 157 QKEMEDFLFKLLGEGFQLSRDVIREVLDSCGYDMQKSMSKLID 199 (495)
Q Consensus 157 ~~d~E~FL~~MLG~gf~L~~~vIr~VL~~cGyDv~ks~d~LLd 199 (495)
.=+.|.+|..||.++ -..+..+|..||-|+++-.++|-.
T Consensus 12 ~i~~eHlL~all~~~----~~~~~~il~~~~id~~~l~~~i~~ 50 (53)
T PF02861_consen 12 YISPEHLLLALLEDP----DSIAARILKKLGIDPEQLKAAIEK 50 (53)
T ss_dssp SE-HHHHHHHHHHHT----TSHHHHHHHHTTCHHHHHHHHHHH
T ss_pred cccHHHHHHHHHhhh----hHHHHHHHHHcCCCHHHHHHHHHH
Confidence 336899999999754 358999999999999888777654
No 50
>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=34.52 E-value=1.3e+02 Score=24.04 Aligned_cols=65 Identities=14% Similarity=0.087 Sum_probs=44.8
Q ss_pred eecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCCceEee-CCCeEEEEEe
Q 011024 408 LDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE-GNAGTILIPL 482 (495)
Q Consensus 408 IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi~~~e~-~n~G~IlI~L 482 (495)
||+-|+.==.=+-.++..|..+. ....|.|++.-.. -..-|..|+++.|++.... .+.|.+.+.|
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---PGDTLLVLATDPS-------TTRDIPKFCTFLGHELLAQETEDEPYRYLI 67 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCC---CCCEEEEEeCCCc-------hHHHHHHHHHHcCCEEEEEEEcCCEEEEEE
Confidence 67778776666777788887663 3367888875221 2345889999999988642 2577776655
No 51
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=34.50 E-value=28 Score=25.49 Aligned_cols=22 Identities=32% Similarity=0.199 Sum_probs=18.2
Q ss_pred HHHHHHHHHhCCCchhhhhhhh
Q 011024 26 QEIALACRNAGRNPDLAGESLC 47 (495)
Q Consensus 26 ~~ia~Ay~~A~~d~~~A~eiL~ 47 (495)
+=|..|+.+.+||+..||++|+
T Consensus 8 ~~i~~aL~~~~gn~~~aA~~Lg 29 (42)
T PF02954_consen 8 QLIRQALERCGGNVSKAARLLG 29 (42)
T ss_dssp HHHHHHHHHTTT-HHHHHHHHT
T ss_pred HHHHHHHHHhCCCHHHHHHHHC
Confidence 3467889999999999999996
No 52
>PF14164 YqzH: YqzH-like protein
Probab=34.18 E-value=21 Score=29.46 Aligned_cols=13 Identities=38% Similarity=0.726 Sum_probs=11.4
Q ss_pred HHHHHHhcCCcHH
Q 011024 179 IREVLDSCGYDMQ 191 (495)
Q Consensus 179 Ir~VL~~cGyDv~ 191 (495)
|+.+|.|+|||++
T Consensus 10 i~~~l~QYg~d~~ 22 (64)
T PF14164_consen 10 IINCLRQYGYDVE 22 (64)
T ss_pred HHHHHHHhCCccc
Confidence 6789999999975
No 53
>PRK03954 ribonuclease P protein component 4; Validated
Probab=32.17 E-value=1.5e+02 Score=27.35 Aligned_cols=37 Identities=16% Similarity=0.098 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHH
Q 011024 346 GTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKARE 383 (495)
Q Consensus 346 ~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmre 383 (495)
+.++-+|+.|..++ ..+.++|.+|...++....+++-
T Consensus 20 eRi~~L~~~A~~~~-~~~pelar~Yv~lar~Is~K~ri 56 (121)
T PRK03954 20 ERIDTLFTLAERVF-PYSPELANRYVELALAVQQKAKV 56 (121)
T ss_pred HHHHHHHHHHHHHh-hcCHHHHHHHHHHHHHHHHHhcc
Confidence 55667999998888 55788888888887776665553
No 54
>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=31.84 E-value=86 Score=29.73 Aligned_cols=38 Identities=5% Similarity=0.051 Sum_probs=30.3
Q ss_pred cCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCC
Q 011024 410 LHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTT 450 (495)
Q Consensus 410 LHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g 450 (495)
+-|.+|.+|+.+|+--|..-..+ .+.+-.-|.|+|+..
T Consensus 33 IrG~~v~~A~~~L~~V~~~k~~v---Pf~r~~~~~g~~~~~ 70 (150)
T TIGR01038 33 IRGMELDKARKYLEDVIEMKRAV---PFRRYNGKVGHRRGL 70 (150)
T ss_pred HcCCcHHHHHHHHHHHHhccccc---ceeeecCCccccccc
Confidence 36999999999999888765555 456677899999985
No 55
>PRK01773 hscB co-chaperone HscB; Provisional
Probab=31.23 E-value=2.3e+02 Score=27.35 Aligned_cols=54 Identities=13% Similarity=0.095 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHH
Q 011024 333 SFQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADE 386 (495)
Q Consensus 333 ~Y~~~R~~A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~ 386 (495)
+...+.+...+....+.+|.++-.+||..+|.+.|..+..+=+++.++..+.+.
T Consensus 112 d~~~L~~l~~~v~~~~~~~~~~l~~~~~~~d~~~A~~~~~rL~y~~kl~~ei~~ 165 (173)
T PRK01773 112 DEDALTAFSKEIKQEQQAILTELSTALNSQQWQQASQINDRLRFIKKLIIEIER 165 (173)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456688888888889999999999999999999999999999999988887754
No 56
>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=30.79 E-value=62 Score=28.55 Aligned_cols=31 Identities=13% Similarity=0.004 Sum_probs=25.6
Q ss_pred EEEEecCCCCCCCCcchHHHHHHHHHcCCceEee
Q 011024 439 KVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE 472 (495)
Q Consensus 439 rVItG~G~HS~g~~k~kpAV~klL~eegi~~~e~ 472 (495)
-||+|+|.+-. .+.|.+.++|++.||.....
T Consensus 55 iliiGTG~~~~---~~~~~~~~~l~~~gI~vE~m 85 (109)
T cd00248 55 ILLIGTGAEIA---FLPRALRAALRAAGIGVEVM 85 (109)
T ss_pred EEEEcCCCCCC---cCCHHHHHHHHHcCCeEEEe
Confidence 59999999863 45678999999999987665
No 57
>PRK11018 hypothetical protein; Provisional
Probab=27.30 E-value=3.6e+02 Score=22.30 Aligned_cols=68 Identities=13% Similarity=0.046 Sum_probs=46.5
Q ss_pred CCeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCCceEe-eCCCeEEEEEe
Q 011024 405 DLLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTE-EGNAGTILIPL 482 (495)
Q Consensus 405 ~~tIDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi~~~e-~~n~G~IlI~L 482 (495)
..+||+-|+.==.=+-.++..|..+. ....|.||+-.. .-..-|..++++.|++... +...|.+.|.|
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~---~G~~L~V~~d~~-------~a~~di~~~~~~~G~~v~~~~~~~g~~~~~I 76 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLK---KGEILEVVSDCP-------QSINNIPLDARNHGYTVLDIQQDGPTIRYLI 76 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCC---CCCEEEEEeCCc-------cHHHHHHHHHHHcCCEEEEEEecCCeEEEEE
Confidence 47899999986666666677776654 336788876421 1233588999999998753 33567777665
No 58
>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=26.99 E-value=75 Score=28.59 Aligned_cols=51 Identities=8% Similarity=-0.009 Sum_probs=32.6
Q ss_pred HHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCCceEee
Q 011024 418 AIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE 472 (495)
Q Consensus 418 Ai~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi~~~e~ 472 (495)
.-++-.++|..+..... +.=-||+|+|.+ ...+.|.+.++|++.|+.....
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 33444555554432211 222489999998 3346778999999999986654
No 59
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=26.49 E-value=32 Score=34.62 Aligned_cols=29 Identities=31% Similarity=0.604 Sum_probs=24.7
Q ss_pred hhHHHHHHHHHhcCccccCHHHHHHHHHh
Q 011024 157 QKEMEDFLFKLLGEGFQLSRDVIREVLDS 185 (495)
Q Consensus 157 ~~d~E~FL~~MLG~gf~L~~~vIr~VL~~ 185 (495)
.++-|+|=..+|+++|.+|.++||.||..
T Consensus 24 ~~~p~~~t~~~Lae~F~vspe~irrILks 52 (225)
T PF06413_consen 24 KEDPEEWTVERLAESFKVSPEAIRRILKS 52 (225)
T ss_pred HhCccccCHHHHHhhCCCCHHHHHHHHhc
Confidence 44556688999999999999999999954
No 60
>TIGR02977 phageshock_pspA phage shock protein A. Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.
Probab=26.39 E-value=4.2e+02 Score=26.02 Aligned_cols=50 Identities=18% Similarity=0.125 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHH
Q 011024 334 FQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKARE 383 (495)
Q Consensus 334 Y~~~R~~A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmre 383 (495)
...+.+...++...-.++.++|..|...|+-.+|+.-..+-+.|...+..
T Consensus 54 ~k~~e~~~~~~~~~~~~~~~~A~~Al~~G~EdLAr~Al~~k~~~~~~~~~ 103 (219)
T TIGR02977 54 KKELERRVSRLEAQVADWQEKAELALSKGREDLARAALIEKQKAQELAEA 103 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 33455555666677788999999999999999999876665555554433
No 61
>PF09644 Mg296: Mg296 protein; InterPro: IPR019097 This protein of 129 residues is expressed in bacteria. It consists of three identical chains of five alpha helices. Two copies of each chain associate into a complex of six units of possible biological significance but of unknown function. ; PDB: 2I15_A.
Probab=26.08 E-value=18 Score=32.69 Aligned_cols=25 Identities=20% Similarity=0.402 Sum_probs=17.8
Q ss_pred hHHHHHHHHHhcCccccCHHHHHHH
Q 011024 158 KEMEDFLFKLLGEGFQLSRDVIREV 182 (495)
Q Consensus 158 ~d~E~FL~~MLG~gf~L~~~vIr~V 182 (495)
+|.-=|+-+||||+|=+.-.||++|
T Consensus 47 dd~~FF~Kpm~sd~~fi~~evikql 71 (121)
T PF09644_consen 47 DDQDFFEKPMLSDLFFIKNEVIKQL 71 (121)
T ss_dssp -S-HHHHHHHHHHHHHHHHHHH---
T ss_pred chhhHHHhhhhhhHHHHHHHHHHHH
Confidence 4445588999999999999999886
No 62
>TIGR00714 hscB Fe-S protein assembly co-chaperone HscB. This model describes the small subunit, Hsc20 (20K heat shock cognate protein) of a pair of proteins Hsc66-Hsc20, related to the DnaK-DnaJ heat shock proteins, which also serve as molecular chaperones. Hsc20, unlike DnaJ, appears not to have chaperone activity on its own, but to act solely as a regulatory subunit for Hsc66 (i.e., to be a co-chaperone). The gene for Hsc20 in E. coli, hscB, is not induced by heat shock.
Probab=25.83 E-value=3.8e+02 Score=25.22 Aligned_cols=53 Identities=8% Similarity=0.131 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHH
Q 011024 334 FQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADE 386 (495)
Q Consensus 334 Y~~~R~~A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~ 386 (495)
...+.....+....+.+|...-.+||..+|.+.|..+..+=+++..+..+.++
T Consensus 99 ~~~L~~l~~~~~~~~~~~~~~l~~~~~~~d~~~A~~~~~kLky~~kl~~~i~~ 151 (157)
T TIGR00714 99 EARLESFIKRVKKMFQTRHQLLVEQLDNQTWAAAADYTRKLRFLDKLRSSAEQ 151 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677777888888899999999999999999999999999999988887764
No 63
>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=24.94 E-value=94 Score=27.51 Aligned_cols=31 Identities=10% Similarity=0.067 Sum_probs=25.0
Q ss_pred EEEEecCCCCCCCCcchHHHHHHHHHcCCceEee
Q 011024 439 KVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE 472 (495)
Q Consensus 439 rVItG~G~HS~g~~k~kpAV~klL~eegi~~~e~ 472 (495)
-||+|+|.+-.- +.|++.++|++.|+.....
T Consensus 55 iliiGTG~~~~~---~~~~~~~~l~~~gi~vE~m 85 (109)
T cd05560 55 VILLGTGERQRF---PPPALLAPLLARGIGVEVM 85 (109)
T ss_pred EEEEecCCCCCc---CCHHHHHHHHHcCCeEEEE
Confidence 599999998542 3578999999999987665
No 64
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=24.22 E-value=1.1e+02 Score=26.60 Aligned_cols=48 Identities=10% Similarity=0.280 Sum_probs=33.9
Q ss_pred hhHHHHHHHHHhcCccc---------cCHHHHHHHHHhcCCcHHHHHHHHHccccccc
Q 011024 157 QKEMEDFLFKLLGEGFQ---------LSRDVIREVLDSCGYDMQKSMSKLIDHSAETL 205 (495)
Q Consensus 157 ~~d~E~FL~~MLG~gf~---------L~~~vIr~VL~~cGyDv~ks~d~LLd~s~~~~ 205 (495)
..-+++|+-.+.|++-. +...+|+++|.+||+++.++. .+|.++..++
T Consensus 29 ~~~l~~~~~~l~~~~~~~~~~~~l~~~Er~~i~~aL~~~~gn~s~AA-r~LGIsRsTL 85 (95)
T PRK00430 29 KQALKNYFAQLNGQDVNDLYELVLAEVEAPLLDMVMQYTRGNQTRAA-LMLGINRGTL 85 (95)
T ss_pred HHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHHHHHcCCCHHHHH-HHhCCCHHHH
Confidence 45556666666555431 345689999999999999986 6777776654
No 65
>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].
Probab=23.69 E-value=6.5e+02 Score=24.34 Aligned_cols=53 Identities=21% Similarity=0.155 Sum_probs=39.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHH
Q 011024 332 DSFQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREA 384 (495)
Q Consensus 332 ~~Y~~~R~~A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrea 384 (495)
.....+.+...++...-.++..+|..|...|+-.+|..+..+=..+...+..+
T Consensus 51 a~~~~le~~~~~~~~~~~~~~~~A~~Al~~g~edLAr~al~~k~~~e~~~~~l 103 (221)
T PF04012_consen 51 ANQKRLERKLDEAEEEAEKWEKQAELALAAGREDLAREALQRKADLEEQAERL 103 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34455666666777777889999999999999999988777666555444433
No 66
>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]
Probab=23.03 E-value=5.6e+02 Score=25.78 Aligned_cols=47 Identities=17% Similarity=0.162 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHH
Q 011024 339 TAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREAD 385 (495)
Q Consensus 339 ~~A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean 385 (495)
+...+......++..+|..|...|+-.+|.+..++-+.|........
T Consensus 59 ~~~~~~~~~~~k~e~~A~~Al~~g~E~LAr~al~~~~~le~~~~~~~ 105 (225)
T COG1842 59 RKLEEAQARAEKLEEKAELALQAGNEDLAREALEEKQSLEDLAKALE 105 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445556677899999999999999999999888877766665443
No 67
>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=22.86 E-value=3.9e+02 Score=21.44 Aligned_cols=65 Identities=18% Similarity=0.063 Sum_probs=42.1
Q ss_pred eecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCCceEe-eCCCeEEEEEe
Q 011024 408 LDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTE-EGNAGTILIPL 482 (495)
Q Consensus 408 IDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi~~~e-~~n~G~IlI~L 482 (495)
||+-|+.==.=+-.++..|..+. ....|.|++-.. .-..-|.+++++.|+++.+ ....|.+.|.|
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 66777665555566677777653 336788876321 1234588999999998864 22457776655
No 68
>PRK01356 hscB co-chaperone HscB; Provisional
Probab=22.10 E-value=4.9e+02 Score=24.80 Aligned_cols=53 Identities=15% Similarity=0.105 Sum_probs=44.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHH
Q 011024 335 QHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEE 387 (495)
Q Consensus 335 ~~~R~~A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmrean~~ 387 (495)
..+.+...+.-...+.|.++-.+||..+|...|..+..+=+++.++..+...+
T Consensus 109 ~~L~~l~~~~~~~~~~~~~~l~~~f~~~d~~~A~~~~~~L~y~~kl~~~i~~k 161 (166)
T PRK01356 109 SDLEKIKNKYELMYKNEIDSLKQAFEEQNLSDATIKTSKLKYIGTLLNKLQEK 161 (166)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34677777777788889999999999999999999999999998888876653
No 69
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=22.07 E-value=4.7e+02 Score=26.28 Aligned_cols=51 Identities=22% Similarity=0.234 Sum_probs=42.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHH
Q 011024 332 DSFQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAR 382 (495)
Q Consensus 332 ~~Y~~~R~~A~~h~~~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~kmr 382 (495)
++++..|.+|.+..+..-.+...|.-+..+||.+.|..--+++...-.+.+
T Consensus 13 ~e~d~~REE~l~lsRei~r~s~~aI~~~H~~~~eeA~~~l~~a~~~v~~Lk 63 (204)
T COG2178 13 QEKDKAREEALKLSREIVRLSGEAIFLLHRGDFEEAEKKLKKASEAVEKLK 63 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999999999999999999988776666655444443
No 70
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=21.92 E-value=1.2e+02 Score=24.73 Aligned_cols=33 Identities=12% Similarity=0.073 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHH
Q 011024 347 TMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYE 379 (495)
Q Consensus 347 ~Rne~f~kAa~AY~kGd~a~A~~LSeqGk~~~~ 379 (495)
..+-+|+.|...+..++.+.|.+|....+...+
T Consensus 2 Ri~~L~~~a~~~~~~~~~~lsr~y~~~~~~i~~ 34 (85)
T PF04032_consen 2 RINFLYQAAHLLLADGSPSLSRHYMKLMRKISK 34 (85)
T ss_dssp HHHHHHHHHH-HHCCC-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Confidence 456778877778999999988888776665444
No 71
>KOG2617 consensus Citrate synthase [Energy production and conversion]
Probab=21.76 E-value=64 Score=35.44 Aligned_cols=58 Identities=14% Similarity=0.107 Sum_probs=37.2
Q ss_pred eecCCCCHHHHHHHHHHHHHhhcCCCC-----------cceEEEEEecCCCCCCCC-cchHHHHHHHHHc
Q 011024 408 LDLHDHGAKEAIRLLKCHLSSLSGIPT-----------IKYLKVILEMNDEDTTKG-GRRRRVMKLLEEE 465 (495)
Q Consensus 408 IDLHGLhVkEAi~iLk~~L~~l~~~~s-----------~~~LrVItG~G~HS~g~~-k~kpAV~klL~ee 465 (495)
=-||||-.+|.|++|..-...+....+ ...=+||+|.||----+. .+-.++.+|-.++
T Consensus 287 GPLHGlAnqEvl~~L~~~~~Eig~~~s~e~ikeyiw~~ln~~rvvpGyGHavlr~tDPR~~~~~efA~k~ 356 (458)
T KOG2617|consen 287 GPLHGLANQEVLRFLGKLIEEIGKDLSKENIKEYIWKTLNSGRVVPGYGHAVLRKTDPRYKVQREFALKH 356 (458)
T ss_pred cccccCchHHHHHHHHHhHHHhccccchhhhhHhhHHhhcccccccccccccccCCCchhhHHHHHHHhc
Confidence 359999999999999866555442221 123469999998643222 2333566666665
No 72
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=21.73 E-value=1.8e+02 Score=29.30 Aligned_cols=46 Identities=22% Similarity=0.280 Sum_probs=39.5
Q ss_pred ccchhHHHHHHHHHhc-CccccCHHHHHHHHHhcCCcHHHHHHHHHc
Q 011024 154 DHLQKEMEDFLFKLLG-EGFQLSRDVIREVLDSCGYDMQKSMSKLID 199 (495)
Q Consensus 154 ~~~~~d~E~FL~~MLG-~gf~L~~~vIr~VL~~cGyDv~ks~d~LLd 199 (495)
.+..+++.++|-.++. +|..++.++++..+..||.|+.+++..|-.
T Consensus 183 ~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~ 229 (337)
T PRK12402 183 APTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQT 229 (337)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3457899999998775 688999999999999999999999887754
No 73
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=21.55 E-value=1.1e+02 Score=21.44 Aligned_cols=31 Identities=16% Similarity=0.303 Sum_probs=27.8
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 011024 330 EEDSFQHLRTAVMEYRGTMKEYCKAAIDAFA 360 (495)
Q Consensus 330 ~d~~Y~~~R~~A~~h~~~Rne~f~kAa~AY~ 360 (495)
.++.|..+.+.|.+....+.++...|...|.
T Consensus 7 ~~~~~~~l~~~a~~~g~s~s~~ir~ai~~~l 37 (39)
T PF01402_consen 7 PDELYERLDELAKELGRSRSELIREAIREYL 37 (39)
T ss_dssp EHHHHHHHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4578999999999999999999999988875
No 74
>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=21.41 E-value=1.1e+02 Score=26.78 Aligned_cols=31 Identities=10% Similarity=0.005 Sum_probs=23.4
Q ss_pred EEEEecCCCCCCCCcchHHHHHHHHHcCCceEee
Q 011024 439 KVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE 472 (495)
Q Consensus 439 rVItG~G~HS~g~~k~kpAV~klL~eegi~~~e~ 472 (495)
-||+|+|.. ...+.|.+.++|++.||.....
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 3446789999999999976554
No 75
>PF12854 PPR_1: PPR repeat
Probab=20.96 E-value=78 Score=21.99 Aligned_cols=27 Identities=22% Similarity=0.117 Sum_probs=22.4
Q ss_pred cCHHHHHHHHHHhCCCchhhhhhhhccc
Q 011024 23 FTMQEIALACRNAGRNPDLAGESLCDKQ 50 (495)
Q Consensus 23 fSl~~ia~Ay~~A~~d~~~A~eiL~~~~ 50 (495)
+|..-+-.+||++| +++.|-++|-.|+
T Consensus 8 ~ty~~lI~~~Ck~G-~~~~A~~l~~~M~ 34 (34)
T PF12854_consen 8 VTYNTLIDGYCKAG-RVDEAFELFDEMK 34 (34)
T ss_pred hHHHHHHHHHHHCC-CHHHHHHHHHhCc
Confidence 66777899999975 7999999998774
No 76
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=20.95 E-value=5.3e+02 Score=24.84 Aligned_cols=55 Identities=20% Similarity=0.199 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CChHHHHHHHHHHHHHHHHHHHHHHH
Q 011024 333 SFQHLRTAVMEYRGTMKEYCKAAIDAFAQ-GDHVQAEKLLEQGKFFYEKAREADEE 387 (495)
Q Consensus 333 ~Y~~~R~~A~~h~~~Rne~f~kAa~AY~k-Gd~a~A~~LSeqGk~~~~kmrean~~ 387 (495)
+...++....+.......|.++..++|.. +|...|..+..+=+++.+...+.+..
T Consensus 115 d~~~L~~l~~e~~~~~~~~~~~l~~~~~~~~d~~~A~~~~~kL~y~~kl~~ei~~~ 170 (176)
T PRK03578 115 DVDALDALLAELRDERRERYAELGALLDSRGDDQAAAEAVRQLMFIEKLAQEIGAA 170 (176)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35678888888899999999999999988 88899999999999998888877643
No 77
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=20.80 E-value=3.6e+02 Score=22.49 Aligned_cols=69 Identities=13% Similarity=0.079 Sum_probs=48.3
Q ss_pred CCeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCcchHHHHHHHHHcCCceEe-eCCCeEEEEEeC
Q 011024 405 DLLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTE-EGNAGTILIPLD 483 (495)
Q Consensus 405 ~~tIDLHGLhVkEAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~eegi~~~e-~~n~G~IlI~L~ 483 (495)
..+||+-|+.==.=+-.+++.|..+. ....|.||+.-. . -..-|..++++.|++... +...|.+.+.|.
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~---~G~~l~V~~dd~-~------~~~di~~~~~~~G~~~~~~~~~~g~~~~~I~ 78 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQ---PGETLLIIADDP-A------TTRDIPSFCRFMDHELLAQETEQLPYRYLIR 78 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCC---CCCEEEEEeCCc-c------HHHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 47899999987777777888887764 236788887521 1 234588899999998753 225677766653
No 78
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=20.07 E-value=1.1e+02 Score=25.84 Aligned_cols=34 Identities=12% Similarity=0.126 Sum_probs=28.6
Q ss_pred ccccCHHHHHHHHHhcCCcHHHHHHHHHcccccc
Q 011024 171 GFQLSRDVIREVLDSCGYDMQKSMSKLIDHSAET 204 (495)
Q Consensus 171 gf~L~~~vIr~VL~~cGyDv~ks~d~LLd~s~~~ 204 (495)
.|.+++..|-++|-.|.+|+..+...+|+.....
T Consensus 6 ~~g~~~~~v~~aL~~tSgd~~~a~~~vl~~l~~g 39 (87)
T PF11626_consen 6 ELGYSREFVTHALYATSGDPELARRFVLNFLQAG 39 (87)
T ss_dssp HHTB-HHHHHHHHHHTTTBHHHHHHHHHHCHCHT
T ss_pred HhCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHcC
Confidence 4678999999999999999999999899886543
No 79
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=20.01 E-value=1.5e+02 Score=22.77 Aligned_cols=26 Identities=15% Similarity=0.387 Sum_probs=20.6
Q ss_pred chHHHHHHHHHcCCceEeeCCCeEEEE
Q 011024 454 RRRRVMKLLEEESIEWTEEGNAGTILI 480 (495)
Q Consensus 454 ~kpAV~klL~eegi~~~e~~n~G~IlI 480 (495)
.+.+..+.|+++||.|... ..|..+|
T Consensus 16 ~~~~Q~~~L~~~Gi~~~~~-~~G~p~V 41 (47)
T PF13986_consen 16 RPSKQIRWLRRNGIPFVVR-ADGRPIV 41 (47)
T ss_pred CHHHHHHHHHHCCCeeEEC-CCCCEEe
Confidence 4557899999999999887 5676555
No 80
>PF14863 Alkyl_sulf_dimr: Alkyl sulfatase dimerisation; PDB: 2YHE_C 2CG2_A 2CG3_A 2CFU_A 2CFZ_A.
Probab=20.01 E-value=4.2e+02 Score=24.72 Aligned_cols=55 Identities=24% Similarity=0.239 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHH---HHHHHHHHHHHHcCChHHHHHHHHHHHHHH---HHHHHHHHHHHHH
Q 011024 337 LRTAVMEYRGTM---KEYCKAAIDAFAQGDHVQAEKLLEQGKFFY---EKAREADEESNKK 391 (495)
Q Consensus 337 ~R~~A~~h~~~R---ne~f~kAa~AY~kGd~a~A~~LSeqGk~~~---~kmrean~~AA~~ 391 (495)
-...|.++...+ ....++|.+++.+||..-|-+|.+.--... +.++++-..|-+.
T Consensus 56 p~~~A~~~v~l~GG~d~vl~~A~~~~~~gd~~wA~~L~d~l~~adp~n~~ar~l~A~al~~ 116 (141)
T PF14863_consen 56 PEEEAKRYVELAGGADKVLERAQAALAAGDYQWAAELLDHLVFADPDNEEARQLKADALEQ 116 (141)
T ss_dssp HHHHHHHHHHHTTCHHHHHHHHHHHHHCT-HHHHHHHHHHHHHH-TT-HHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHH
Confidence 345566666665 789999999999999999999988764433 3344444443333
Done!