Query 010943
Match_columns 497
No_of_seqs 122 out of 244
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 06:19:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010943.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010943hhsearch_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 3.8E-17 8.2E-22 131.5 1.0 65 335-401 1-65 (66)
2 smart00463 SMR Small MutS-rela 99.6 6.4E-15 1.4E-19 121.3 7.8 78 408-485 2-80 (80)
3 PF01713 Smr: Smr domain; Int 99.5 3E-14 6.5E-19 118.1 5.2 73 410-485 1-83 (83)
4 KOG2401 Predicted MutS-related 98.9 7.6E-10 1.6E-14 118.1 5.9 402 20-474 24-429 (448)
5 COG2840 Uncharacterized protei 98.0 1.2E-05 2.5E-10 77.5 7.4 79 406-486 95-180 (184)
6 PRK04946 hypothetical protein; 98.0 1.7E-05 3.7E-10 76.2 7.1 76 406-487 94-175 (181)
7 PRK00409 recombination and DNA 97.4 0.00029 6.4E-09 80.7 7.7 73 407-485 704-782 (782)
8 TIGR01069 mutS2 MutS2 family p 97.3 0.00048 1E-08 78.9 7.2 72 407-484 693-770 (771)
9 KOG2401 Predicted MutS-related 96.2 0.0094 2E-07 64.3 6.9 356 23-474 16-378 (448)
10 PF02845 CUE: CUE domain; Int 96.0 0.015 3.4E-07 42.8 4.9 40 159-201 3-42 (42)
11 smart00546 CUE Domain that may 94.9 0.069 1.5E-06 39.4 5.3 40 159-201 4-43 (43)
12 cd00194 UBA Ubiquitin Associat 94.8 0.058 1.2E-06 38.4 4.5 35 163-199 4-38 (38)
13 PF00627 UBA: UBA/TS-N domain; 89.9 0.34 7.3E-06 34.7 2.9 31 162-197 7-37 (37)
14 smart00165 UBA Ubiquitin assoc 89.7 0.4 8.8E-06 33.9 3.2 25 174-198 13-37 (37)
15 PF08938 HBS1_N: HBS1 N-termin 83.6 0.67 1.5E-05 38.8 1.7 39 165-204 36-74 (79)
16 cd00194 UBA Ubiquitin Associat 83.5 1.1 2.3E-05 31.8 2.5 29 20-48 10-38 (38)
17 PF03474 DMA: DMRTA motif; In 81.5 1.5 3.4E-05 32.7 2.7 26 173-198 14-39 (39)
18 PF00627 UBA: UBA/TS-N domain; 80.4 1.6 3.4E-05 31.2 2.5 25 22-46 13-37 (37)
19 smart00165 UBA Ubiquitin assoc 78.2 2.1 4.6E-05 30.2 2.5 28 20-47 10-37 (37)
20 PF14346 DUF4398: Domain of un 70.6 32 0.00068 29.7 8.4 42 345-386 40-81 (103)
21 PF14555 UBA_4: UBA-like domai 68.7 14 0.0003 27.3 5.0 38 158-200 2-39 (43)
22 COG1193 Mismatch repair ATPase 67.4 8.1 0.00018 45.0 5.2 72 407-484 676-753 (753)
23 PF02954 HTH_8: Bacterial regu 65.5 5 0.00011 29.5 2.1 31 174-205 5-35 (42)
24 cd00291 SirA_YedF_YeeD SirA, Y 63.5 19 0.00041 28.2 5.2 66 409-484 1-67 (69)
25 PF11848 DUF3368: Domain of un 63.0 9.7 0.00021 29.0 3.3 29 159-187 20-48 (48)
26 PF01963 TraB: TraB family; I 61.2 65 0.0014 31.3 9.6 89 345-470 167-255 (259)
27 PRK09591 celC cellobiose phosp 60.6 76 0.0016 28.3 9.0 69 343-419 13-81 (104)
28 PRK01905 DNA-binding protein F 60.3 14 0.00029 30.7 4.0 49 156-205 10-67 (77)
29 cd00215 PTS_IIA_lac PTS_IIA, P 57.7 44 0.00096 29.3 6.9 50 346-398 11-60 (97)
30 TIGR00823 EIIA-LAC phosphotran 56.8 46 0.001 29.3 6.9 43 346-388 13-55 (99)
31 cd03421 SirA_like_N SirA_like_ 54.0 62 0.0013 25.6 6.7 65 409-484 1-65 (67)
32 PF04505 Dispanin: Interferon- 53.6 14 0.00031 31.3 3.1 27 355-381 42-68 (82)
33 PF03357 Snf7: Snf7; InterPro 53.5 63 0.0014 29.4 7.6 54 336-389 10-63 (171)
34 PLN03218 maturation of RBCL 1; 50.8 25 0.00053 42.7 5.6 77 407-483 921-1011(1060)
35 PRK10454 PTS system N,N'-diace 49.6 66 0.0014 29.2 6.9 53 343-398 24-76 (115)
36 PF02255 PTS_IIA: PTS system, 48.1 84 0.0018 27.5 7.1 49 347-398 11-59 (96)
37 PF01206 TusA: Sulfurtransfera 47.8 85 0.0018 24.8 6.6 66 409-484 2-68 (70)
38 COG2023 RPR2 RNase P subunit R 47.6 59 0.0013 29.3 6.1 42 342-384 6-47 (105)
39 PF13763 DUF4167: Domain of un 47.6 81 0.0018 27.2 6.7 38 351-388 40-77 (80)
40 smart00685 DM14 Repeats in fly 44.2 93 0.002 25.3 6.2 39 348-386 5-44 (59)
41 PF02845 CUE: CUE domain; Int 40.3 20 0.00044 26.2 1.8 27 23-49 15-41 (42)
42 cd03420 SirA_RHOD_Pry_redox Si 37.8 94 0.002 25.0 5.5 66 409-484 1-67 (69)
43 PF06972 DUF1296: Protein of u 37.7 42 0.00091 27.4 3.3 28 174-201 19-46 (60)
44 PF10006 DUF2249: Uncharacteri 37.2 1.7E+02 0.0036 23.5 6.8 64 409-484 1-67 (69)
45 COG1447 CelC Phosphotransferas 37.0 1.1E+02 0.0024 27.6 6.2 38 348-386 18-55 (105)
46 PF02403 Seryl_tRNA_N: Seryl-t 36.9 1.6E+02 0.0035 25.4 7.2 60 330-391 32-91 (108)
47 PF06972 DUF1296: Protein of u 36.9 30 0.00065 28.3 2.4 29 20-49 17-45 (60)
48 PF02861 Clp_N: Clp amino term 36.3 44 0.00096 24.6 3.1 39 157-199 12-50 (53)
49 PF02954 HTH_8: Bacterial regu 34.0 29 0.00062 25.5 1.7 22 26-47 8-29 (42)
50 PF07743 HSCB_C: HSCB C-termin 33.7 2.6E+02 0.0056 22.7 8.3 51 337-387 27-77 (78)
51 PF14164 YqzH: YqzH-like prote 33.7 22 0.00047 29.4 1.1 13 179-191 10-22 (64)
52 PRK03954 ribonuclease P protei 32.2 1.4E+02 0.0031 27.4 6.3 38 347-385 19-56 (121)
53 cd03423 SirA SirA (also known 29.4 1.8E+02 0.004 23.2 5.9 65 410-484 2-67 (69)
54 PRK01773 hscB co-chaperone Hsc 29.0 2.9E+02 0.0063 26.6 8.1 54 335-388 112-165 (173)
55 cd00248 Mth938-like Mth938-lik 28.3 72 0.0016 28.2 3.6 31 441-474 55-85 (109)
56 TIGR01038 L22_arch ribosomal p 27.5 1.1E+02 0.0024 29.1 4.8 38 412-452 33-70 (150)
57 PRK11018 hypothetical protein; 26.5 3.7E+02 0.0081 22.2 7.6 68 407-484 8-76 (78)
58 TIGR00714 hscB Fe-S protein as 26.1 3.3E+02 0.0071 25.7 7.8 53 336-388 99-151 (157)
59 PF06413 Neugrin: Neugrin; In 26.0 32 0.0007 34.6 1.1 29 157-185 24-52 (225)
60 PF09644 Mg296: Mg296 protein; 25.9 19 0.0004 32.7 -0.5 25 158-182 47-71 (121)
61 cd05125 Mth938_2P1-like Mth938 25.6 85 0.0018 28.3 3.6 51 420-474 37-87 (114)
62 TIGR02977 phageshock_pspA phag 24.8 4.4E+02 0.0096 25.9 8.8 48 337-384 55-102 (219)
63 PRK00430 fis global DNA-bindin 23.8 1.1E+02 0.0025 26.5 4.0 48 157-205 29-85 (95)
64 PF10231 DUF2315: Uncharacteri 22.1 6.4E+02 0.014 23.4 8.8 34 330-363 26-63 (126)
65 PF04012 PspA_IM30: PspA/IM30 22.1 7.2E+02 0.016 24.0 9.6 52 334-385 51-102 (221)
66 cd05560 Xcc1710_like Xcc1710_l 22.0 1.1E+02 0.0025 27.0 3.7 31 441-474 55-85 (109)
67 cd05126 Mth938 Mth938 domain. 21.7 1.2E+02 0.0027 27.3 3.9 51 411-474 42-92 (117)
68 cd03422 YedF YedF is a bacteri 21.5 4.3E+02 0.0093 21.2 6.7 65 410-484 2-67 (69)
69 PRK12402 replication factor C 21.5 1.8E+02 0.0039 29.2 5.5 46 154-199 183-229 (337)
70 COG2250 Uncharacterized conser 21.1 3.6E+02 0.0077 24.7 6.8 39 340-378 3-41 (132)
71 COG1842 PspA Phage shock prote 20.7 6.7E+02 0.014 25.3 9.2 44 343-386 61-104 (225)
72 PF13986 DUF4224: Domain of un 20.4 1.4E+02 0.0031 22.9 3.4 26 456-482 16-41 (47)
73 COG2178 Predicted RNA-binding 20.4 5.3E+02 0.012 25.9 8.2 51 334-384 13-63 (204)
74 PF04430 DUF498: Protein of un 20.2 1.1E+02 0.0025 26.7 3.3 31 441-474 56-86 (110)
75 PF12854 PPR_1: PPR repeat 20.2 81 0.0017 22.0 1.9 27 23-50 8-34 (34)
76 PF04032 Rpr2: RNAse P Rpr2/Rp 20.0 1.4E+02 0.0031 24.4 3.7 34 349-382 2-35 (85)
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=99.64 E-value=3.8e-17 Score=131.48 Aligned_cols=65 Identities=32% Similarity=0.502 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Q 010943 335 SFQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETSGRN 401 (497)
Q Consensus 335 ~Y~~~R~~A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean~~AA~~If~~r~~N 401 (497)
+|+.+|.+|.+|++.|++||++|++||++||++.|++||++||.|.++|+++|.+||++||..+ |
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=99.57 E-value=6.4e-15 Score=121.28 Aligned_cols=78 Identities=27% Similarity=0.344 Sum_probs=68.2
Q ss_pred CeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCC-CCccHHHHHHHHHHcCCceEeeCCCeEEEEEeC
Q 010943 408 LLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTT-KGGRRRRVMKLLEEESIEWTEEGNAGTILIPLD 485 (497)
Q Consensus 408 ~tIDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g-~~k~kpAV~klL~kegi~w~e~~n~GvIlI~L~ 485 (497)
++|||||++|.||+..|+..|..+...+..+.+.||||+|+||.+ ...++++|.++|...+|.|.++.|.|+++|.|.
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 689999999999999999999988764322689999999999984 456888999999999999987569999999874
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=99.48 E-value=3e-14 Score=118.07 Aligned_cols=73 Identities=29% Similarity=0.449 Sum_probs=58.5
Q ss_pred eecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCCceEe----------eCCCeE
Q 010943 410 LDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTE----------EGNAGT 479 (497)
Q Consensus 410 IDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi~w~e----------~~n~Gv 479 (497)
|||||++++||++.|+..|..+... ....++||||+|+||.++. ++++|.++|.+ ++.|.+ ..|.|+
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 8999999999999999999987654 3489999999999999886 99999999988 766543 139999
Q ss_pred EEEEeC
Q 010943 480 ILIPLD 485 (497)
Q Consensus 480 IlI~L~ 485 (497)
++|.|.
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=98.95 E-value=7.6e-10 Score=118.11 Aligned_cols=402 Identities=13% Similarity=0.042 Sum_probs=216.0
Q ss_pred CCccCHHHHHHHHHHhCCCchhhhhhhccccCCCCCcccCCCCCccCCCCCCCCCCCCccccccccCCCCCCCCCcceec
Q 010943 20 GSVFTMQEIALACRNAGRNPDLAGESLCDKQANASTSSIHPSTGEARGKESSKSSNSNISEKSFYANGKSKPPKTKWHPV 99 (497)
Q Consensus 20 gs~fSl~~ia~Ay~~A~~d~~~A~eiL~~~~~~~sts~~~~s~~~~~~~~~~~~~~~~~~e~~~~~~~~~k~~k~k~~~v 99 (497)
++.|.+.++..|+++++..+++...++.+++..++...-.-.+.+.+ .+++......++..... ..+....+....
T Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~-~~s~~~~~~~~~~~~~~---~~~~~~~~~~~~ 99 (448)
T KOG2401|consen 24 SFSFKLVDLKAASEESSDEVDLGPPELSEMATSTSSADRLQYTIELL-EPSPSSVSFESLRARAS---DENVDRGNQERI 99 (448)
T ss_pred hhhhhhHhhhhcccccccccccCCCcchhhccccchhhhhccccccc-CCCcccccccccccchh---hhccccHHHHhh
Confidence 56688888999999999999988888888876553222222333322 11111111111111111 011122333444
Q ss_pred ccccccccccccccccCCCCCCCcccCCCCcCCCCCCCccccccCCC-CCCCCCCccchhHHHHHHHHHhcCccccCHHH
Q 010943 100 SGGTVSSFLGKDYVKPAQPTNGTGLASKPLKLDPKEFPMSALWGEET-KPKQSKGDHLQKEMEDFLFKLLGEGFQLSRDV 178 (497)
Q Consensus 100 s~GtVSsviGK~y~r~~~~~~~~~~~~kp~k~~~k~~~~~~~w~~~~-~~~~~~~~~~~~d~E~FL~~MLG~gf~L~~~v 178 (497)
.-....++.|+.+++............+++..+.+.+|....|.++. -++.+.........+++|+.|..+++.-+--.
T Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~n~~ 179 (448)
T KOG2401|consen 100 LDRSRNQVAGKLKVSFVEKKLNEEEPQKEINPDGRILPEDPSFEESFRVENGFDPGEAIAFKIEDLPQKQVEGEDVDNCK 179 (448)
T ss_pred cccccccccccccccccccccCccccccccCCcccccccccchHHHHHHhccCccchhhhcchhhhccccccccccccce
Confidence 55678889999999999888888888888888887777766554333 33333333333344444444444444333333
Q ss_pred HHHHHHhcCCcHHHHHHHHHcccccccccccccccccccccccccCCcCcchhHhhhhhhccCCCCCcCCCCCCcccccC
Q 010943 179 IREVLDSCGYDMQKSMSKLIDHSAETLGEKTKFLGKSSEKCMDICSTFGGSQRERKLQQLNSSGGRAKEDPNTNKGELLK 258 (497)
Q Consensus 179 Ir~VL~~cGyDv~ks~d~LLd~s~~~~~k~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~ 258 (497)
|. ...+|.+|..++..-.++-+.+.... ..... ++ .-.+ .+........
T Consensus 180 ~~-~~~~~~~d~~~~~~~~~~~~~~~~~~----~~~~~---------------~~-~~~~--~~~~~~~~~~-------- 228 (448)
T KOG2401|consen 180 VK-NQITNSSDSKMATEPGLNDSLKKAYE----NVDSS---------------EE-SVEL--LRKEGFSVDV-------- 228 (448)
T ss_pred ee-ccccccccccccccccccchhhcccc----ccCcc---------------hh-hhhh--hccCCCCccC--------
Confidence 33 33444444444333333333222110 00001 00 0000 0000000000
Q ss_pred CCcchhhhHHHHHHHhccCCCCCCcchhhH-HhhhcccccCCccccCCCCCCcccccccccccccccCCcc-cccchHHH
Q 010943 259 HPKDRNELQKEVFAALFSAPKKSDEFPEIM-VKTKRRSKALGKVVSGPPEDLVPEYKANVVHLQQDNQNIA-DNVEEDSF 336 (497)
Q Consensus 259 ~~~~~~~l~~evlesLF~~~e~~e~~p~~~-~~~~~k~~~~~~~v~~p~~D~~~~~~~~~~~~~~~~~~~~-~~~~d~~Y 336 (497)
.......-...+.+..+..++.....+.+. -...+++-.-+++.+++.++...... .....-+|...+ .......|
T Consensus 229 ~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~--~~~~~d~~~~~~~~~~~~~~~ 306 (448)
T KOG2401|consen 229 PSNAEKNSAKRLEELQKSQPEEDKAKKLRDQLYKSKRPAGSGKCLRKRHELSDKPRG--VLQAEDDYNADELSDEFGNKE 306 (448)
T ss_pred cchhhcccccchhhcchhhhccchhhhHHHhhhhhcccccccchhhhhhhhhhhhhh--hhhcccccchhhhhhhhhhhh
Confidence 000111123334444444444444333222 22344444444566555544433322 112222333322 12333334
Q ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCeeecCCC
Q 010943 337 QHLRTAVMEYRG-TMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETSGRNRDTKNDLLLDLHDH 415 (497)
Q Consensus 337 ~~~R~~A~eh~~-~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean~~AA~~If~~r~~N~~~~n~~tIDLHGL 415 (497)
......+++..+ .+..++++|+.++..+....|.++.-.+......+......+-+.+.... |.......+.++|+.
T Consensus 307 s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~a~~~~~~--~~~~~r~~~~~~~~~ 384 (448)
T KOG2401|consen 307 SIKSEREIDNQRLYKKAAEQKAQPEIEDAINLQASELKPKVSLAVKGSYAVAKLKPATQWKLD--NEEIERRSEVGEHGE 384 (448)
T ss_pred hhhhhHHhhhhhHHHHHHHhhhhhhhhhhhhhhhhhhchhhhhcccccchhhhcchHHHHHHh--hhhhhcccccccchh
Confidence 444444555555 77889999999999999999999998887766555555444444455555 445555688999999
Q ss_pred CHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCCceEee
Q 010943 416 GAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE 474 (497)
Q Consensus 416 hV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi~w~e~ 474 (497)
+|.++...++ +.|++|+|.||.+...+.+++.+.+...++.+...
T Consensus 385 ~i~~~~~~~~--------------~qv~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~ 429 (448)
T KOG2401|consen 385 KISELSRRLK--------------LQVLFGRGIHSRGEARLPRAEKRSYEDPPQGFVEE 429 (448)
T ss_pred hhHhHhhhcc--------------ccccccccccCccchhhhhhhhhhccCCccceeee
Confidence 9988776543 45889999999998888888888788888765443
No 5
>COG2840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.04 E-value=1.2e-05 Score=77.49 Aligned_cols=79 Identities=18% Similarity=0.259 Sum_probs=63.3
Q ss_pred CCCeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCc-cHHHHHHHHHHcCC--ceEee----CCCe
Q 010943 406 NDLLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGG-RRRRVMKLLEEESI--EWTEE----GNAG 478 (497)
Q Consensus 406 n~~tIDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k-~kpAV~klL~kegi--~w~e~----~n~G 478 (497)
.+..|||||++++||-..|-..|..+... ....+.||+|+|. |.|+.. ++++|-.+|.+.-- -|++. ...|
T Consensus 95 ~e~~LDLHG~tq~eAr~~L~~Fi~~a~~~-~~rcv~VihGkG~-s~g~~~vLK~~Vp~WL~qhp~V~a~~~a~~~hGG~G 172 (184)
T COG2840 95 PEARLDLHGLTQEEARQELGAFIARARAE-GLRCVLVIHGKGR-SKGSKPVLKSQVPRWLTQHPDVLAFHQAPRRHGGDG 172 (184)
T ss_pred cceeeeccCCCHHHHHHHHHHHHHHHHHh-CCcEEEEEeCCCc-CCCCchhHHHHHHHHHHhChHHHhhcccchhcCCce
Confidence 46889999999999999999999987653 4578999999999 998655 67899999998532 24442 2778
Q ss_pred EEEEEeCC
Q 010943 479 TILIPLDK 486 (497)
Q Consensus 479 vIlI~L~g 486 (497)
.|+|.|.-
T Consensus 173 AlyVlL~~ 180 (184)
T COG2840 173 ALYVLLRR 180 (184)
T ss_pred EEEEEEec
Confidence 99998854
No 6
>PRK04946 hypothetical protein; Provisional
Probab=97.97 E-value=1.7e-05 Score=76.20 Aligned_cols=76 Identities=14% Similarity=0.168 Sum_probs=61.5
Q ss_pred CCCeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCC--ceEee----CCCeE
Q 010943 406 NDLLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESI--EWTEE----GNAGT 479 (497)
Q Consensus 406 n~~tIDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi--~w~e~----~n~Gv 479 (497)
...+|||||+.+.||...|...|..+... +...+.||.|+|. +.++.+|..+|.+.-. .|+.. .+.|.
T Consensus 94 ~~~~LDLhG~~~eeA~~~L~~fl~~a~~~-g~r~v~IIHGkG~-----gvLk~~V~~wL~q~~~V~af~~A~~~~GG~GA 167 (181)
T PRK04946 94 PELFLDLHGLTQLQAKQELGALIAACRKE-HVFCACVMHGHGK-----HILKQQTPLWLAQHPDVMAFHQAPKEWGGDAA 167 (181)
T ss_pred CceEEECCCCCHHHHHHHHHHHHHHHHHc-CCCEEEEEcCCCH-----hHHHHHHHHHHcCCchhheeeccCcccCCceE
Confidence 46899999999999999999999886542 4578999999996 4578899999987654 46542 37899
Q ss_pred EEEEeCCC
Q 010943 480 ILIPLDKV 487 (497)
Q Consensus 480 IlI~L~gi 487 (497)
++|.|...
T Consensus 168 ~~VlLk~~ 175 (181)
T PRK04946 168 LLVLIEIE 175 (181)
T ss_pred EEEEEecC
Confidence 99998764
No 7
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=97.42 E-value=0.00029 Score=80.68 Aligned_cols=73 Identities=22% Similarity=0.275 Sum_probs=59.4
Q ss_pred CCeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCC--ceEee----CCCeEE
Q 010943 407 DLLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESI--EWTEE----GNAGTI 480 (497)
Q Consensus 407 ~~tIDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi--~w~e~----~n~GvI 480 (497)
..+|||||+.|.||+..|...|..+... +...++||.|+|. +.++.+|.+||+++-+ .|+.. .+.|+.
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 4588999999984 4688899999998865 35542 278999
Q ss_pred EEEeC
Q 010943 481 LIPLD 485 (497)
Q Consensus 481 lI~L~ 485 (497)
+|.|.
T Consensus 778 ~V~lk 782 (782)
T PRK00409 778 IVELK 782 (782)
T ss_pred EEEEC
Confidence 98873
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=97.28 E-value=0.00048 Score=78.88 Aligned_cols=72 Identities=24% Similarity=0.352 Sum_probs=58.5
Q ss_pred CCeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCC--ceEee----CCCeEE
Q 010943 407 DLLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESI--EWTEE----GNAGTI 480 (497)
Q Consensus 407 ~~tIDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi--~w~e~----~n~GvI 480 (497)
..+|||||+.+.||+..|...|..+.-. +...++||.|+|. +.++.+|..||++.-+ .|+.. .+.|+.
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 SLTLDLRGQRSEEALDRLEKFLNDALLA-GYEVVLIIHGKGS-----GKLRKGVQELLKNHPKVKSFRDAPPNDGGSGVT 766 (771)
T ss_pred CceEECCCCCHHHHHHHHHHHHHHHHHC-CCCEEEEEcCCCh-----hHHHHHHHHHhcCCcceeeecccCcccCCceEE
Confidence 5799999999999999999999876432 4578999999985 4688999999999765 35432 278899
Q ss_pred EEEe
Q 010943 481 LIPL 484 (497)
Q Consensus 481 lI~L 484 (497)
+|.|
T Consensus 767 ~V~l 770 (771)
T TIGR01069 767 IVYL 770 (771)
T ss_pred EEEE
Confidence 8877
No 9
>KOG2401 consensus Predicted MutS-related protein involved in mismatch repair [Replication, recombination and repair]
Probab=96.24 E-value=0.0094 Score=64.28 Aligned_cols=356 Identities=13% Similarity=0.038 Sum_probs=212.9
Q ss_pred cCHHHHHHHHHHhCCCchhhhhhhccccCCCCCcccCCCCCcc------CCCCCCCCCCCCccccccccCCCCCCCCCcc
Q 010943 23 FTMQEIALACRNAGRNPDLAGESLCDKQANASTSSIHPSTGEA------RGKESSKSSNSNISEKSFYANGKSKPPKTKW 96 (497)
Q Consensus 23 fSl~~ia~Ay~~A~~d~~~A~eiL~~~~~~~sts~~~~s~~~~------~~~~~~~~~~~~~~e~~~~~~~~~k~~k~k~ 96 (497)
.++.-.+..|...+.+.+.|.+.+...-+...+-.++....++ .+....+.++..+ +.. ....+..+
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~s~~~~---~~~-~~~~~~~~--- 88 (448)
T KOG2401|consen 16 LTLSLAAFSFSFKLVDLKAASEESSDEVDLGPPELSEMATSTSSADRLQYTIELLEPSPSSV---SFE-SLRARASD--- 88 (448)
T ss_pred chhccchhhhhhhhHhhhhcccccccccccCCCcchhhccccchhhhhcccccccCCCcccc---ccc-ccccchhh---
Confidence 4566678899999999999999998887776555554333322 1011111111111 000 00011100
Q ss_pred eecccccccccccccccccCCCCCCCcccCCCCcCCCCCCCccccccCCCCCCCCCCccchhHHHHHHHHHhcCccccCH
Q 010943 97 HPVSGGTVSSFLGKDYVKPAQPTNGTGLASKPLKLDPKEFPMSALWGEETKPKQSKGDHLQKEMEDFLFKLLGEGFQLSR 176 (497)
Q Consensus 97 ~~vs~GtVSsviGK~y~r~~~~~~~~~~~~kp~k~~~k~~~~~~~w~~~~~~~~~~~~~~~~d~E~FL~~MLG~gf~L~~ 176 (497)
..+-.|+ --.+++.+..+....-. ....+.+++. ++|+.. |. -..+......-.++++-.+++......+
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 12345555444432211 1223333331 122222 11 1122333466778888889999999999
Q ss_pred HHHHHHHHhcCCcHHHHHHHHHcccccccccccccccccccccccccCCcCcchhHhhhhhhccCCCCCcCCCCCCcccc
Q 010943 177 DVIREVLDSCGYDMQKSMSKLIDHSAETLGEKTKFLGKSSEKCMDICSTFGGSQRERKLQQLNSSGGRAKEDPNTNKGEL 256 (497)
Q Consensus 177 ~vIr~VL~~cGyDv~ks~d~LLd~s~~~~~k~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~ 256 (497)
..+.+.|.+|.+...-+.....+...+ ..- +.+.......+..
T Consensus 159 ~~~~~~~~~~~~~~~~~~n~~~~~~~~-~~~------------------------------------d~~~~~~~~~~~~ 201 (448)
T KOG2401|consen 159 AFKIEDLPQKQVEGEDVDNCKVKNQIT-NSS------------------------------------DSKMATEPGLNDS 201 (448)
T ss_pred hcchhhhccccccccccccceeecccc-ccc------------------------------------cccccccccccch
Confidence 999999999998776555544441111 000 0000000000111
Q ss_pred cCCCcchhhhHHHHHHHhccCCCCCCcchhhHHhhhcccccCCccccCCCCCCcccccccccccccccCCcccccchHHH
Q 010943 257 LKHPKDRNELQKEVFAALFSAPKKSDEFPEIMVKTKRRSKALGKVVSGPPEDLVPEYKANVVHLQQDNQNIADNVEEDSF 336 (497)
Q Consensus 257 ~~~~~~~~~l~~evlesLF~~~e~~e~~p~~~~~~~~k~~~~~~~v~~p~~D~~~~~~~~~~~~~~~~~~~~~~~~d~~Y 336 (497)
......-..++.+.+..+|+. +.++. .+.... .+ ......+|
T Consensus 202 ~~~~~~~~~~~~~~~~~~~~~---------------------~~~~~-----~~~~~~----------~~--~~~~~~~~ 243 (448)
T KOG2401|consen 202 LKKAYENVDSSEESVELLRKE---------------------GFSVD-----VPSNAE----------KN--SAKRLEEL 243 (448)
T ss_pred hhccccccCcchhhhhhhccC---------------------CCCcc-----Ccchhh----------cc--cccchhhc
Confidence 111111123344455555544 12221 111111 11 23456778
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCeeecCCCC
Q 010943 337 QHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETSGRNRDTKNDLLLDLHDHG 416 (497)
Q Consensus 337 ~~~R~~A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean~~AA~~If~~r~~N~~~~n~~tIDLHGLh 416 (497)
+..+.........+...|..+.-|+..+....+..++.+.+......+..+.++....|.-. +.. .....+|+|+++
T Consensus 244 ~~~~~~~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~--~s~-~~~~~~~~~~~~ 320 (448)
T KOG2401|consen 244 QKSQPEEDKAKKLRDQLYKSKRPAGSGKCLRKRHELSDKPRGVLQAEDDYNADELSDEFGNK--ESI-KSEREIDNQRLY 320 (448)
T ss_pred chhhhccchhhhHHHhhhhhcccccccchhhhhhhhhhhhhhhhhcccccchhhhhhhhhhh--hhh-hhhHHhhhhhHH
Confidence 88888888888999999999999999999999999999999999999999999999988877 533 346889999999
Q ss_pred HHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCC-CccHHHHHHHHHHcCCceEee
Q 010943 417 AKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTK-GGRRRRVMKLLEEESIEWTEE 474 (497)
Q Consensus 417 V~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~-~k~kpAV~klL~kegi~w~e~ 474 (497)
++.|...+...+...... ...++.++.+.++|.... .+++|++...+..+.+.-...
T Consensus 321 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~v~~~~~a~~~~~~~~~~~r~~~ 378 (448)
T KOG2401|consen 321 KKAAEQKAQPEIEDAINL-QASELKPKVSLAVKGSYAVAKLKPATQWKLDNEEIERRSE 378 (448)
T ss_pred HHHHHhhhhhhhhhhhhh-hhhhhchhhhhcccccchhhhcchHHHHHHhhhhhhcccc
Confidence 999999998887765443 347899999999999754 568899999999988764443
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=95.97 E-value=0.015 Score=42.81 Aligned_cols=40 Identities=30% Similarity=0.471 Sum_probs=33.3
Q ss_pred HHHHHHHHHhcCccccCHHHHHHHHHhcCCcHHHHHHHHHccc
Q 010943 159 EMEDFLFKLLGEGFQLSRDVIREVLDSCGYDMQKSMSKLIDHS 201 (497)
Q Consensus 159 d~E~FL~~MLG~gf~L~~~vIr~VL~~cGyDv~ks~d~LLd~s 201 (497)
++-+.|..|+- +++.++|+.||.+|++||+.+++.||+++
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=94.90 E-value=0.069 Score=39.41 Aligned_cols=40 Identities=23% Similarity=0.382 Sum_probs=33.4
Q ss_pred HHHHHHHHHhcCccccCHHHHHHHHHhcCCcHHHHHHHHHccc
Q 010943 159 EMEDFLFKLLGEGFQLSRDVIREVLDSCGYDMQKSMSKLIDHS 201 (497)
Q Consensus 159 d~E~FL~~MLG~gf~L~~~vIr~VL~~cGyDv~ks~d~LLd~s 201 (497)
++-+.|..|+- +|+..+|+.+|-.|++||+.+++.||..+
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 45556666632 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=94.83 E-value=0.058 Score=38.40 Aligned_cols=35 Identities=26% Similarity=0.462 Sum_probs=28.6
Q ss_pred HHHHHhcCccccCHHHHHHHHHhcCCcHHHHHHHHHc
Q 010943 163 FLFKLLGEGFQLSRDVIREVLDSCGYDMQKSMSKLID 199 (497)
Q Consensus 163 FL~~MLG~gf~L~~~vIr~VL~~cGyDv~ks~d~LLd 199 (497)
-+..|..-||. +..++++|..|++|+++|++.|++
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=89.88 E-value=0.34 Score=34.72 Aligned_cols=31 Identities=32% Similarity=0.665 Sum_probs=25.3
Q ss_pred HHHHHHhcCccccCHHHHHHHHHhcCCcHHHHHHHH
Q 010943 162 DFLFKLLGEGFQLSRDVIREVLDSCGYDMQKSMSKL 197 (497)
Q Consensus 162 ~FL~~MLG~gf~L~~~vIr~VL~~cGyDv~ks~d~L 197 (497)
+=|..| || +...+++.|-.|++||++|++.|
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=89.70 E-value=0.4 Score=33.87 Aligned_cols=25 Identities=16% Similarity=0.311 Sum_probs=22.3
Q ss_pred cCHHHHHHHHHhcCCcHHHHHHHHH
Q 010943 174 LSRDVIREVLDSCGYDMQKSMSKLI 198 (497)
Q Consensus 174 L~~~vIr~VL~~cGyDv~ks~d~LL 198 (497)
.+...++.+|-.|++|+++|++-|+
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
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=83.62 E-value=0.67 Score=38.80 Aligned_cols=39 Identities=21% Similarity=0.344 Sum_probs=31.1
Q ss_pred HHHhcCccccCHHHHHHHHHhcCCcHHHHHHHHHcccccc
Q 010943 165 FKLLGEGFQLSRDVIREVLDSCGYDMQKSMSKLIDHSAET 204 (497)
Q Consensus 165 ~~MLG~gf~L~~~vIr~VL~~cGyDv~ks~d~LLd~s~~~ 204 (497)
-.-||+... +-..|+++|=.|.|||+||++.||.-....
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 889999999999999999999999876553
No 16
>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=83.46 E-value=1.1 Score=31.81 Aligned_cols=29 Identities=28% Similarity=0.195 Sum_probs=26.0
Q ss_pred CCccCHHHHHHHHHHhCCCchhhhhhhcc
Q 010943 20 GSVFTMQEIALACRNAGRNPDLAGESLCD 48 (497)
Q Consensus 20 gs~fSl~~ia~Ay~~A~~d~~~A~eiL~~ 48 (497)
.-+|+-+++..|+...++|++.|++.|.+
T Consensus 10 ~mGf~~~~~~~AL~~~~~d~~~A~~~L~~ 38 (38)
T cd00194 10 EMGFSREEARKALRATNNNVERAVEWLLE 38 (38)
T ss_pred HcCCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence 45699999999999999999999999853
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=81.53 E-value=1.5 Score=32.72 Aligned_cols=26 Identities=19% Similarity=0.524 Sum_probs=23.2
Q ss_pred ccCHHHHHHHHHhcCCcHHHHHHHHH
Q 010943 173 QLSRDVIREVLDSCGYDMQKSMSKLI 198 (497)
Q Consensus 173 ~L~~~vIr~VL~~cGyDv~ks~d~LL 198 (497)
+-.+.++.-||..|+.||=+|||.+|
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=80.37 E-value=1.6 Score=31.24 Aligned_cols=25 Identities=24% Similarity=0.174 Sum_probs=22.7
Q ss_pred ccCHHHHHHHHHHhCCCchhhhhhh
Q 010943 22 VFTMQEIALACRNAGRNPDLAGESL 46 (497)
Q Consensus 22 ~fSl~~ia~Ay~~A~~d~~~A~eiL 46 (497)
+|+-+++-.|+...++|++.|.++|
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=78.22 E-value=2.1 Score=30.18 Aligned_cols=28 Identities=32% Similarity=0.230 Sum_probs=25.4
Q ss_pred CCccCHHHHHHHHHHhCCCchhhhhhhc
Q 010943 20 GSVFTMQEIALACRNAGRNPDLAGESLC 47 (497)
Q Consensus 20 gs~fSl~~ia~Ay~~A~~d~~~A~eiL~ 47 (497)
.-+|+-+++..|+...++|++.|.+.|.
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
>PF14346 DUF4398: Domain of unknown function (DUF4398)
Probab=70.60 E-value=32 Score=29.66 Aligned_cols=42 Identities=26% Similarity=0.162 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHH
Q 010943 345 EYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREA 386 (497)
Q Consensus 345 eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karea 386 (497)
.++..-.+.+.+|..+|..|+...|..|..+++.+.+++...
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 366777888999999999999999999999999987777653
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=68.74 E-value=14 Score=27.32 Aligned_cols=38 Identities=18% Similarity=0.506 Sum_probs=29.4
Q ss_pred hHHHHHHHHHhcCccccCHHHHHHHHHhcCCcHHHHHHHHHcc
Q 010943 158 KEMEDFLFKLLGEGFQLSRDVIREVLDSCGYDMQKSMSKLIDH 200 (497)
Q Consensus 158 ~d~E~FL~~MLG~gf~L~~~vIr~VL~~cGyDv~ks~d~LLd~ 200 (497)
+.+++|. +..| .+.++-+..|..|++|++.|++.-++-
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
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=67.39 E-value=8.1 Score=45.04 Aligned_cols=72 Identities=19% Similarity=0.284 Sum_probs=52.5
Q ss_pred CCeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCC--ceEe--e--CCCeEE
Q 010943 407 DLLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESI--EWTE--E--GNAGTI 480 (497)
Q Consensus 407 ~~tIDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi--~w~e--~--~n~GvI 480 (497)
..+|||+|.-+.+|+..|...+..+-- .++..+.||=|.| -++++..|.++|+++-- .|+. . ...|+=
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 369999999999999999999976532 2457788886654 46688899999999843 2332 1 256666
Q ss_pred EEEe
Q 010943 481 LIPL 484 (497)
Q Consensus 481 lI~L 484 (497)
+|.|
T Consensus 750 iv~l 753 (753)
T COG1193 750 IVEL 753 (753)
T ss_pred EEeC
Confidence 6654
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=65.46 E-value=5 Score=29.49 Aligned_cols=31 Identities=32% Similarity=0.638 Sum_probs=22.1
Q ss_pred cCHHHHHHHHHhcCCcHHHHHHHHHccccccc
Q 010943 174 LSRDVIREVLDSCGYDMQKSMSKLIDHSAETL 205 (497)
Q Consensus 174 L~~~vIr~VL~~cGyDv~ks~d~LLd~s~~~~ 205 (497)
+...+|+++|..||+++.++-. +|.++-.++
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=63.49 E-value=19 Score=28.24 Aligned_cols=66 Identities=21% Similarity=0.163 Sum_probs=46.4
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCCceEeeC-CCeEEEEEe
Q 010943 409 LLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEEG-NAGTILIPL 484 (497)
Q Consensus 409 tIDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi~w~e~~-n~GvIlI~L 484 (497)
+||+.|+.==.-+-.+++.|..+. ....|.||+.... -..-|.++|++.|++|.... ..|...|.+
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 3377888875322 23458999999999986532 445555544
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=62.97 E-value=9.7 Score=29.04 Aligned_cols=29 Identities=34% Similarity=0.627 Sum_probs=28.0
Q ss_pred HHHHHHHHHhcCccccCHHHHHHHHHhcC
Q 010943 159 EMEDFLFKLLGEGFQLSRDVIREVLDSCG 187 (497)
Q Consensus 159 d~E~FL~~MLG~gf~L~~~vIr~VL~~cG 187 (497)
+++.+|..|.--||=||..+++++|..+|
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=61.21 E-value=65 Score=31.31 Aligned_cols=89 Identities=15% Similarity=0.150 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCeeecCCCCHHHHHHHH
Q 010943 345 EYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETSGRNRDTKNDLLLDLHDHGAKEAIRLL 424 (497)
Q Consensus 345 eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean~~AA~~If~~r~~N~~~~n~~tIDLHGLhV~EAi~iL 424 (497)
.......+.+.+-.+||..||...-..+..... ......+.|+..| |.. ++
T Consensus 167 ~~~~~~~~~~~~~~~~~~~gd~~~l~~~~~~~~--------~~p~~~~~ll~~R--N~~-------------------~~ 217 (259)
T PF01963_consen 167 DDIEDGEKMLEQLIEAWKNGDLDALMELMKEDE--------SFPELYEVLLDER--NRR-------------------WA 217 (259)
T ss_pred hccccchHHHHHHHHHHHccCHHHHHHHHHhcc--------cCHHHHHHHHHHH--hHH-------------------HH
Confidence 335666888999999999999754333311111 4445556788888 732 11
Q ss_pred HHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCCc
Q 010943 425 KCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIE 470 (497)
Q Consensus 425 k~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi~ 470 (497)
+.-...+.. + +...|+||.||----. -|..+|++.||+
T Consensus 218 ~~i~~~l~~-~--~~~fvvVGa~HL~G~~-----gvl~lLr~~Gy~ 255 (259)
T PF01963_consen 218 EKIEELLKE-G--GTVFVVVGAGHLPGED-----GVLDLLRKKGYT 255 (259)
T ss_pred HHHHHHHhc-C--CCEEEEEcchhccchh-----hHHHHHHhCCce
Confidence 111112221 1 4688999999985411 288999999954
No 27
>PRK09591 celC cellobiose phosphotransferase system IIA component; Reviewed
Probab=60.60 E-value=76 Score=28.27 Aligned_cols=69 Identities=19% Similarity=0.221 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCeeecCCCCHHH
Q 010943 343 VMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETSGRNRDTKNDLLLDLHDHGAKE 419 (497)
Q Consensus 343 A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean~~AA~~If~~r~~N~~~~n~~tIDLHGLhV~E 419 (497)
-.-|+-.-+.+|-+|-++.+.||.+.|..+..+|+.....+.+.+ .+-|-..- +-. ...+.|==.|..+
T Consensus 13 II~~aG~Ars~~~eAl~~ak~gdf~~A~~~l~eA~~~l~~AH~~q---t~liq~Ea--~g~---~~~~slLlvHAQD 81 (104)
T PRK09591 13 IILHSGNARTEVHEAFAAMREGNFDLAEQKLNQSNEELLEAHHAQ---TKLLQEYA--SGT---EIKIEIIMVHAQD 81 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHh--CCC---CCccceeehhHHH
Confidence 344555556677789999999999999999999998877777665 34444433 211 2345554444443
No 28
>PRK01905 DNA-binding protein Fis; Provisional
Probab=60.28 E-value=14 Score=30.74 Aligned_cols=49 Identities=12% Similarity=0.317 Sum_probs=38.3
Q ss_pred chhHHHHHHHHHhcCc---------cccCHHHHHHHHHhcCCcHHHHHHHHHccccccc
Q 010943 156 LQKEMEDFLFKLLGEG---------FQLSRDVIREVLDSCGYDMQKSMSKLIDHSAETL 205 (497)
Q Consensus 156 ~~~d~E~FL~~MLG~g---------f~L~~~vIr~VL~~cGyDv~ks~d~LLd~s~~~~ 205 (497)
.++.++.||-.++|.+ -++.+..|+++|..||.++.++- .+|.++..++
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=57.71 E-value=44 Score=29.34 Aligned_cols=50 Identities=26% Similarity=0.339 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 010943 346 YRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETS 398 (497)
Q Consensus 346 h~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean~~AA~~If~~r 398 (497)
|+-.-+.||-+|-++.+.||.+.|..+..+|+....++.+.+ .+-|-..-
T Consensus 11 ~aG~Ars~~~eAl~~a~~g~fe~A~~~l~ea~~~l~~AH~~q---t~liq~ea 60 (97)
T cd00215 11 HAGNARSKALEALKAAKEGDFAEAEELLEEANDSLNEAHHAQ---TKLLQQEA 60 (97)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHh
Confidence 344455677779999999999999999999999888777766 34454443
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=56.76 E-value=46 Score=29.33 Aligned_cols=43 Identities=28% Similarity=0.393 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHH
Q 010943 346 YRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADE 388 (497)
Q Consensus 346 h~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean~ 388 (497)
++-.-+.||-+|-++.+.||.+.|..+.++|+.....+.+.+-
T Consensus 13 ~aG~Ars~~~eAl~~a~~gdfe~A~~~l~eA~~~l~~AH~~qt 55 (99)
T TIGR00823 13 YAGDARSKALEALKAAKAGDFAKARALVEQAGMCLNEAHLAQT 55 (99)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444556777799999999999999999999998887777663
No 31
>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=54.03 E-value=62 Score=25.56 Aligned_cols=65 Identities=17% Similarity=0.236 Sum_probs=44.3
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCCceEeeCCCeEEEEEe
Q 010943 409 LLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEEGNAGTILIPL 484 (497)
Q Consensus 409 tIDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi~w~e~~n~GvIlI~L 484 (497)
+||+-|+.==+-+-.+++.| .+. ....|.||+-. .+ -..-|..+|++.|+.+......|.+.|.+
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 48899998877888888888 443 22578887532 11 23358999999999986443555666654
No 32
>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=53.61 E-value=14 Score=31.27 Aligned_cols=27 Identities=19% Similarity=0.178 Sum_probs=24.2
Q ss_pred HHHHHHHHcCChHHHHHHHHHHHHHHH
Q 010943 355 KAAIDAFAQGDHVQAEKLLEQGKFFYE 381 (497)
Q Consensus 355 ~kA~~AY~~Gd~a~A~~LSeqGk~~~~ 381 (497)
.|+..+|++||.+.|.+.|.++|.+.-
T Consensus 42 ~kv~~~~~~Gd~~~A~~aS~~Ak~~~~ 68 (82)
T PF04505_consen 42 SKVRSRYAAGDYEGARRASRKAKKWSI 68 (82)
T ss_pred hhhHHHHHCCCHHHHHHHHHHhHHHHH
Confidence 578999999999999999999998764
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=53.46 E-value=63 Score=29.44 Aligned_cols=54 Identities=17% Similarity=0.229 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHH
Q 010943 336 FQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEE 389 (497)
Q Consensus 336 Y~~~R~~A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean~~ 389 (497)
...+.+.+...-..-.++..+|..|.++|++..|+.|..+-+.+.+........
T Consensus 10 ~~~L~~~~~~le~~i~~~~~~~k~~~~~~~~~~A~~~lk~~k~~~k~~~~~~~~ 63 (171)
T PF03357_consen 10 IRRLEKQIKRLEKKIKKLEKKAKKAIKKGNKERAKIYLKRKKRLEKQLEKLLNQ 63 (171)
T ss_dssp HHHHHHHHHHHHHHHHHCHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667777788888899999999999999999999999988887766665543
No 34
>PLN03218 maturation of RBCL 1; Provisional
Probab=50.79 E-value=25 Score=42.65 Aligned_cols=77 Identities=13% Similarity=0.178 Sum_probs=52.5
Q ss_pred CCeeecCCCCHHHHHHHHHHHH-------HhhcCCCCcce------EEEEEecCCCCCCCC-ccHHHHHHHHHHcCCceE
Q 010943 407 DLLLDLHDHGAKEAIRLLKCHL-------SSLSGIPTIKY------LKVILEMNDEDTTKG-GRRRRVMKLLEEESIEWT 472 (497)
Q Consensus 407 ~~tIDLHGLhV~EAi~iLk~~L-------~~l~~~~s~~~------LrVItG~G~HS~g~~-k~kpAV~klL~kegi~w~ 472 (497)
.+.||+|.+-|--|.-.|-..| ......|...- =.|.||.|.|+.... ++..+|..+|++-++.|.
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 5899999999999876665444 43333443111 125566666654432 345699999999999999
Q ss_pred eeCCCeEEEEE
Q 010943 473 EEGNAGTILIP 483 (497)
Q Consensus 473 e~~n~GvIlI~ 483 (497)
+....|.|.+.
T Consensus 1001 ~~~~~g~~~~~ 1011 (1060)
T PLN03218 1001 GSESHGKLRIN 1011 (1060)
T ss_pred CCCCCCeEEec
Confidence 87655988873
No 35
>PRK10454 PTS system N,N'-diacetylchitobiose-specific transporter subunit IIA; Provisional
Probab=49.60 E-value=66 Score=29.25 Aligned_cols=53 Identities=21% Similarity=0.298 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 010943 343 VMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETS 398 (497)
Q Consensus 343 A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean~~AA~~If~~r 398 (497)
-.-|+-.-+.||-+|-++.+.||.+.|..|.++|+....++.+.+ .+-|-..-
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 344455555666779999999999999999999999877777666 44554444
No 36
>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=48.14 E-value=84 Score=27.46 Aligned_cols=49 Identities=22% Similarity=0.295 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 010943 347 RGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESNKKIFETS 398 (497)
Q Consensus 347 ~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean~~AA~~If~~r 398 (497)
+-.-+.+|-+|-++.+.||.+.|..+..+|+....++.+.+- +-|-..-
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 334455677799999999999999999999988777776654 3444444
No 37
>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=47.77 E-value=85 Score=24.83 Aligned_cols=66 Identities=21% Similarity=0.198 Sum_probs=46.1
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCCceEee-CCCeEEEEEe
Q 010943 409 LLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE-GNAGTILIPL 484 (497)
Q Consensus 409 tIDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi~w~e~-~n~GvIlI~L 484 (497)
+||+-|+.==.-+-.+++.|..+.. ...|.||+-.. .-..-|..+|++.|+.+.+. ...|.+.|.|
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 37899987432 12356999999999875442 3666666554
No 38
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=47.63 E-value=59 Score=29.33 Aligned_cols=42 Identities=14% Similarity=0.070 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHH
Q 010943 342 AVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAR 384 (497)
Q Consensus 342 ~A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~kar 384 (497)
....+....+.+|+-|..+|+.| .++|..|.+.++...++++
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 34556667788999999999999 6777777777766665554
No 39
>PF13763 DUF4167: Domain of unknown function (DUF4167)
Probab=47.58 E-value=81 Score=27.18 Aligned_cols=38 Identities=29% Similarity=0.470 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHH
Q 010943 351 KEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADE 388 (497)
Q Consensus 351 ne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean~ 388 (497)
.+|-+-|.+|-..||.-.|..|.+-+-+|...+.++..
T Consensus 40 EKY~~LArDA~ssGDrV~aEny~QHAeHY~Ril~~~~~ 77 (80)
T PF13763_consen 40 EKYNQLARDAQSSGDRVLAENYLQHAEHYFRILAAAQA 77 (80)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666699999999999999999999999988877654
No 40
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=44.21 E-value=93 Score=25.29 Aligned_cols=39 Identities=31% Similarity=0.386 Sum_probs=29.4
Q ss_pred HHHHH-HHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHH
Q 010943 348 GTMKE-YCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREA 386 (497)
Q Consensus 348 ~~Rne-~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karea 386 (497)
..|.+ |=+.|.+|=+.||.+.|+.+....|.|....+.+
T Consensus 5 ~~R~~~yk~Aa~~AK~~gd~~kAr~~~R~~K~~~~~I~~~ 44 (59)
T smart00685 5 QQRQEQYKQAALQAKRAGDEEKARRHLRIAKQFDDAIKAA 44 (59)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhhHHHHHHHH
Confidence 44444 5556778999999999998888888887766654
No 41
>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=40.27 E-value=20 Score=26.24 Aligned_cols=27 Identities=11% Similarity=0.116 Sum_probs=23.9
Q ss_pred cCHHHHHHHHHHhCCCchhhhhhhccc
Q 010943 23 FTMQEIALACRNAGRNPDLAGESLCDK 49 (497)
Q Consensus 23 fSl~~ia~Ay~~A~~d~~~A~eiL~~~ 49 (497)
++.+.|..++.+.+||++.|-+.|..+
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 788999999999999999999988765
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=37.80 E-value=94 Score=24.99 Aligned_cols=66 Identities=15% Similarity=0.060 Sum_probs=46.4
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCCceEe-eCCCeEEEEEe
Q 010943 409 LLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTE-EGNAGTILIPL 484 (497)
Q Consensus 409 tIDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi~w~e-~~n~GvIlI~L 484 (497)
+||+.|+.==.-+-.++..|..+.. ...|.||+... . -..-|..++++.|+++.. ....|.+.|.+
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 36788888622 1 234588999999998864 22567777655
No 43
>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=37.72 E-value=42 Score=27.43 Aligned_cols=28 Identities=21% Similarity=0.483 Sum_probs=24.4
Q ss_pred cCHHHHHHHHHhcCCcHHHHHHHHHccc
Q 010943 174 LSRDVIREVLDSCGYDMQKSMSKLIDHS 201 (497)
Q Consensus 174 L~~~vIr~VL~~cGyDv~ks~d~LLd~s 201 (497)
-+-+-|-.+|.-|+.|...+..+||++-
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 44
>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=37.18 E-value=1.7e+02 Score=23.46 Aligned_cols=64 Identities=20% Similarity=0.296 Sum_probs=44.3
Q ss_pred eeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHc-CC-ceEe-eCCCeEEEEEe
Q 010943 409 LLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEE-SI-EWTE-EGNAGTILIPL 484 (497)
Q Consensus 409 tIDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~ke-gi-~w~e-~~n~GvIlI~L 484 (497)
+||+.|+...+....+-..+..+.. ...|.||.- | .. . -+...|... |+ .|.. ...+|...|++
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---GETLELVND---H--DP---R-PLYPQLEERRGFFSWEYEEQGPGEWRVRI 67 (69)
T ss_pred CEECCCCCCcChHHHHHHHHHcCCC---CCEEEEEeC---C--CC---H-HHHHHHHHhCCCceEEEEEcCCCEEEEEE
Confidence 5899999888888888888887753 367777742 2 11 2 355566666 88 8864 44777777765
No 45
>COG1447 CelC Phosphotransferase system cellobiose-specific component IIA [Carbohydrate transport and metabolism]
Probab=37.03 E-value=1.1e+02 Score=27.63 Aligned_cols=38 Identities=21% Similarity=0.295 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHH
Q 010943 348 GTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREA 386 (497)
Q Consensus 348 ~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karea 386 (497)
+.|..+| +|-++.+.|+.+.|..+.++|+..-..+..+
T Consensus 18 ~ArS~~~-eAl~~Ak~g~f~~A~~~i~eA~~~l~eAH~~ 55 (105)
T COG1447 18 NARSKAY-EALKAAKEGDFEEAEELIQEANDALNEAHHV 55 (105)
T ss_pred cHhHHHH-HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4555555 5999999999999999999998765554443
No 46
>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=36.94 E-value=1.6e+02 Score=25.40 Aligned_cols=60 Identities=22% Similarity=0.186 Sum_probs=48.6
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 010943 330 NVEEDSFQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADEESN 391 (497)
Q Consensus 330 ~~~d~~Y~~~R~~A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean~~AA 391 (497)
-..+..|..+..+.......||++..+=..+...| +.+..|.++++...+.......+..
T Consensus 32 ~~ld~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~--~~~~~l~~e~~~lk~~i~~le~~~~ 91 (108)
T PF02403_consen 32 IELDQERRELQQELEELRAERNELSKEIGKLKKAG--EDAEELKAEVKELKEEIKELEEQLK 91 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTT--CCTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhCc--ccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34678888899999999999999999999999988 5567788888888777777655443
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=36.92 E-value=30 Score=28.26 Aligned_cols=29 Identities=21% Similarity=0.311 Sum_probs=26.4
Q ss_pred CCccCHHHHHHHHHHhCCCchhhhhhhccc
Q 010943 20 GSVFTMQEIALACRNAGRNPDLAGESLCDK 49 (497)
Q Consensus 20 gs~fSl~~ia~Ay~~A~~d~~~A~eiL~~~ 49 (497)
|+ .|=+||-+.+++.|-|+|.|++=|...
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 899999999999999999999988753
No 48
>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=36.31 E-value=44 Score=24.58 Aligned_cols=39 Identities=18% Similarity=0.272 Sum_probs=30.7
Q ss_pred hhHHHHHHHHHhcCccccCHHHHHHHHHhcCCcHHHHHHHHHc
Q 010943 157 QKEMEDFLFKLLGEGFQLSRDVIREVLDSCGYDMQKSMSKLID 199 (497)
Q Consensus 157 ~~d~E~FL~~MLG~gf~L~~~vIr~VL~~cGyDv~ks~d~LLd 199 (497)
.=+.|.+|..||.++ -..+..+|..||-|+++-.++|-.
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 49
>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=34.00 E-value=29 Score=25.48 Aligned_cols=22 Identities=32% Similarity=0.199 Sum_probs=18.2
Q ss_pred HHHHHHHHHhCCCchhhhhhhc
Q 010943 26 QEIALACRNAGRNPDLAGESLC 47 (497)
Q Consensus 26 ~~ia~Ay~~A~~d~~~A~eiL~ 47 (497)
+=|..|+.+.+||+..||++|+
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 50
>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=33.69 E-value=2.6e+02 Score=22.71 Aligned_cols=51 Identities=24% Similarity=0.272 Sum_probs=44.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHH
Q 010943 337 QHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREAD 387 (497)
Q Consensus 337 ~~~R~~A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean 387 (497)
..+.....+.....++|.++-..+|..+|...|..+..+=+++....++..
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 678888888889999999999999999999999999999999888776653
No 51
>PF14164 YqzH: YqzH-like protein
Probab=33.67 E-value=22 Score=29.42 Aligned_cols=13 Identities=38% Similarity=0.726 Sum_probs=11.4
Q ss_pred HHHHHHhcCCcHH
Q 010943 179 IREVLDSCGYDMQ 191 (497)
Q Consensus 179 Ir~VL~~cGyDv~ 191 (497)
|+.+|.|+|||++
T Consensus 10 i~~~l~QYg~d~~ 22 (64)
T PF14164_consen 10 IINCLRQYGYDVE 22 (64)
T ss_pred HHHHHHHhCCccc
Confidence 6789999999975
No 52
>PRK03954 ribonuclease P protein component 4; Validated
Probab=32.25 E-value=1.4e+02 Score=27.39 Aligned_cols=38 Identities=18% Similarity=0.136 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHH
Q 010943 347 RGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKARE 385 (497)
Q Consensus 347 ~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~kare 385 (497)
.+.++-+|+.|..++ ..+.++|.+|...++....+++-
T Consensus 19 ~eRi~~L~~~A~~~~-~~~pelar~Yv~lar~Is~K~ri 56 (121)
T PRK03954 19 RERIDTLFTLAERVF-PYSPELANRYVELALAVQQKAKV 56 (121)
T ss_pred HHHHHHHHHHHHHHh-hcCHHHHHHHHHHHHHHHHHhcc
Confidence 355667999998888 56789898888888777666654
No 53
>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=29.44 E-value=1.8e+02 Score=23.25 Aligned_cols=65 Identities=14% Similarity=0.087 Sum_probs=44.1
Q ss_pred eecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCCceEee-CCCeEEEEEe
Q 010943 410 LDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE-GNAGTILIPL 484 (497)
Q Consensus 410 IDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi~w~e~-~n~GvIlI~L 484 (497)
||+-|+.==.=+-.++..|..+. ....|.|++.-.. -..-|..++++.|++.... .+.|.+.+.+
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 67777776666777788877663 2367888875221 2345889999999987642 2567666654
No 54
>PRK01773 hscB co-chaperone HscB; Provisional
Probab=28.97 E-value=2.9e+02 Score=26.64 Aligned_cols=54 Identities=13% Similarity=0.095 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHH
Q 010943 335 SFQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADE 388 (497)
Q Consensus 335 ~Y~~~R~~A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean~ 388 (497)
+...+.+...+....+.+|.++-.+||..+|.+.|+.+..+=+++.....+.+.
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 456788888888899999999999999999999999999999998888877653
No 55
>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=28.32 E-value=72 Score=28.19 Aligned_cols=31 Identities=13% Similarity=0.004 Sum_probs=25.3
Q ss_pred EEEEecCCCCCCCCccHHHHHHHHHHcCCceEee
Q 010943 441 KVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE 474 (497)
Q Consensus 441 rVItG~G~HS~g~~k~kpAV~klL~kegi~w~e~ 474 (497)
-||+|+|.+-. .+.|.+.++|++.||.....
T Consensus 55 iliiGTG~~~~---~~~~~~~~~l~~~gI~vE~m 85 (109)
T cd00248 55 ILLIGTGAEIA---FLPRALRAALRAAGIGVEVM 85 (109)
T ss_pred EEEEcCCCCCC---cCCHHHHHHHHHcCCeEEEe
Confidence 58999999863 35678999999999987664
No 56
>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=27.46 E-value=1.1e+02 Score=29.07 Aligned_cols=38 Identities=5% Similarity=0.051 Sum_probs=30.2
Q ss_pred cCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCC
Q 010943 412 LHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTT 452 (497)
Q Consensus 412 LHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g 452 (497)
+-|.+|.+|+.+|+--|..-..+ .+.+-.-|.|+|+..
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 36999999999999887765554 456677889999874
No 57
>PRK11018 hypothetical protein; Provisional
Probab=26.53 E-value=3.7e+02 Score=22.23 Aligned_cols=68 Identities=13% Similarity=0.047 Sum_probs=46.0
Q ss_pred CCeeecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCCceEe-eCCCeEEEEEe
Q 010943 407 DLLLDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTE-EGNAGTILIPL 484 (497)
Q Consensus 407 ~~tIDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi~w~e-~~n~GvIlI~L 484 (497)
..+||+-|+.==.=+-.++..|..+. ..+.|.||+-. .. -..-|..++++.|++... +...|.+.+.|
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---KGEILEVVSDC------PQ-SINNIPLDARNHGYTVLDIQQDGPTIRYLI 76 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCC---CCCEEEEEeCC------cc-HHHHHHHHHHHcCCEEEEEEecCCeEEEEE
Confidence 47899999986666666677776664 23678887642 11 233588999999998753 33567766654
No 58
>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=26.11 E-value=3.3e+02 Score=25.69 Aligned_cols=53 Identities=8% Similarity=0.131 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHH
Q 010943 336 FQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREADE 388 (497)
Q Consensus 336 Y~~~R~~A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karean~ 388 (497)
...+.....+....+.+|...-.+||..+|.+.|..+..+=+++.....+.+.
T Consensus 99 ~~~L~~l~~~~~~~~~~~~~~l~~~~~~~d~~~A~~~~~kLky~~kl~~~i~~ 151 (157)
T TIGR00714 99 EARLESFIKRVKKMFQTRHQLLVEQLDNQTWAAAADYTRKLRFLDKLRSSAEQ 151 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677888888888999999999999999999999999999999888777654
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=26.05 E-value=32 Score=34.55 Aligned_cols=29 Identities=31% Similarity=0.604 Sum_probs=24.7
Q ss_pred hhHHHHHHHHHhcCccccCHHHHHHHHHh
Q 010943 157 QKEMEDFLFKLLGEGFQLSRDVIREVLDS 185 (497)
Q Consensus 157 ~~d~E~FL~~MLG~gf~L~~~vIr~VL~~ 185 (497)
.++-|+|=..+|+++|.+|.++||.+|..
T Consensus 24 ~~~p~~~t~~~Lae~F~vspe~irrILks 52 (225)
T PF06413_consen 24 KEDPEEWTVERLAESFKVSPEAIRRILKS 52 (225)
T ss_pred HhCccccCHHHHHhhCCCCHHHHHHHHhc
Confidence 44556688899999999999999999954
No 60
>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=25.93 E-value=19 Score=32.70 Aligned_cols=25 Identities=20% Similarity=0.402 Sum_probs=17.8
Q ss_pred hHHHHHHHHHhcCccccCHHHHHHH
Q 010943 158 KEMEDFLFKLLGEGFQLSRDVIREV 182 (497)
Q Consensus 158 ~d~E~FL~~MLG~gf~L~~~vIr~V 182 (497)
+|.-=|+-+||||+|=+.-.||++|
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 4445588999999999999999986
No 61
>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=25.64 E-value=85 Score=28.27 Aligned_cols=51 Identities=8% Similarity=-0.009 Sum_probs=32.3
Q ss_pred HHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCCceEee
Q 010943 420 AIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE 474 (497)
Q Consensus 420 Ai~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi~w~e~ 474 (497)
.-++-.+++..+..... +.=-||+|+|.+ ...+.|.+.++|++.||.....
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 33444455554432111 222489999998 3346678999999999986654
No 62
>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=24.85 E-value=4.4e+02 Score=25.87 Aligned_cols=48 Identities=19% Similarity=0.153 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHH
Q 010943 337 QHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAR 384 (497)
Q Consensus 337 ~~~R~~A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~kar 384 (497)
..+.+...++...-.++.++|..|...|+-.+|+.-..+-+.|.+.+.
T Consensus 55 k~~e~~~~~~~~~~~~~~~~A~~Al~~G~EdLAr~Al~~k~~~~~~~~ 102 (219)
T TIGR02977 55 KELERRVSRLEAQVADWQEKAELALSKGREDLARAALIEKQKAQELAE 102 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 344455556666777899999999999999998877666555554443
No 63
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=23.77 E-value=1.1e+02 Score=26.54 Aligned_cols=48 Identities=10% Similarity=0.280 Sum_probs=33.9
Q ss_pred hhHHHHHHHHHhcCccc---------cCHHHHHHHHHhcCCcHHHHHHHHHccccccc
Q 010943 157 QKEMEDFLFKLLGEGFQ---------LSRDVIREVLDSCGYDMQKSMSKLIDHSAETL 205 (497)
Q Consensus 157 ~~d~E~FL~~MLG~gf~---------L~~~vIr~VL~~cGyDv~ks~d~LLd~s~~~~ 205 (497)
..-+++|+-.+.|++-. +...+|+++|.+||+++.++. .+|.++..++
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 64
>PF10231 DUF2315: Uncharacterised conserved protein (DUF2315); InterPro: IPR018796 This entry consists of small conserved proteins found from worms to humans. Their function is not known.
Probab=22.14 E-value=6.4e+02 Score=23.37 Aligned_cols=34 Identities=15% Similarity=0.185 Sum_probs=28.8
Q ss_pred ccchHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHc
Q 010943 330 NVEEDSFQHLRTAV----MEYRGTMKEYCKAAIDAFAQ 363 (497)
Q Consensus 330 ~~~d~~Y~~~R~~A----~eh~~~Rne~f~kA~~AY~~ 363 (497)
-..+..|..+|.+. .++|..-|..|.++.+||..
T Consensus 26 t~lE~klR~~Rqe~~~wNq~FW~~~N~~F~~~K~~fi~ 63 (126)
T PF10231_consen 26 TPLERKLRLLRQETQEWNQEFWAKHNIRFSKEKEEFIE 63 (126)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677888888886 46789999999999999998
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=22.09 E-value=7.2e+02 Score=24.02 Aligned_cols=52 Identities=21% Similarity=0.165 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHH
Q 010943 334 DSFQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKARE 385 (497)
Q Consensus 334 ~~Y~~~R~~A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~kare 385 (497)
.....+.....++...-.++..+|..|...|+-..|..+..+=..+...+..
T Consensus 51 a~~~~le~~~~~~~~~~~~~~~~A~~Al~~g~edLAr~al~~k~~~e~~~~~ 102 (221)
T PF04012_consen 51 ANQKRLERKLDEAEEEAEKWEKQAELALAAGREDLAREALQRKADLEEQAER 102 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHH
Confidence 3444555666666677778899999999999999988777765555444433
No 66
>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=21.96 E-value=1.1e+02 Score=26.99 Aligned_cols=31 Identities=10% Similarity=0.035 Sum_probs=24.7
Q ss_pred EEEEecCCCCCCCCccHHHHHHHHHHcCCceEee
Q 010943 441 KVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE 474 (497)
Q Consensus 441 rVItG~G~HS~g~~k~kpAV~klL~kegi~w~e~ 474 (497)
-||+|+|.+-. -+.|++.++|++.||.....
T Consensus 55 iliiGTG~~~~---~~~~~~~~~l~~~gi~vE~m 85 (109)
T cd05560 55 VILLGTGERQR---FPPPALLAPLLARGIGVEVM 85 (109)
T ss_pred EEEEecCCCCC---cCCHHHHHHHHHcCCeEEEE
Confidence 58999999854 23578999999999987654
No 67
>cd05126 Mth938 Mth938 domain. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. The function of the protein has not been determined.
Probab=21.73 E-value=1.2e+02 Score=27.30 Aligned_cols=51 Identities=14% Similarity=0.097 Sum_probs=37.8
Q ss_pred ecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCCceEee
Q 010943 411 DLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE 474 (497)
Q Consensus 411 DLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi~w~e~ 474 (497)
+.|.|...+..++|... | . -||+|+|.+-. -.+.|++.++|++.||.....
T Consensus 42 ~~~~l~~~~l~~ll~~~-------p--e--ivliGTG~~~~--~~~~~~~~~~l~~~Gi~ve~m 92 (117)
T cd05126 42 TSHGLQPEELEELLEEG-------V--E--VIVIGTGQSGA--LKVPPETVEKLEKRGVEVLVL 92 (117)
T ss_pred CcccCCHHHHHHHHhcC-------C--C--EEEEcCCCCcc--ccCCHHHHHHHHhcCCEEEEc
Confidence 88999998877777531 2 1 59999998743 124678889999999987653
No 68
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=21.47 E-value=4.3e+02 Score=21.18 Aligned_cols=65 Identities=18% Similarity=0.065 Sum_probs=41.7
Q ss_pred eecCCCCHHHHHHHHHHHHHhhcCCCCcceEEEEEecCCCCCCCCccHHHHHHHHHHcCCceEe-eCCCeEEEEEe
Q 010943 410 LDLHDHGAKEAIRLLKCHLSSLSGIPTIKYLKVILEMNDEDTTKGGRRRRVMKLLEEESIEWTE-EGNAGTILIPL 484 (497)
Q Consensus 410 IDLHGLhV~EAi~iLk~~L~~l~~~~s~~~LrVItG~G~HS~g~~k~kpAV~klL~kegi~w~e-~~n~GvIlI~L 484 (497)
||+-|+.==.=+-.+++.|..+. ....|.|++-. . .-..-|.+++++.|+++.+ +...|.+.|.|
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~---~G~~l~V~~d~------~-~s~~ni~~~~~~~g~~v~~~~~~~~~~~~~i 67 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLK---PGEILEVISDC------P-QSINNIPIDARNHGYKVLAIEQSGPTIRYLI 67 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCC---CCCEEEEEecC------c-hHHHHHHHHHHHcCCEEEEEEecCCEEEEEE
Confidence 66667665555566677777654 33678887632 1 1234588999999998864 22456666654
No 69
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=21.45 E-value=1.8e+02 Score=29.24 Aligned_cols=46 Identities=22% Similarity=0.280 Sum_probs=39.5
Q ss_pred ccchhHHHHHHHHHhc-CccccCHHHHHHHHHhcCCcHHHHHHHHHc
Q 010943 154 DHLQKEMEDFLFKLLG-EGFQLSRDVIREVLDSCGYDMQKSMSKLID 199 (497)
Q Consensus 154 ~~~~~d~E~FL~~MLG-~gf~L~~~vIr~VL~~cGyDv~ks~d~LLd 199 (497)
.+..+++.++|-.++. +|..++.+++...+..||.|+.+++..|-.
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 70
>COG2250 Uncharacterized conserved protein related to C-terminal domain of eukaryotic chaperone, SACSIN [Function unknown]
Probab=21.06 E-value=3.6e+02 Score=24.70 Aligned_cols=39 Identities=18% Similarity=0.004 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHH
Q 010943 340 RTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKF 378 (497)
Q Consensus 340 R~~A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~ 378 (497)
|..+....+.....+..|...+..|+...|-++|+|+=+
T Consensus 3 ~~~~~~~~~rA~~~l~~A~~~le~G~y~~a~f~aqQAve 41 (132)
T COG2250 3 REEAEKWLRRAERDLKLAKRDLELGDYDLACFHAQQAVE 41 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHH
Confidence 566777777788889999999999999999999888644
No 71
>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]
Probab=20.71 E-value=6.7e+02 Score=25.28 Aligned_cols=44 Identities=18% Similarity=0.157 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHH
Q 010943 343 VMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAREA 386 (497)
Q Consensus 343 A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~karea 386 (497)
..+......++..+|..|...|+-..|.+..++-..|.......
T Consensus 61 ~~~~~~~~~k~e~~A~~Al~~g~E~LAr~al~~~~~le~~~~~~ 104 (225)
T COG1842 61 LEEAQARAEKLEEKAELALQAGNEDLAREALEEKQSLEDLAKAL 104 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 34445566789999999999999999999888877766555543
No 72
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=20.42 E-value=1.4e+02 Score=22.86 Aligned_cols=26 Identities=15% Similarity=0.387 Sum_probs=20.6
Q ss_pred cHHHHHHHHHHcCCceEeeCCCeEEEE
Q 010943 456 RRRRVMKLLEEESIEWTEEGNAGTILI 482 (497)
Q Consensus 456 ~kpAV~klL~kegi~w~e~~n~GvIlI 482 (497)
.+.+..+.|+++||.|... ..|..+|
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 73
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=20.41 E-value=5.3e+02 Score=25.93 Aligned_cols=51 Identities=22% Similarity=0.234 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHH
Q 010943 334 DSFQHLRTAVMEYRGTMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEKAR 384 (497)
Q Consensus 334 ~~Y~~~R~~A~eh~~~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~kar 384 (497)
+++++.|.+|.+..+..-.+...|.-+..+||.+.|..--+++...-++.+
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 567789999999999999999999999999999988776666655444444
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=20.25 E-value=1.1e+02 Score=26.72 Aligned_cols=31 Identities=10% Similarity=0.005 Sum_probs=23.0
Q ss_pred EEEEecCCCCCCCCccHHHHHHHHHHcCCceEee
Q 010943 441 KVILEMNDEDTTKGGRRRRVMKLLEEESIEWTEE 474 (497)
Q Consensus 441 rVItG~G~HS~g~~k~kpAV~klL~kegi~w~e~ 474 (497)
-||+|+|.. ...+.|.+.++|++.||.....
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 3446789999999999876543
No 75
>PF12854 PPR_1: PPR repeat
Probab=20.24 E-value=81 Score=21.95 Aligned_cols=27 Identities=22% Similarity=0.117 Sum_probs=22.4
Q ss_pred cCHHHHHHHHHHhCCCchhhhhhhcccc
Q 010943 23 FTMQEIALACRNAGRNPDLAGESLCDKQ 50 (497)
Q Consensus 23 fSl~~ia~Ay~~A~~d~~~A~eiL~~~~ 50 (497)
+|..-+-.+||++| +++.|-++|-.|+
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 7999999988774
No 76
>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=20.04 E-value=1.4e+02 Score=24.37 Aligned_cols=34 Identities=15% Similarity=0.102 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHH
Q 010943 349 TMKEYCKAAIDAFAQGDHVQAEKLLEQGKFFYEK 382 (497)
Q Consensus 349 ~Rne~f~kA~~AY~~Gd~a~A~~LSeqGk~~~~k 382 (497)
..+-+|+.|...+..++.+.|.+|....+...++
T Consensus 2 Ri~~L~~~a~~~~~~~~~~lsr~y~~~~~~i~~k 35 (85)
T PF04032_consen 2 RINFLYQAAHLLLADGSPSLSRHYMKLMRKISKK 35 (85)
T ss_dssp HHHHHHHHHH-HHCCC-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Confidence 4566777777689999999888887776655443
Done!