Query 043016
Match_columns 511
No_of_seqs 169 out of 575
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 11:58:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043016.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043016hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00463 SMR Small MutS-rela 99.6 1.1E-15 2.4E-20 126.4 8.7 77 432-508 2-80 (80)
2 PF01713 Smr: Smr domain; Int 99.6 8E-15 1.7E-19 122.1 7.1 72 434-508 1-83 (83)
3 PF08590 DUF1771: Domain of un 99.5 8.7E-15 1.9E-19 118.2 1.4 66 361-426 1-66 (66)
4 COG2840 Uncharacterized protei 99.1 5E-10 1.1E-14 107.6 9.5 83 425-509 90-180 (184)
5 PRK04946 hypothetical protein; 98.9 7.6E-09 1.6E-13 99.4 9.0 78 426-509 90-174 (181)
6 KOG2401 Predicted MutS-related 98.4 3.8E-06 8.2E-11 90.5 13.0 411 41-497 10-428 (448)
7 PRK00409 recombination and DNA 98.2 3.5E-06 7.6E-11 96.6 8.5 72 431-508 704-782 (782)
8 TIGR01069 mutS2 MutS2 family p 98.1 6.7E-06 1.5E-10 94.2 8.5 72 431-508 693-771 (771)
9 PF02845 CUE: CUE domain; Int 96.1 0.0099 2.1E-07 44.0 4.6 41 179-222 2-42 (42)
10 PF02845 CUE: CUE domain; Int 95.3 0.047 1E-06 40.3 5.4 39 45-83 3-41 (42)
11 cd00194 UBA Ubiquitin Associat 94.9 0.045 9.7E-07 39.1 4.2 34 185-220 5-38 (38)
12 COG1193 Mismatch repair ATPase 94.2 0.093 2E-06 60.7 6.9 70 432-507 677-753 (753)
13 smart00546 CUE Domain that may 94.1 0.13 2.7E-06 38.1 5.2 41 179-222 3-43 (43)
14 cd00194 UBA Ubiquitin Associat 92.3 0.32 7E-06 34.6 4.8 35 45-81 3-37 (38)
15 PF00627 UBA: UBA/TS-N domain; 91.4 0.54 1.2E-05 33.8 5.0 35 44-80 3-37 (37)
16 smart00546 CUE Domain that may 90.9 0.59 1.3E-05 34.5 5.0 39 45-83 4-42 (43)
17 smart00165 UBA Ubiquitin assoc 90.6 0.32 7E-06 34.5 3.2 25 195-219 13-37 (37)
18 PF00627 UBA: UBA/TS-N domain; 88.9 0.84 1.8E-05 32.8 4.4 31 183-218 7-37 (37)
19 PF08938 HBS1_N: HBS1 N-termin 86.1 0.44 9.5E-06 40.0 1.7 38 186-224 36-73 (79)
20 cd00291 SirA_YedF_YeeD SirA, Y 85.6 3.7 8.1E-05 32.5 6.8 66 433-508 1-68 (69)
21 smart00165 UBA Ubiquitin assoc 84.9 2.2 4.8E-05 30.1 4.7 35 45-81 3-37 (37)
22 PF01206 TusA: Sulfurtransfera 81.6 5.3 0.00011 32.0 6.2 66 433-508 2-69 (70)
23 PF06972 DUF1296: Protein of u 80.8 4 8.7E-05 33.2 5.0 40 43-82 5-44 (60)
24 PF03474 DMA: DMRTA motif; In 78.1 2.3 4.9E-05 31.9 2.7 25 195-219 15-39 (39)
25 cd03420 SirA_RHOD_Pry_redox Si 76.5 12 0.00027 30.2 6.9 66 433-508 1-68 (69)
26 cd03421 SirA_like_N SirA_like_ 75.7 14 0.00031 29.4 7.0 65 433-508 1-66 (67)
27 cd03423 SirA SirA (also known 68.8 23 0.0005 28.6 6.8 65 434-508 2-68 (69)
28 PF14555 UBA_4: UBA-like domai 68.1 13 0.00029 27.5 4.9 38 179-221 2-39 (43)
29 PF02954 HTH_8: Bacterial regu 67.8 5.2 0.00011 29.5 2.6 27 195-222 5-31 (42)
30 PLN03218 maturation of RBCL 1; 66.8 12 0.00025 45.5 6.6 76 431-506 921-1011(1060)
31 PRK01905 DNA-binding protein F 66.1 10 0.00023 31.5 4.4 48 177-225 10-66 (77)
32 PRK11018 hypothetical protein; 65.5 46 0.001 27.7 8.1 68 431-508 8-77 (78)
33 smart00685 DM14 Repeats in fly 64.7 32 0.00069 28.0 6.7 38 374-411 5-43 (59)
34 PF01963 TraB: TraB family; I 62.3 55 0.0012 32.0 9.4 89 373-496 169-257 (259)
35 KOG2401 Predicted MutS-related 60.4 3.7 8E-05 44.8 0.8 136 359-496 240-376 (448)
36 COG4008 Predicted metal-bindin 58.2 18 0.00039 33.8 4.7 37 44-83 115-151 (153)
37 PF11848 DUF3368: Domain of un 58.0 12 0.00025 28.7 3.0 29 180-208 20-48 (48)
38 PRK00299 sulfur transfer prote 57.5 59 0.0013 27.3 7.5 68 431-508 9-78 (81)
39 PF14346 DUF4398: Domain of un 57.2 81 0.0018 27.2 8.5 45 372-416 41-85 (103)
40 PF13763 DUF4167: Domain of un 56.4 49 0.0011 28.5 6.7 38 377-414 40-77 (80)
41 cd03422 YedF YedF is a bacteri 53.5 63 0.0014 26.1 6.8 65 434-508 2-68 (69)
42 PF10006 DUF2249: Uncharacteri 52.2 56 0.0012 26.3 6.3 64 433-508 1-68 (69)
43 TIGR01689 EcbF-BcbF capsule bi 48.1 37 0.0008 31.2 5.1 36 462-497 41-82 (126)
44 PRK06851 hypothetical protein; 47.0 4.1E+02 0.0088 28.8 14.1 124 360-496 115-246 (367)
45 COG0425 SirA Predicted redox p 46.4 74 0.0016 26.8 6.3 68 431-508 5-75 (78)
46 PF04505 Dispanin: Interferon- 43.4 35 0.00076 29.0 3.9 28 381-408 42-69 (82)
47 PF02861 Clp_N: Clp amino term 41.0 30 0.00064 25.6 2.8 37 180-220 14-50 (53)
48 PF03357 Snf7: Snf7; InterPro 39.9 1.5E+02 0.0032 27.1 7.9 55 362-416 10-64 (171)
49 PF12854 PPR_1: PPR repeat 39.2 33 0.00071 24.0 2.7 27 57-84 8-34 (34)
50 PF02954 HTH_8: Bacterial regu 38.6 29 0.00064 25.5 2.4 20 62-81 10-29 (42)
51 PF09644 Mg296: Mg296 protein; 37.0 12 0.00026 33.9 0.1 25 179-203 47-71 (121)
52 TIGR00823 EIIA-LAC phosphotran 37.0 1.1E+02 0.0024 27.0 6.2 47 377-426 18-64 (99)
53 PF06972 DUF1296: Protein of u 35.5 44 0.00095 27.4 3.1 27 195-221 19-45 (60)
54 TIGR03527 selenium_YedF seleni 35.1 1.3E+02 0.0028 29.6 6.9 65 434-508 1-67 (194)
55 PRK09591 celC cellobiose phosp 35.0 1.2E+02 0.0027 27.0 6.2 53 372-427 16-68 (104)
56 cd00215 PTS_IIA_lac PTS_IIA, P 34.7 1.3E+02 0.0028 26.6 6.2 48 377-427 16-63 (97)
57 PF13986 DUF4224: Domain of un 33.4 59 0.0013 25.0 3.4 27 480-506 16-42 (47)
58 PF14164 YqzH: YqzH-like prote 30.3 26 0.00056 29.0 1.0 20 182-212 3-22 (64)
59 COG2250 Uncharacterized conser 30.2 1.9E+02 0.0041 26.6 6.8 40 366-405 3-42 (132)
60 PF09507 CDC27: DNA polymerase 30.0 58 0.0013 34.5 3.9 38 438-475 13-52 (430)
61 PF02255 PTS_IIA: PTS system, 29.8 1.8E+02 0.0039 25.5 6.3 47 377-426 15-61 (96)
62 PF04858 TH1: TH1 protein; In 27.0 1.3E+02 0.0028 34.6 6.1 43 40-82 31-79 (584)
63 PF06413 Neugrin: Neugrin; In 26.7 28 0.00062 35.1 0.9 27 179-205 25-51 (225)
64 PF03948 Ribosomal_L9_C: Ribos 24.6 41 0.0009 28.8 1.4 24 53-76 28-52 (87)
65 COG2023 RPR2 RNase P subunit R 24.1 2.5E+02 0.0054 25.5 6.1 39 371-410 9-47 (105)
66 PF02403 Seryl_tRNA_N: Seryl-t 23.8 3.3E+02 0.0071 23.5 6.9 61 355-417 31-91 (108)
67 PRK00430 fis global DNA-bindin 23.7 1.2E+02 0.0027 26.4 4.1 30 195-225 55-84 (95)
68 KOG3837 Uncharacterized conser 23.3 2E+02 0.0043 32.1 6.4 36 378-413 214-249 (523)
69 smart00380 AP2 DNA-binding dom 23.0 65 0.0014 25.6 2.1 16 54-69 28-44 (64)
70 PF13812 PPR_3: Pentatricopept 22.0 1.2E+02 0.0025 19.9 3.0 28 58-86 3-30 (34)
71 PRK10454 PTS system N,N'-diace 21.5 5.7E+02 0.012 23.4 8.1 65 372-439 27-91 (115)
72 cd00018 AP2 DNA-binding domain 21.3 75 0.0016 24.9 2.2 16 54-69 29-45 (61)
73 PF08542 Rep_fac_C: Replicatio 21.0 1.5E+02 0.0032 24.4 4.0 47 177-224 4-50 (89)
74 PF05491 RuvB_C: Holliday junc 20.8 99 0.0021 26.4 2.9 29 40-68 7-37 (76)
No 1
>smart00463 SMR Small MutS-related domain.
Probab=99.63 E-value=1.1e-15 Score=126.41 Aligned_cols=77 Identities=34% Similarity=0.505 Sum_probs=70.4
Q ss_pred ceeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCC-CCcchHHHHHHHHHhCCCceee-CCCcEEEEEec
Q 043016 432 ITIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGV-GKSKLKQSVIELVENEGLHWSE-ENRGTVLIKLD 508 (511)
Q Consensus 432 ~~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~-G~akLKpAV~~~Lek~gi~~~e-~n~G~IlV~L~ 508 (511)
++|||||+++.||+.+|..+|..+...+..+.+.||||+|+||. |+++|+++|.++|...+|.|.+ .|.|+++|.|.
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 58999999999999999999998887653268999999999998 7999999999999999999988 79999999874
No 2
>PF01713 Smr: Smr domain; InterPro: IPR002625 This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 (P23909 from SWISSPROT) protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2, P94545 from SWISSPROT [].; PDB: 3QD7_X 2D9I_A 3FAU_A 2VKC_A 2ZQE_A.
Probab=99.55 E-value=8e-15 Score=122.08 Aligned_cols=72 Identities=36% Similarity=0.585 Sum_probs=58.0
Q ss_pred eecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCCceee-----------CCCcE
Q 043016 434 IDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGLHWSE-----------ENRGT 502 (511)
Q Consensus 434 IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi~~~e-----------~n~G~ 502 (511)
|||||+++.||+.+|+++|..+...+ ...++||||+|+||.+.. ||++|..||.+ ++.|.+ .|+|+
T Consensus 1 iDLHG~~~~eA~~~l~~~l~~~~~~~-~~~~~II~G~G~hS~~g~-Lk~~V~~~L~~-~~~~~~v~~~~~~~~~~g~~G~ 77 (83)
T PF01713_consen 1 IDLHGLTVEEALRALEEFLDEARQRG-IRELRIITGKGNHSKGGV-LKRAVRRWLEE-GYQYEEVLAYRDAEPEDGNSGA 77 (83)
T ss_dssp EE-TTS-HHHHHHHHHHHHHHHHHTT-HSEEEEE--STCTCCTSH-HHHHHHHHHHH-THCCTTEEEEEE--CCCTGGGE
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHHcC-CCEEEEEeccCCCCCCCc-HHHHHHHHHHh-hhccchhheeeecCCCCCCCeE
Confidence 89999999999999999999887654 479999999999999643 99999999988 766542 48999
Q ss_pred EEEEec
Q 043016 503 VLIKLD 508 (511)
Q Consensus 503 IlV~L~ 508 (511)
++|.|+
T Consensus 78 ~~V~lk 83 (83)
T PF01713_consen 78 TIVYLK 83 (83)
T ss_dssp EEEEE-
T ss_pred EEEEeC
Confidence 999884
No 3
>PF08590 DUF1771: Domain of unknown function (DUF1771); InterPro: IPR013899 This domain is almost always found adjacent to IPR002625 from INTERPRO. ; PDB: 2VKC_A.
Probab=99.48 E-value=8.7e-15 Score=118.25 Aligned_cols=66 Identities=35% Similarity=0.622 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 043016 361 EYQVFRKDAKQHWNSMKSCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQKADEKASHDIFKARNK 426 (511)
Q Consensus 361 ~Y~~lR~~A~e~~~~Rne~~~kAa~Ay~rGd~~~A~~Lseegr~~~~karean~~AA~~If~~rN~ 426 (511)
+|..+|.+|.+|++.|++||++|++||++||++.|++||++|+.|..+|+++|.+||+.||..+|.
T Consensus 1 ~Y~~~R~~A~~~~~~r~~~~~~A~~Ay~~Gd~~~A~~ls~~gk~~~~~~~~~n~~AA~~I~~~~N~ 66 (66)
T PF08590_consen 1 DYEKLRAEADEHARKRNECFQKAAEAYRRGDKAAAKELSEEGKQHNEKMKEANRQAAEAIFEERNA 66 (66)
T ss_dssp --------------------------------------------------SHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 599999999999999999999999999999999999999999999999999999999999999983
No 4
>COG2840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.07 E-value=5e-10 Score=107.56 Aligned_cols=83 Identities=20% Similarity=0.277 Sum_probs=70.5
Q ss_pred cCCCCCcceeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCC-CcchHHHHHHHHHhCCC--ceee----
Q 043016 425 NKSFENVITIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVG-KSKLKQSVIELVENEGL--HWSE---- 497 (511)
Q Consensus 425 N~~~~~~~~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G-~akLKpAV~~~Lek~gi--~~~e---- 497 (511)
+...+.+..||||||++.||-..|-.+|..+...+ +.++.||||+|. |.| .+.||++|-.||.++-- .|.+
T Consensus 90 rG~~~~e~~LDLHG~tq~eAr~~L~~Fi~~a~~~~-~rcv~VihGkG~-s~g~~~vLK~~Vp~WL~qhp~V~a~~~a~~~ 167 (184)
T COG2840 90 RGRYPPEARLDLHGLTQEEARQELGAFIARARAEG-LRCVLVIHGKGR-SKGSKPVLKSQVPRWLTQHPDVLAFHQAPRR 167 (184)
T ss_pred cCCCCcceeeeccCCCHHHHHHHHHHHHHHHHHhC-CcEEEEEeCCCc-CCCCchhHHHHHHHHHHhChHHHhhcccchh
Confidence 34445678999999999999999999999998664 679999999999 988 89999999999999653 4442
Q ss_pred -CCCcEEEEEecC
Q 043016 498 -ENRGTVLIKLDG 509 (511)
Q Consensus 498 -~n~G~IlV~L~~ 509 (511)
++.|.|+|.|.-
T Consensus 168 hGG~GAlyVlL~~ 180 (184)
T COG2840 168 HGGDGALYVLLRR 180 (184)
T ss_pred cCCceEEEEEEec
Confidence 578899999864
No 5
>PRK04946 hypothetical protein; Provisional
Probab=98.87 E-value=7.6e-09 Score=99.36 Aligned_cols=78 Identities=18% Similarity=0.179 Sum_probs=65.8
Q ss_pred CCCCCcceeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCC--cee-----eC
Q 043016 426 KSFENVITIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGL--HWS-----EE 498 (511)
Q Consensus 426 ~~~~~~~~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi--~~~-----e~ 498 (511)
....-+.+|||||+++.||...|..+|..+...+ ..++.||+|+|. ++||.+|..||.+... .|. ++
T Consensus 90 G~~~~~~~LDLhG~~~eeA~~~L~~fl~~a~~~g-~r~v~IIHGkG~-----gvLk~~V~~wL~q~~~V~af~~A~~~~G 163 (181)
T PRK04946 90 GDYSPELFLDLHGLTQLQAKQELGALIAACRKEH-VFCACVMHGHGK-----HILKQQTPLWLAQHPDVMAFHQAPKEWG 163 (181)
T ss_pred CCCCCceEEECCCCCHHHHHHHHHHHHHHHHHcC-CCEEEEEcCCCH-----hHHHHHHHHHHcCCchhheeeccCcccC
Confidence 3344578999999999999999999999987654 679999999995 7899999999998764 454 36
Q ss_pred CCcEEEEEecC
Q 043016 499 NRGTVLIKLDG 509 (511)
Q Consensus 499 n~G~IlV~L~~ 509 (511)
+.|+++|.|+.
T Consensus 164 G~GA~~VlLk~ 174 (181)
T PRK04946 164 GDAALLVLIEI 174 (181)
T ss_pred CceEEEEEEec
Confidence 89999999875
No 6
>KOG2401 consensus Predicted MutS-related protein involved in mismatch repair [Replication, recombination and repair]
Probab=98.36 E-value=3.8e-06 Score=90.54 Aligned_cols=411 Identities=16% Similarity=0.076 Sum_probs=238.9
Q ss_pred chhHHHHHHHHHhhCC-CCHHHHHHHHHHhcCChhHHHHHHHhhcCCCCCCCCCCCcc-cCCCCCCCCCCCCCCCCCCCC
Q 043016 41 DTKNQIIHSLTEAFGS-VSLEEATSAFCEANGDVNKAEELLTALTEGNSEDPLTSSSV-SGGSSSLDSGSSSGSWLGFGE 118 (511)
Q Consensus 41 ~~~~k~l~~LleaFgs-~Sl~~ia~Ay~~A~~d~~~A~eiL~~~~~~~~~~~~~~s~~-~~~~~~~~~~~~~~~~~~~~~ 118 (511)
+.+---+.-++++|+. |.+.++..|+++++..++....++.++.-..+ +.. +-.....+.++.+. .-+..
T Consensus 10 ~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~------~~~~~~~~~~~~~~s~~~--~~~~~ 81 (448)
T KOG2401|consen 10 DSDFMSLTLSLAAFSFSFKLVDLKAASEESSDEVDLGPPELSEMATSTS------SADRLQYTIELLEPSPSS--VSFES 81 (448)
T ss_pred chhhccchhccchhhhhhhhHhhhhcccccccccccCCCcchhhccccc------hhhhhcccccccCCCccc--ccccc
Confidence 3334556667888886 68999999999999888888888887644311 000 00001111111000 01111
Q ss_pred cccCCCCCcCCCCCCCCCcceeeeeccccccccccccccccCCCCCCC---CCC-CCCCCCccHHHHHHHHHHhhccccc
Q 043016 119 TSCVQNPVDYGNKKGGSRQKRVVAVSGMVANMLGKDYVRASPRKSGRF---KGV-GDDQSGFDKEEMEQFLYSMLGDECQ 194 (511)
Q Consensus 119 ~~~~~~~~~~~~~~~~~k~k~~~~s~GtVSsviGK~y~r~~~~~~~~~---~~~-~~~~~~~~~~d~E~FL~sMLGdgfq 194 (511)
+..... .. .....+.-...-.....+.|++++..++.+.+.. ..+ ..........-.++++-.|++....
T Consensus 82 ~~~~~~---~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~f~~~ 155 (448)
T KOG2401|consen 82 LRARAS---DE---NVDRGNQERILDRSRNQVAGKLKVSFVEKKLNEEEPQKEINPDGRILPEDPSFEESFRVENGFDPG 155 (448)
T ss_pred cccchh---hh---ccccHHHHhhcccccccccccccccccccccCccccccccCCcccccccccchHHHHHHhccCccc
Confidence 111111 00 0112233345566778899999999887764411 111 1123333567788888899999999
Q ss_pred cchHHHHHHHhhcCCcHHHHHHHHHcccCCCCCCCCCCCCCCcccccccccccCCcccccccCCCCCCCccccccccccc
Q 043016 195 FSMAVVRDVLCQCGYNVEKAMDVLLDLSAPSNERSMNDDDDFTFKEDRRFITEHTDNFTDRASDCTSYSSESDLYDSIWS 274 (511)
Q Consensus 195 L~~~vIrdVL~~cGyDv~ks~d~LLd~S~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~se~~~~~~~~~ 274 (511)
..+..+.+.|.||.+...-+.....++. +++. .+..+.. +...+ +.++-...++ ..+++ .-+++|-
T Consensus 156 ~~~~~~~~~~~~~~~~~~~~~n~~~~~~-~~~~-~d~~~~~-------~~~~~--~~~~~~~~~~--~~~~~-~~~~~~~ 221 (448)
T KOG2401|consen 156 EAIAFKIEDLPQKQVEGEDVDNCKVKNQ-ITNS-SDSKMAT-------EPGLN--DSLKKAYENV--DSSEE-SVELLRK 221 (448)
T ss_pred hhhhcchhhhccccccccccccceeecc-cccc-ccccccc-------ccccc--chhhcccccc--Ccchh-hhhhhcc
Confidence 9999999999999998888777777622 2221 1111111 11110 0011111111 11111 2233442
Q ss_pred cCCCcCCcchhhccCCCCCCCC-CCcCCCchHHHHHhhhcCCCCCCCCCCcccchhhhhhhhccCCCCCcccCCccccch
Q 043016 275 TGYNYRNNSKVLIGSEVPSPLK-ASDQSDLPQKVLESLFNISKSPQHEPTTMNWRNVVKKLQALGPRFDVSHSSSTEHQQ 353 (511)
Q Consensus 275 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~vLeslF~~per~e~~p~~~~w~~v~k~~~~~~~~~~~~~s~~~s~~~ 353 (511)
-++..+.+..+.+.....--.- .......++..|...|..-.++...+++..|+-.-+..... ..... ......+
T Consensus 222 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~---~~~~~-d~~~~~~ 297 (448)
T KOG2401|consen 222 EGFSVDVPSNAEKNSAKRLEELQKSQPEEDKAKKLRDQLYKSKRPAGSGKCLRKRHELSDKPRG---VLQAE-DDYNADE 297 (448)
T ss_pred CCCCccCcchhhcccccchhhcchhhhccchhhhHHHhhhhhcccccccchhhhhhhhhhhhhh---hhhcc-cccchhh
Confidence 2222223333322222211111 13456667888888888888888888888663332221111 11111 1111111
Q ss_pred hhhhcchHHHHHHHHHHHHHH-HHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcc
Q 043016 354 ELCAKGDEYQVFRKDAKQHWN-SMKSCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQKADEKASHDIFKARNKSFENVI 432 (511)
Q Consensus 354 ~~~~~~~~Y~~lR~~A~e~~~-~Rne~~~kAa~Ay~rGd~~~A~~Lseegr~~~~karean~~AA~~If~~rN~~~~~~~ 432 (511)
....-...+......+.+..+ .+..++++++..+..+....|.++.-.+......+......+-..+....+..+....
T Consensus 298 ~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~a~~~~~~~~~~~r~~ 377 (448)
T KOG2401|consen 298 LSDEFGNKESIKSEREIDNQRLYKKAAEQKAQPEIEDAINLQASELKPKVSLAVKGSYAVAKLKPATQWKLDNEEIERRS 377 (448)
T ss_pred hhhhhhhhhhhhhhHHhhhhhHHHHHHHhhhhhhhhhhhhhhhhhhchhhhhcccccchhhhcchHHHHHHhhhhhhccc
Confidence 122233333334444444444 7788889999999999999999999998888888888888888888888877777677
Q ss_pred eeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCCceee
Q 043016 433 TIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGLHWSE 497 (511)
Q Consensus 433 ~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi~~~e 497 (511)
..++|+..+.++... ..+.+++|+|.||.+.+++.+++...++..++.+.+
T Consensus 378 ~~~~~~~~i~~~~~~--------------~~~qv~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~ 428 (448)
T KOG2401|consen 378 EVGEHGEKISELSRR--------------LKLQVLFGRGIHSRGEARLPRAEKRSYEDPPQGFVE 428 (448)
T ss_pred ccccchhhhHhHhhh--------------ccccccccccccCccchhhhhhhhhhccCCccceee
Confidence 888888887766543 257789999999999998999988889988888865
No 7
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=98.19 E-value=3.5e-06 Score=96.59 Aligned_cols=72 Identities=24% Similarity=0.366 Sum_probs=61.5
Q ss_pred cceeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCC--cee-----eCCCcEE
Q 043016 431 VITIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGL--HWS-----EENRGTV 503 (511)
Q Consensus 431 ~~~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi--~~~-----e~n~G~I 503 (511)
..+|||||+++.||+..|..+|..+...+ ...++||+|+|. ++||.+|..||.++.+ .|. +++.|+.
T Consensus 704 ~~~lDL~G~~~eeA~~~l~~fl~~a~~~g-~~~v~IIHGkGt-----G~Lr~~v~~~L~~~~~V~~f~~a~~~~GG~Gat 777 (782)
T PRK00409 704 SLELDLRGMRYEEALERLDKYLDDALLAG-YGEVLIIHGKGT-----GKLRKGVQEFLKKHPSVKSFRDAPPNEGGFGVT 777 (782)
T ss_pred CceEECCCCCHHHHHHHHHHHHHHHHHcC-CCEEEEEcCCCh-----hHHHHHHHHHHcCCCceeeeeecCcccCCCeEE
Confidence 45899999999999999999999887554 579999999995 6899999999999875 343 4689999
Q ss_pred EEEec
Q 043016 504 LIKLD 508 (511)
Q Consensus 504 lV~L~ 508 (511)
+|.|+
T Consensus 778 ~V~lk 782 (782)
T PRK00409 778 IVELK 782 (782)
T ss_pred EEEEC
Confidence 99874
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=98.10 E-value=6.7e-06 Score=94.18 Aligned_cols=72 Identities=29% Similarity=0.452 Sum_probs=61.6
Q ss_pred cceeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCC--cee-----eCCCcEE
Q 043016 431 VITIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGL--HWS-----EENRGTV 503 (511)
Q Consensus 431 ~~~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi--~~~-----e~n~G~I 503 (511)
..+|||||+++.||+..|..+|..+...+ ...++||+|+|. +.||.+|..||.++.+ .|+ +++.|+.
T Consensus 693 ~~~ldl~G~~~~eA~~~l~~~ld~a~~~g-~~~v~IIHGkGt-----G~Lr~~v~~~L~~~~~V~~f~~a~~~~GG~G~t 766 (771)
T TIGR01069 693 SLTLDLRGQRSEEALDRLEKFLNDALLAG-YEVVLIIHGKGS-----GKLRKGVQELLKNHPKVKSFRDAPPNDGGSGVT 766 (771)
T ss_pred CceEECCCCCHHHHHHHHHHHHHHHHHCC-CCEEEEEcCCCh-----hHHHHHHHHHhcCCcceeeecccCcccCCceEE
Confidence 45899999999999999999999887654 579999999995 6799999999999875 343 4678999
Q ss_pred EEEec
Q 043016 504 LIKLD 508 (511)
Q Consensus 504 lV~L~ 508 (511)
+|.|.
T Consensus 767 ~V~l~ 771 (771)
T TIGR01069 767 IVYLE 771 (771)
T ss_pred EEEEC
Confidence 99873
No 9
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=96.15 E-value=0.0099 Score=43.96 Aligned_cols=41 Identities=39% Similarity=0.479 Sum_probs=35.1
Q ss_pred HHHHHHHHHhhccccccchHHHHHHHhhcCCcHHHHHHHHHccc
Q 043016 179 EEMEQFLYSMLGDECQFSMAVVRDVLCQCGYNVEKAMDVLLDLS 222 (511)
Q Consensus 179 ~d~E~FL~sMLGdgfqL~~~vIrdVL~~cGyDv~ks~d~LLd~S 222 (511)
+++-+.|..|+- +++.++|+.||.+|++||+.+++.||++|
T Consensus 2 ~~~v~~L~~mFP---~~~~~~I~~~L~~~~~~ve~ai~~LL~~~ 42 (42)
T PF02845_consen 2 EEMVQQLQEMFP---DLDREVIEAVLQANNGDVEAAIDALLEMS 42 (42)
T ss_dssp HHHHHHHHHHSS---SS-HHHHHHHHHHTTTTHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCC---CCCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence 345577888887 49999999999999999999999999875
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=95.30 E-value=0.047 Score=40.34 Aligned_cols=39 Identities=26% Similarity=0.417 Sum_probs=35.7
Q ss_pred HHHHHHHHhhCCCCHHHHHHHHHHhcCChhHHHHHHHhh
Q 043016 45 QIIHSLTEAFGSVSLEEATSAFCEANGDVNKAEELLTAL 83 (511)
Q Consensus 45 k~l~~LleaFgs~Sl~~ia~Ay~~A~~d~~~A~eiL~~~ 83 (511)
..++.|.+.|+.++.+.|..++.+.+||++.|-+.|.++
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~ 41 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEM 41 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 568899999999999999999999999999999999875
No 11
>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=94.92 E-value=0.045 Score=39.10 Aligned_cols=34 Identities=29% Similarity=0.328 Sum_probs=27.5
Q ss_pred HHHhhccccccchHHHHHHHhhcCCcHHHHHHHHHc
Q 043016 185 LYSMLGDECQFSMAVVRDVLCQCGYNVEKAMDVLLD 220 (511)
Q Consensus 185 L~sMLGdgfqL~~~vIrdVL~~cGyDv~ks~d~LLd 220 (511)
+-.|..-||. ...++++|..|++|+++|++.|++
T Consensus 5 v~~L~~mGf~--~~~~~~AL~~~~~d~~~A~~~L~~ 38 (38)
T cd00194 5 LEQLLEMGFS--REEARKALRATNNNVERAVEWLLE 38 (38)
T ss_pred HHHHHHcCCC--HHHHHHHHHHhCCCHHHHHHHHhC
Confidence 3344444665 999999999999999999999974
No 12
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=94.23 E-value=0.093 Score=60.68 Aligned_cols=70 Identities=21% Similarity=0.345 Sum_probs=57.3
Q ss_pred ceeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCCc----ee---eCCCcEEE
Q 043016 432 ITIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGLH----WS---EENRGTVL 504 (511)
Q Consensus 432 ~~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi~----~~---e~n~G~Il 504 (511)
..|||+|..+.+|+..|..++..+--.+ ...+.||+|+|. ++|+..|.++|+++..- +. +++.|+=+
T Consensus 677 ~~ldLrg~r~e~a~~~l~k~i~eail~~-~~~v~iihgkGt-----G~lre~v~~~Lk~~~~v~~~~~~~~~~GG~G~ti 750 (753)
T COG1193 677 NRLDLRGERSEEALDELDKSIDEAILEG-YEKVSIIHGKGT-----GKLREGVQEYLKKHKKVKSFRDAPPNEGGSGVTI 750 (753)
T ss_pred ccccccccccHHHHHHHHhhhHHHHHcC-CcceeEEeeeec-----hHHHHHHHHHHHhCCCccCcCCCCcCCCCCCeeE
Confidence 6999999999999999999998876443 568999999996 88999999999998642 22 35677766
Q ss_pred EEe
Q 043016 505 IKL 507 (511)
Q Consensus 505 V~L 507 (511)
|.|
T Consensus 751 v~l 753 (753)
T COG1193 751 VEL 753 (753)
T ss_pred EeC
Confidence 654
No 13
>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=94.14 E-value=0.13 Score=38.12 Aligned_cols=41 Identities=29% Similarity=0.306 Sum_probs=35.8
Q ss_pred HHHHHHHHHhhccccccchHHHHHHHhhcCCcHHHHHHHHHccc
Q 043016 179 EEMEQFLYSMLGDECQFSMAVVRDVLCQCGYNVEKAMDVLLDLS 222 (511)
Q Consensus 179 ~d~E~FL~sMLGdgfqL~~~vIrdVL~~cGyDv~ks~d~LLd~S 222 (511)
.++-+.|..|+- +|+..+|+.+|-.|++||+.+++.||..|
T Consensus 3 ~~~v~~L~~mFP---~l~~~~I~~~L~~~~g~ve~~i~~LL~~~ 43 (43)
T smart00546 3 DEALHDLKDMFP---NLDEEVIKAVLEANNGNVEATINNLLEGS 43 (43)
T ss_pred HHHHHHHHHHCC---CCCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence 456677888876 59999999999999999999999999764
No 14
>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=92.33 E-value=0.32 Score=34.60 Aligned_cols=35 Identities=37% Similarity=0.471 Sum_probs=30.0
Q ss_pred HHHHHHHHhhCCCCHHHHHHHHHHhcCChhHHHHHHH
Q 043016 45 QIIHSLTEAFGSVSLEEATSAFCEANGDVNKAEELLT 81 (511)
Q Consensus 45 k~l~~LleaFgs~Sl~~ia~Ay~~A~~d~~~A~eiL~ 81 (511)
+.++.|++ +| |+-+++..|+...++|++.|.+.|.
T Consensus 3 ~~v~~L~~-mG-f~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 3 EKLEQLLE-MG-FSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHH-cC-CCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 45666666 55 8999999999999999999999986
No 15
>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=91.35 E-value=0.54 Score=33.76 Aligned_cols=35 Identities=31% Similarity=0.461 Sum_probs=31.0
Q ss_pred HHHHHHHHHhhCCCCHHHHHHHHHHhcCChhHHHHHH
Q 043016 44 NQIIHSLTEAFGSVSLEEATSAFCEANGDVNKAEELL 80 (511)
Q Consensus 44 ~k~l~~LleaFgs~Sl~~ia~Ay~~A~~d~~~A~eiL 80 (511)
.+.|+.|++- .|+-+++-.|+...++|++.|.++|
T Consensus 3 ~~~v~~L~~m--Gf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 3 EEKVQQLMEM--GFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHH--TS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHHc--CCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 4678888888 5999999999999999999999987
No 16
>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=90.85 E-value=0.59 Score=34.52 Aligned_cols=39 Identities=21% Similarity=0.289 Sum_probs=36.0
Q ss_pred HHHHHHHHhhCCCCHHHHHHHHHHhcCChhHHHHHHHhh
Q 043016 45 QIIHSLTEAFGSVSLEEATSAFCEANGDVNKAEELLTAL 83 (511)
Q Consensus 45 k~l~~LleaFgs~Sl~~ia~Ay~~A~~d~~~A~eiL~~~ 83 (511)
..++.|.+.|+.++.+.|...+...+||++.|-+.|..+
T Consensus 4 ~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~ 42 (43)
T smart00546 4 EALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG 42 (43)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 578899999999999999999999999999999988753
No 17
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=90.57 E-value=0.32 Score=34.49 Aligned_cols=25 Identities=36% Similarity=0.367 Sum_probs=22.5
Q ss_pred cchHHHHHHHhhcCCcHHHHHHHHH
Q 043016 195 FSMAVVRDVLCQCGYNVEKAMDVLL 219 (511)
Q Consensus 195 L~~~vIrdVL~~cGyDv~ks~d~LL 219 (511)
++...++.+|-.|++|+++|++.|+
T Consensus 13 f~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 13 FSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 5666999999999999999999885
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=88.94 E-value=0.84 Score=32.75 Aligned_cols=31 Identities=42% Similarity=0.501 Sum_probs=25.3
Q ss_pred HHHHHhhccccccchHHHHHHHhhcCCcHHHHHHHH
Q 043016 183 QFLYSMLGDECQFSMAVVRDVLCQCGYNVEKAMDVL 218 (511)
Q Consensus 183 ~FL~sMLGdgfqL~~~vIrdVL~~cGyDv~ks~d~L 218 (511)
+=|..| || +...+++.|-.||+||++|++.|
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 44 56699999999999999999976
No 19
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=86.11 E-value=0.44 Score=40.05 Aligned_cols=38 Identities=29% Similarity=0.409 Sum_probs=29.8
Q ss_pred HHhhccccccchHHHHHHHhhcCCcHHHHHHHHHcccCC
Q 043016 186 YSMLGDECQFSMAVVRDVLCQCGYNVEKAMDVLLDLSAP 224 (511)
Q Consensus 186 ~sMLGdgfqL~~~vIrdVL~~cGyDv~ks~d~LLd~S~~ 224 (511)
-.-||+... +-..|+++|=.|.|||+||++.||.-...
T Consensus 36 r~~Lg~~~~-~e~~i~eal~~~~fDvekAl~~Ll~~~~~ 73 (79)
T PF08938_consen 36 REVLGDYVP-PEEQIKEALWHYYFDVEKALDYLLSKFKK 73 (79)
T ss_dssp HHHCCCCC---CCHHHHHHHHTTT-CCHHHHHHHHCCHS
T ss_pred HHHHcccCC-CHHHHHHHHHHHcCCHHHHHHHHHHhccC
Confidence 345888887 88899999999999999999999975543
No 20
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=85.61 E-value=3.7 Score=32.45 Aligned_cols=66 Identities=21% Similarity=0.188 Sum_probs=49.9
Q ss_pred eeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCCceee--CCCcEEEEEec
Q 043016 433 TIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGLHWSE--ENRGTVLIKLD 508 (511)
Q Consensus 433 ~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi~~~e--~n~G~IlV~L~ 508 (511)
+||+.|+....-+-.++..|..+. ....|.|++.... -..-|..||++.|+.+.. ..+|.+.|.|.
T Consensus 1 ~lD~rg~~CP~Pl~~~~~~l~~l~---~g~~l~v~~d~~~-------~~~~i~~~~~~~g~~~~~~~~~~~~~~i~i~ 68 (69)
T cd00291 1 TLDLRGLPCPLPVLKTKKALEKLK---SGEVLEVLLDDPG-------AVEDIPAWAKETGHEVLEVEEEGGVYRILIR 68 (69)
T ss_pred CccccCCcCCHHHHHHHHHHhcCC---CCCEEEEEecCCc-------HHHHHHHHHHHcCCEEEEEEEeCCEEEEEEE
Confidence 489999999999999998887753 3457888887553 355699999999999863 34556666553
No 21
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=84.90 E-value=2.2 Score=30.14 Aligned_cols=35 Identities=46% Similarity=0.573 Sum_probs=28.5
Q ss_pred HHHHHHHHhhCCCCHHHHHHHHHHhcCChhHHHHHHH
Q 043016 45 QIIHSLTEAFGSVSLEEATSAFCEANGDVNKAEELLT 81 (511)
Q Consensus 45 k~l~~LleaFgs~Sl~~ia~Ay~~A~~d~~~A~eiL~ 81 (511)
+.|+.|++ +| |+.+++..|+...++|++.|.++|.
T Consensus 3 ~~v~~L~~-mG-f~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 3 EKIDQLLE-MG-FSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred HHHHHHHH-cC-CCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 44544444 45 9999999999999999999999883
No 22
>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=81.56 E-value=5.3 Score=31.95 Aligned_cols=66 Identities=21% Similarity=0.233 Sum_probs=50.1
Q ss_pred eeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCCceee--CCCcEEEEEec
Q 043016 433 TIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGLHWSE--ENRGTVLIKLD 508 (511)
Q Consensus 433 ~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi~~~e--~n~G~IlV~L~ 508 (511)
+||+-|+.-..-+-.++..|..+. ....|.|++-... -..-|..|++..|+.+.+ ..+|.+.|.|.
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~---~G~~l~v~~d~~~-------~~~di~~~~~~~g~~~~~~~~~~~~~~i~I~ 69 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELP---PGEVLEVLVDDPA-------AVEDIPRWCEENGYEVVEVEEEGGEYRILIR 69 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSG---TT-EEEEEESSTT-------HHHHHHHHHHHHTEEEEEEEESSSSEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcC---CCCEEEEEECCcc-------HHHHHHHHHHHCCCEEEEEEEeCCEEEEEEE
Confidence 699999999999999999988764 3457888886553 456799999999999753 46777776653
No 23
>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=80.75 E-value=4 Score=33.20 Aligned_cols=40 Identities=30% Similarity=0.317 Sum_probs=37.5
Q ss_pred hHHHHHHHHHhhCCCCHHHHHHHHHHhcCChhHHHHHHHh
Q 043016 43 KNQIIHSLTEAFGSVSLEEATSAFCEANGDVNKAEELLTA 82 (511)
Q Consensus 43 ~~k~l~~LleaFgs~Sl~~ia~Ay~~A~~d~~~A~eiL~~ 82 (511)
-+|.++.|-|.-|..|=+||-+.+++.|-|+|.|++=|..
T Consensus 5 ~rk~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~ 44 (60)
T PF06972_consen 5 SRKTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLS 44 (60)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHh
Confidence 3789999999999999999999999999999999998874
No 24
>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=78.13 E-value=2.3 Score=31.86 Aligned_cols=25 Identities=24% Similarity=0.400 Sum_probs=22.2
Q ss_pred cchHHHHHHHhhcCCcHHHHHHHHH
Q 043016 195 FSMAVVRDVLCQCGYNVEKAMDVLL 219 (511)
Q Consensus 195 L~~~vIrdVL~~cGyDv~ks~d~LL 219 (511)
-.+.++.-||..|+.||=+|||.+|
T Consensus 15 ~kr~~Le~iL~~C~GDvv~AIE~~l 39 (39)
T PF03474_consen 15 QKRSVLELILQRCNGDVVQAIEQFL 39 (39)
T ss_pred CChHHHHHHHHHcCCcHHHHHHHhC
Confidence 3578899999999999999999875
No 25
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=76.53 E-value=12 Score=30.21 Aligned_cols=66 Identities=15% Similarity=0.189 Sum_probs=51.4
Q ss_pred eeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCCcee--eCCCcEEEEEec
Q 043016 433 TIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGLHWS--EENRGTVLIKLD 508 (511)
Q Consensus 433 ~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi~~~--e~n~G~IlV~L~ 508 (511)
.||+.|+.-..-+-.++..|..+. ....|.|++.-.. -..-|..|++..|+.+. +...|.+.+.|.
T Consensus 1 ~lD~rG~~CP~Pvl~~kkal~~l~---~G~~l~V~~d~~~-------a~~di~~~~~~~G~~~~~~~~~~~~~~~~I~ 68 (69)
T cd03420 1 EVDACGLQCPGPILKLKKEIDKLQ---DGEQLEVKASDPG-------FARDAQAWCKSTGNTLISLETEKGKVKAVIE 68 (69)
T ss_pred CcccCCCcCCHHHHHHHHHHHcCC---CCCEEEEEECCcc-------HHHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 489999999999999999988764 3357888887542 45569999999999996 345788877764
No 26
>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=75.68 E-value=14 Score=29.38 Aligned_cols=65 Identities=23% Similarity=0.253 Sum_probs=47.1
Q ss_pred eeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCCceee-CCCcEEEEEec
Q 043016 433 TIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGLHWSE-ENRGTVLIKLD 508 (511)
Q Consensus 433 ~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi~~~e-~n~G~IlV~L~ 508 (511)
.||+-|+.-.+-+-.++..| .+. ....|.|++-.. .-..-|..|+++.|+.+.. ...|.+.|.|.
T Consensus 1 ~lD~rG~~CP~P~l~~k~al-~~~---~g~~l~v~~d~~-------~s~~~i~~~~~~~G~~~~~~~~~~~~~i~I~ 66 (67)
T cd03421 1 TIDARGLACPQPVIKTKKAL-ELE---AGGEIEVLVDNE-------VAKENVSRFAESRGYEVSVEEKGGEFEITIT 66 (67)
T ss_pred CcccCCCCCCHHHHHHHHHH-hcC---CCCEEEEEEcCh-------hHHHHHHHHHHHcCCEEEEEecCCEEEEEEE
Confidence 48999999999999999999 553 234677775432 1344699999999999963 34557766654
No 27
>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=68.85 E-value=23 Score=28.58 Aligned_cols=65 Identities=12% Similarity=0.106 Sum_probs=49.9
Q ss_pred eecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCCceee--CCCcEEEEEec
Q 043016 434 IDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGLHWSE--ENRGTVLIKLD 508 (511)
Q Consensus 434 IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi~~~e--~n~G~IlV~L~ 508 (511)
||+-|+.-..=+-.++..|..+. ....|.|++.-.. -..-|..|+++.|+.+.. .++|.+.+.|.
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~---~G~~l~V~~dd~~-------s~~di~~~~~~~g~~~~~~~~~~~~~~~~I~ 68 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMK---PGDTLLVLATDPS-------TTRDIPKFCTFLGHELLAQETEDEPYRYLIR 68 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCC---CCCEEEEEeCCCc-------hHHHHHHHHHHcCCEEEEEEEcCCEEEEEEE
Confidence 89999999999999999887663 3456888876442 455699999999999963 46777777654
No 28
>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=68.09 E-value=13 Score=27.47 Aligned_cols=38 Identities=26% Similarity=0.407 Sum_probs=29.4
Q ss_pred HHHHHHHHHhhccccccchHHHHHHHhhcCCcHHHHHHHHHcc
Q 043016 179 EEMEQFLYSMLGDECQFSMAVVRDVLCQCGYNVEKAMDVLLDL 221 (511)
Q Consensus 179 ~d~E~FL~sMLGdgfqL~~~vIrdVL~~cGyDv~ks~d~LLd~ 221 (511)
+.+++|. +..| .+-++-+..|..|++|++.|++.-++-
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 4555 388999999999999999999988764
No 29
>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=67.78 E-value=5.2 Score=29.50 Aligned_cols=27 Identities=41% Similarity=0.688 Sum_probs=20.2
Q ss_pred cchHHHHHHHhhcCCcHHHHHHHHHccc
Q 043016 195 FSMAVVRDVLCQCGYNVEKAMDVLLDLS 222 (511)
Q Consensus 195 L~~~vIrdVL~~cGyDv~ks~d~LLd~S 222 (511)
+...+|+++|..||+++.++-..| .+|
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L-gis 31 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL-GIS 31 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH-TS-
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCC
Confidence 456899999999999999887654 444
No 30
>PLN03218 maturation of RBCL 1; Provisional
Probab=66.80 E-value=12 Score=45.50 Aligned_cols=76 Identities=24% Similarity=0.251 Sum_probs=55.3
Q ss_pred cceeecCCCChHHHHHHHHHHHHHHHh-------cCCCc------eEEEEEccCCCCCC-CcchHHHHHHHHHhCCCcee
Q 043016 431 VITIDLHGQHVKPAMKLLKLHLVMVSY-------AQSVQ------TLRVITGCGSHGVG-KSKLKQSVIELVENEGLHWS 496 (511)
Q Consensus 431 ~~~IDLHGL~V~EAl~~Lk~~L~~~~~-------~~s~~------~L~VITG~G~HS~G-~akLKpAV~~~Lek~gi~~~ 496 (511)
.+.||+|.|.|.-|.-.|..-|..++. .|... .=.|-||+|.|+.. -+++-.+|..+|++-+++|.
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 689999999999998887766654432 23211 11256777777555 36789999999999999998
Q ss_pred e-CCCcEEEEE
Q 043016 497 E-ENRGTVLIK 506 (511)
Q Consensus 497 e-~n~G~IlV~ 506 (511)
+ ...|.|.+.
T Consensus 1001 ~~~~~g~~~~~ 1011 (1060)
T PLN03218 1001 GSESHGKLRIN 1011 (1060)
T ss_pred CCCCCCeEEec
Confidence 6 445988764
No 31
>PRK01905 DNA-binding protein Fis; Provisional
Probab=66.06 E-value=10 Score=31.51 Aligned_cols=48 Identities=17% Similarity=0.263 Sum_probs=36.8
Q ss_pred cHHHHHHHHHHhhccc---------cccchHHHHHHHhhcCCcHHHHHHHHHcccCCC
Q 043016 177 DKEEMEQFLYSMLGDE---------CQFSMAVVRDVLCQCGYNVEKAMDVLLDLSAPS 225 (511)
Q Consensus 177 ~~~d~E~FL~sMLGdg---------fqL~~~vIrdVL~~cGyDv~ks~d~LLd~S~~~ 225 (511)
-++.++.||-.++|.+ -++....|+++|..||.++.++- .+|.++.++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~E~~~i~~aL~~~~gn~s~aA-r~LGIsrst 66 (77)
T PRK01905 10 IRDSLDQYFRDLDGSNPHDVYDMVLSCVEKPLLEVVMEQAGGNQSLAA-EYLGINRNT 66 (77)
T ss_pred HHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHHHHHHcCCCHHHHH-HHHCCCHHH
Confidence 3578899999998855 24567789999999999999985 455665443
No 32
>PRK11018 hypothetical protein; Provisional
Probab=65.53 E-value=46 Score=27.73 Aligned_cols=68 Identities=13% Similarity=0.130 Sum_probs=50.6
Q ss_pred cceeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCCcee--eCCCcEEEEEec
Q 043016 431 VITIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGLHWS--EENRGTVLIKLD 508 (511)
Q Consensus 431 ~~~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi~~~--e~n~G~IlV~L~ 508 (511)
..+||+-|+.-..=+-.++..|..+. ....|.|++--.. -..-|..|+++.|+.+. +...|.+.+.|.
T Consensus 8 ~~~lD~rG~~CP~Pvl~~kk~l~~l~---~G~~L~V~~d~~~-------a~~di~~~~~~~G~~v~~~~~~~g~~~~~I~ 77 (78)
T PRK11018 8 DYRLDMVGEPCPYPAVATLEALPQLK---KGEILEVVSDCPQ-------SINNIPLDARNHGYTVLDIQQDGPTIRYLIQ 77 (78)
T ss_pred CeeEECCCCcCCHHHHHHHHHHHhCC---CCCEEEEEeCCcc-------HHHHHHHHHHHcCCEEEEEEecCCeEEEEEE
Confidence 47899999999988888888887664 3445777765331 34569999999999995 345687777664
No 33
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=64.74 E-value=32 Score=27.97 Aligned_cols=38 Identities=16% Similarity=0.045 Sum_probs=29.4
Q ss_pred HHHH-HHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHH
Q 043016 374 NSMK-SCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQK 411 (511)
Q Consensus 374 ~~Rn-e~~~kAa~Ay~rGd~~~A~~Lseegr~~~~kare 411 (511)
..|. +|-..|.+|-+.||-+.|+.|...++.|....+.
T Consensus 5 ~~R~~~yk~Aa~~AK~~gd~~kAr~~~R~~K~~~~~I~~ 43 (59)
T smart00685 5 QQRQEQYKQAALQAKRAGDEEKARRHLRIAKQFDDAIKA 43 (59)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhhHHHHHHH
Confidence 3444 4555568999999999999999999988875554
No 34
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=62.31 E-value=55 Score=32.03 Aligned_cols=89 Identities=13% Similarity=0.199 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcceeecCCCChHHHHHHHHHHH
Q 043016 373 WNSMKSCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQKADEKASHDIFKARNKSFENVITIDLHGQHVKPAMKLLKLHL 452 (511)
Q Consensus 373 ~~~Rne~~~kAa~Ay~rGd~~~A~~Lseegr~~~~karean~~AA~~If~~rN~~~~~~~~IDLHGL~V~EAl~~Lk~~L 452 (511)
.....+.+.+..++|..||......+..+.. ......+.++..||... -..|
T Consensus 169 ~~~~~~~~~~~~~~~~~gd~~~l~~~~~~~~--------~~p~~~~~ll~~RN~~~--------------------~~~i 220 (259)
T PF01963_consen 169 IEDGEKMLEQLIEAWKNGDLDALMELMKEDE--------SFPELYEVLLDERNRRW--------------------AEKI 220 (259)
T ss_pred cccchHHHHHHHHHHHccCHHHHHHHHHhcc--------cCHHHHHHHHHHHhHHH--------------------HHHH
Confidence 4555778999999999999744433321111 44455677888887421 1122
Q ss_pred HHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCCcee
Q 043016 453 VMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGLHWS 496 (511)
Q Consensus 453 ~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi~~~ 496 (511)
..+-.. .+.+.|++|.||-..-.+ |...|++.||..+
T Consensus 221 ~~~l~~--~~~~fvvVGa~HL~G~~g-----vl~lLr~~Gy~V~ 257 (259)
T PF01963_consen 221 EELLKE--GGTVFVVVGAGHLPGEDG-----VLDLLRKKGYTVE 257 (259)
T ss_pred HHHHhc--CCCEEEEEcchhccchhh-----HHHHHHhCCceee
Confidence 222212 257999999998664222 7799999999875
No 35
>KOG2401 consensus Predicted MutS-related protein involved in mismatch repair [Replication, recombination and repair]
Probab=60.41 E-value=3.7 Score=44.82 Aligned_cols=136 Identities=15% Similarity=0.079 Sum_probs=107.2
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcceeecCC
Q 043016 359 GDEYQVFRKDAKQHWNSMKSCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQKADEKASHDIFKARNKSFENVITIDLHG 438 (511)
Q Consensus 359 ~~~Y~~lR~~A~e~~~~Rne~~~kAa~Ay~rGd~~~A~~Lseegr~~~~karean~~AA~~If~~rN~~~~~~~~IDLHG 438 (511)
...|+..+.........+..+|..+.-|+.-+....+..+..+.+...........++....|...+... ....+|+|+
T Consensus 240 ~~~~~~~~~~~~~~~k~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~s~~-~~~~~~~~~ 318 (448)
T KOG2401|consen 240 LEELQKSQPEEDKAKKLRDQLYKSKRPAGSGKCLRKRHELSDKPRGVLQAEDDYNADELSDEFGNKESIK-SEREIDNQR 318 (448)
T ss_pred hhhcchhhhccchhhhHHHhhhhhcccccccchhhhhhhhhhhhhhhhhcccccchhhhhhhhhhhhhhh-hhHHhhhhh
Confidence 3455556666666677777788888889988888999999999999888888888888888887776543 357899999
Q ss_pred CChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCC-CCcchHHHHHHHHHhCCCcee
Q 043016 439 QHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGV-GKSKLKQSVIELVENEGLHWS 496 (511)
Q Consensus 439 L~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~-G~akLKpAV~~~Lek~gi~~~ 496 (511)
+.+..|...+...+...-.. ....+.++.+.++|.. ++.+++|++..++..+.+...
T Consensus 319 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~v~~~~~a~~~~~~~~~~~r~ 376 (448)
T KOG2401|consen 319 LYKKAAEQKAQPEIEDAINL-QASELKPKVSLAVKGSYAVAKLKPATQWKLDNEEIERR 376 (448)
T ss_pred HHHHHHHhhhhhhhhhhhhh-hhhhhchhhhhcccccchhhhcchHHHHHHhhhhhhcc
Confidence 77777777777666544322 2357999999999986 799999999999999988764
No 36
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=58.21 E-value=18 Score=33.77 Aligned_cols=37 Identities=35% Similarity=0.436 Sum_probs=33.0
Q ss_pred HHHHHHHHHhhCCCCHHHHHHHHHHhcCChhHHHHHHHhh
Q 043016 44 NQIIHSLTEAFGSVSLEEATSAFCEANGDVNKAEELLTAL 83 (511)
Q Consensus 44 ~k~l~~LleaFgs~Sl~~ia~Ay~~A~~d~~~A~eiL~~~ 83 (511)
....++|.||| ++.+++-.|..+|| |+-.|-+||-.+
T Consensus 115 ~e~v~v~a~a~--v~~eeAr~aleeag-Dl~~A~k~l~~~ 151 (153)
T COG4008 115 VEEVEVLADAF--VTPEEAREALEEAG-DLRTAMKILRMK 151 (153)
T ss_pred HHHHHHHHHhc--CCHHHHHHHHHHcC-CHHHHHHHHHHh
Confidence 35678899999 99999999999999 999999999753
No 37
>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=57.97 E-value=12 Score=28.66 Aligned_cols=29 Identities=17% Similarity=0.356 Sum_probs=27.9
Q ss_pred HHHHHHHHhhccccccchHHHHHHHhhcC
Q 043016 180 EMEQFLYSMLGDECQFSMAVVRDVLCQCG 208 (511)
Q Consensus 180 d~E~FL~sMLGdgfqL~~~vIrdVL~~cG 208 (511)
+++.+|-.|.--||=+|-.+++++|..+|
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 38
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=57.49 E-value=59 Score=27.27 Aligned_cols=68 Identities=10% Similarity=0.056 Sum_probs=52.0
Q ss_pred cceeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCCcee--eCCCcEEEEEec
Q 043016 431 VITIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGLHWS--EENRGTVLIKLD 508 (511)
Q Consensus 431 ~~~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi~~~--e~n~G~IlV~L~ 508 (511)
..+||+-|+.-..=+-.++..|..+. ....|.||+.-.. -..-|..|+++.|+++. +..+|.+.+.|.
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~---~G~~l~V~~dd~~-------~~~di~~~~~~~G~~~~~~~~~~g~~~~~I~ 78 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQ---PGETLLIIADDPA-------TTRDIPSFCRFMDHELLAQETEQLPYRYLIR 78 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCC---CCCEEEEEeCCcc-------HHHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 46899999999999999999988764 3456888776332 45668999999999985 345777777664
No 39
>PF14346 DUF4398: Domain of unknown function (DUF4398)
Probab=57.15 E-value=81 Score=27.22 Aligned_cols=45 Identities=29% Similarity=0.386 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHH
Q 043016 372 HWNSMKSCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQKADEKA 416 (511)
Q Consensus 372 ~~~~Rne~~~kAa~Ay~rGd~~~A~~Lseegr~~~~karean~~A 416 (511)
++..-.+.+..|..+|..|+...|..|..+++.+.+.+...-..+
T Consensus 41 el~~A~~~L~~A~~a~~~~~y~~A~~~A~~A~~~A~~A~~~a~~~ 85 (103)
T PF14346_consen 41 ELKEAREKLQRAKAALDDGDYERARRLAEQAQADAELAEAKAEAA 85 (103)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 555556788999999999999999999999999877766544433
No 40
>PF13763 DUF4167: Domain of unknown function (DUF4167)
Probab=56.43 E-value=49 Score=28.55 Aligned_cols=38 Identities=18% Similarity=0.177 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHH
Q 043016 377 KSCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQKADE 414 (511)
Q Consensus 377 ne~~~kAa~Ay~rGd~~~A~~Lseegr~~~~karean~ 414 (511)
.+|.+.|.+|-..||+-.|..|.+-|.+|...+.++..
T Consensus 40 EKY~~LArDA~ssGDrV~aEny~QHAeHY~Ril~~~~~ 77 (80)
T PF13763_consen 40 EKYNQLARDAQSSGDRVLAENYLQHAEHYFRILAAAQA 77 (80)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45888999999999999999999999999988776654
No 41
>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=53.47 E-value=63 Score=26.13 Aligned_cols=65 Identities=17% Similarity=0.166 Sum_probs=47.9
Q ss_pred eecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCCceee--CCCcEEEEEec
Q 043016 434 IDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGLHWSE--ENRGTVLIKLD 508 (511)
Q Consensus 434 IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi~~~e--~n~G~IlV~L~ 508 (511)
||+-|+.-..=+-.++..|..+. ....|.|++--.. -..-|..|+++.|+.+.. ..+|.+.|.|.
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~---~G~~l~V~~d~~~-------s~~ni~~~~~~~g~~v~~~~~~~~~~~~~i~ 68 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLK---PGEILEVISDCPQ-------SINNIPIDARNHGYKVLAIEQSGPTIRYLIQ 68 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCC---CCCEEEEEecCch-------HHHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 89999998888888888887763 3456777765332 455699999999999963 45677777653
No 42
>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=52.24 E-value=56 Score=26.29 Aligned_cols=64 Identities=16% Similarity=0.320 Sum_probs=45.2
Q ss_pred eeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhC-CC-cee--eCCCcEEEEEec
Q 043016 433 TIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENE-GL-HWS--EENRGTVLIKLD 508 (511)
Q Consensus 433 ~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~-gi-~~~--e~n~G~IlV~L~ 508 (511)
+||+.|+...+.+..+-..+..+. ....|.||.-.- -.| +...|+.. |+ .|. +.++|...|.|.
T Consensus 1 ~LDvR~l~~~~p~~~il~~~~~L~---~Ge~l~lv~d~~--------P~p-L~~~l~~~~g~~~~~~~~~~~~~w~v~i~ 68 (69)
T PF10006_consen 1 VLDVRGLPPPEPHERILEALDELP---PGETLELVNDHD--------PRP-LYPQLEERRGFFSWEYEEQGPGEWRVRIT 68 (69)
T ss_pred CEECCCCCCcChHHHHHHHHHcCC---CCCEEEEEeCCC--------CHH-HHHHHHHhCCCceEEEEEcCCCEEEEEEE
Confidence 589999999999999888887774 345677776432 122 55556666 77 774 467888888774
No 43
>TIGR01689 EcbF-BcbF capsule biosynthesis phosphatase. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology.
Probab=48.09 E-value=37 Score=31.17 Aligned_cols=36 Identities=8% Similarity=0.109 Sum_probs=28.8
Q ss_pred ceEEEEEccCCCCC-C-C----cchHHHHHHHHHhCCCceee
Q 043016 462 QTLRVITGCGSHGV-G-K----SKLKQSVIELVENEGLHWSE 497 (511)
Q Consensus 462 ~~L~VITG~G~HS~-G-~----akLKpAV~~~Lek~gi~~~e 497 (511)
..+.|+||+..+.. | . ...-+.+.+||.+++++|.+
T Consensus 41 ~~IiiaTGR~~~~~~~n~~~i~~~~~~~t~~wL~k~~ipYd~ 82 (126)
T TIGR01689 41 FEIVISSSRNMRTYEGNVGKINIHTLPIIILWLNQHNVPYDE 82 (126)
T ss_pred CEEEEECCCCchhhhccccccchhhHHHHHHHHHHcCCCCce
Confidence 46999999998875 2 2 44556899999999999975
No 44
>PRK06851 hypothetical protein; Provisional
Probab=46.99 E-value=4.1e+02 Score=28.81 Aligned_cols=124 Identities=16% Similarity=0.249 Sum_probs=85.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHhcCC--CCCc
Q 043016 360 DEYQVFRKDAKQHWNSMKSCYQKASAAYSKGEWGYAAHLSEQGKSL------TKLAQKADEKASHDIFKARNKS--FENV 431 (511)
Q Consensus 360 ~~Y~~lR~~A~e~~~~Rne~~~kAa~Ay~rGd~~~A~~Lseegr~~------~~karean~~AA~~If~~rN~~--~~~~ 431 (511)
..-..+|++.........++|++|.+.+.. |..+-++-..+ .+++.+.-++=...||...... .+..
T Consensus 115 ~~l~~~k~eI~~~~~~~~~~~~~Ay~~l~~-----A~~ihdd~e~~y~~~md~~k~~~~~~~l~~~l~~~~~~~~~~g~~ 189 (367)
T PRK06851 115 DKLRKHKEEILKINEEISRCFQRAYEYLNE-----ALAIHDEWEKIYIENMDFAKANELTDELIQELFKGAPGKISKGKV 189 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccCcccccCCce
Confidence 445667787778888888888888887765 33333333222 3456666666677777775432 2334
Q ss_pred ceeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCCcee
Q 043016 432 ITIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGLHWS 496 (511)
Q Consensus 432 ~~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi~~~ 496 (511)
..+=+.|.|++-.+.++...+. ....+++|||.- ..|+..|-..|...+.++|+...
T Consensus 190 rh~F~ga~Tp~G~~s~~~~l~~------~~~~~~~i~G~p--G~GKstl~~~i~~~a~~~G~~v~ 246 (367)
T PRK06851 190 RHLFLGAITPKGAVDFVPSLTE------GVKNRYFLKGRP--GTGKSTMLKKIAKAAEERGFDVE 246 (367)
T ss_pred eeeeccccCCCcHHhhHHhHhc------ccceEEEEeCCC--CCcHHHHHHHHHHHHHhCCCeEE
Confidence 5677899999999998887763 235688998853 25778888889999999998653
No 45
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=46.40 E-value=74 Score=26.79 Aligned_cols=68 Identities=21% Similarity=0.219 Sum_probs=50.5
Q ss_pred cceeecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCC-Cceee--CCCcEEEEEe
Q 043016 431 VITIDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEG-LHWSE--ENRGTVLIKL 507 (511)
Q Consensus 431 ~~~IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~g-i~~~e--~n~G~IlV~L 507 (511)
..+|||-|++-..=+-.++..|..+. ....|.||+.-.- -..-|..|+++.+ +...+ ...|.+.+.+
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~---~Ge~LeV~~ddp~-------~~~dIp~~~~~~~~~~ll~~e~~~~~~~~~I 74 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLK---PGEILEVIADDPA-------AKEDIPAWAKKEGGHELLEVEQEGGVYRILI 74 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCC---CCCEEEEEecCcc-------hHHHHHHHHHHcCCcEEEEEEecCCcEEEEE
Confidence 35899999999999999999988775 3567999987653 4467999999777 66643 3455655555
Q ss_pred c
Q 043016 508 D 508 (511)
Q Consensus 508 ~ 508 (511)
.
T Consensus 75 k 75 (78)
T COG0425 75 K 75 (78)
T ss_pred E
Confidence 4
No 46
>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=43.39 E-value=35 Score=28.99 Aligned_cols=28 Identities=21% Similarity=0.376 Sum_probs=24.6
Q ss_pred HHHHHHHHcCChHHHHHHHHHHHHHHHH
Q 043016 381 QKASAAYSKGEWGYAAHLSEQGKSLTKL 408 (511)
Q Consensus 381 ~kAa~Ay~rGd~~~A~~Lseegr~~~~k 408 (511)
.++.++|.+||.+.|...+.+|+.+...
T Consensus 42 ~kv~~~~~~Gd~~~A~~aS~~Ak~~~~i 69 (82)
T PF04505_consen 42 SKVRSRYAAGDYEGARRASRKAKKWSII 69 (82)
T ss_pred hhhHHHHHCCCHHHHHHHHHHhHHHHHH
Confidence 4788999999999999999999988753
No 47
>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=40.95 E-value=30 Score=25.63 Aligned_cols=37 Identities=19% Similarity=0.305 Sum_probs=29.8
Q ss_pred HHHHHHHHhhccccccchHHHHHHHhhcCCcHHHHHHHHHc
Q 043016 180 EMEQFLYSMLGDECQFSMAVVRDVLCQCGYNVEKAMDVLLD 220 (511)
Q Consensus 180 d~E~FL~sMLGdgfqL~~~vIrdVL~~cGyDv~ks~d~LLd 220 (511)
+.|.+|..||.++ -..+..+|..||-|+++-.+.|..
T Consensus 14 ~~eHlL~all~~~----~~~~~~il~~~~id~~~l~~~i~~ 50 (53)
T PF02861_consen 14 SPEHLLLALLEDP----DSIAARILKKLGIDPEQLKAAIEK 50 (53)
T ss_dssp -HHHHHHHHHHHT----TSHHHHHHHHTTCHHHHHHHHHHH
T ss_pred cHHHHHHHHHhhh----hHHHHHHHHHcCCCHHHHHHHHHH
Confidence 5789999998754 258999999999999988777654
No 48
>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=39.85 E-value=1.5e+02 Score=27.13 Aligned_cols=55 Identities=24% Similarity=0.161 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHH
Q 043016 362 YQVFRKDAKQHWNSMKSCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQKADEKA 416 (511)
Q Consensus 362 Y~~lR~~A~e~~~~Rne~~~kAa~Ay~rGd~~~A~~Lseegr~~~~karean~~A 416 (511)
...+.+.+..+...-.++..+|..+.+.|++..|..|..+-+.+...........
T Consensus 10 ~~~L~~~~~~le~~i~~~~~~~k~~~~~~~~~~A~~~lk~~k~~~k~~~~~~~~~ 64 (171)
T PF03357_consen 10 IRRLEKQIKRLEKKIKKLEKKAKKAIKKGNKERAKIYLKRKKRLEKQLEKLLNQL 64 (171)
T ss_dssp HHHHHHHHHHHHHHHHHCHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456677778888888899999999999999999999999888877666655443
No 49
>PF12854 PPR_1: PPR repeat
Probab=39.16 E-value=33 Score=23.98 Aligned_cols=27 Identities=30% Similarity=0.608 Sum_probs=21.8
Q ss_pred CCHHHHHHHHHHhcCChhHHHHHHHhhc
Q 043016 57 VSLEEATSAFCEANGDVNKAEELLTALT 84 (511)
Q Consensus 57 ~Sl~~ia~Ay~~A~~d~~~A~eiL~~~~ 84 (511)
+|.--+-++||++ |+++.|-++|-.|+
T Consensus 8 ~ty~~lI~~~Ck~-G~~~~A~~l~~~M~ 34 (34)
T PF12854_consen 8 VTYNTLIDGYCKA-GRVDEAFELFDEMK 34 (34)
T ss_pred hHHHHHHHHHHHC-CCHHHHHHHHHhCc
Confidence 3556678899997 68999999998874
No 50
>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=38.57 E-value=29 Score=25.47 Aligned_cols=20 Identities=35% Similarity=0.466 Sum_probs=17.1
Q ss_pred HHHHHHHhcCChhHHHHHHH
Q 043016 62 ATSAFCEANGDVNKAEELLT 81 (511)
Q Consensus 62 ia~Ay~~A~~d~~~A~eiL~ 81 (511)
|..|+.+.+||+..||++|.
T Consensus 10 i~~aL~~~~gn~~~aA~~Lg 29 (42)
T PF02954_consen 10 IRQALERCGGNVSKAARLLG 29 (42)
T ss_dssp HHHHHHHTTT-HHHHHHHHT
T ss_pred HHHHHHHhCCCHHHHHHHHC
Confidence 67788999999999999997
No 51
>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=37.05 E-value=12 Score=33.92 Aligned_cols=25 Identities=20% Similarity=0.335 Sum_probs=18.2
Q ss_pred HHHHHHHHHhhccccccchHHHHHH
Q 043016 179 EEMEQFLYSMLGDECQFSMAVVRDV 203 (511)
Q Consensus 179 ~d~E~FL~sMLGdgfqL~~~vIrdV 203 (511)
+|.-=|+-+||||+|=+.-+||++|
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 4555689999999999999999987
No 52
>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=37.00 E-value=1.1e+02 Score=27.04 Aligned_cols=47 Identities=21% Similarity=0.111 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 043016 377 KSCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQKADEKASHDIFKARNK 426 (511)
Q Consensus 377 ne~~~kAa~Ay~rGd~~~A~~Lseegr~~~~karean~~AA~~If~~rN~ 426 (511)
+.+|-+|-++.+.||...|..+..+|+.....+...+- +.|-..-+.
T Consensus 18 rs~~~eAl~~a~~gdfe~A~~~l~eA~~~l~~AH~~qt---~liq~ea~g 64 (99)
T TIGR00823 18 RSKALEALKAAKAGDFAKARALVEQAGMCLNEAHLAQT---SLLAQEAGG 64 (99)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHhcC
Confidence 45778899999999999999999999998887776663 444444443
No 53
>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=35.50 E-value=44 Score=27.36 Aligned_cols=27 Identities=22% Similarity=0.343 Sum_probs=23.8
Q ss_pred cchHHHHHHHhhcCCcHHHHHHHHHcc
Q 043016 195 FSMAVVRDVLCQCGYNVEKAMDVLLDL 221 (511)
Q Consensus 195 L~~~vIrdVL~~cGyDv~ks~d~LLd~ 221 (511)
-+-+-|-.+|.-|+.|...+...||++
T Consensus 19 hse~eIya~L~ecnMDpnea~qrLL~q 45 (60)
T PF06972_consen 19 HSEEEIYAMLKECNMDPNEAVQRLLSQ 45 (60)
T ss_pred CCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence 456678889999999999999999986
No 54
>TIGR03527 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis.
Probab=35.08 E-value=1.3e+02 Score=29.61 Aligned_cols=65 Identities=20% Similarity=0.229 Sum_probs=48.7
Q ss_pred eecCCCChHHHHHHHHHHHHHHHhcCCCceEEEEEccCCCCCCCcchHHHHHHHHHhCCCceee--CCCcEEEEEec
Q 043016 434 IDLHGQHVKPAMKLLKLHLVMVSYAQSVQTLRVITGCGSHGVGKSKLKQSVIELVENEGLHWSE--ENRGTVLIKLD 508 (511)
Q Consensus 434 IDLHGL~V~EAl~~Lk~~L~~~~~~~s~~~L~VITG~G~HS~G~akLKpAV~~~Lek~gi~~~e--~n~G~IlV~L~ 508 (511)
||+.|+.-..-+-.++..|..+. ....|.||+-... -+.-|.+|++..|+.+.. ..+|.+.|.+.
T Consensus 1 ID~rGl~CP~Pvi~tKkal~~l~---~g~~L~VlvD~~~-------a~~nV~~~~~~~G~~v~~~e~~~~~~~i~i~ 67 (194)
T TIGR03527 1 IDARGLACPQPVILTKKALDELG---EEGVLTVIVDNEA-------AKENVSKFATSLGYEVEVEEKEEGYWILIIK 67 (194)
T ss_pred CCCCCCCCCHHHHHHHHHHHcCC---CCCEEEEEECCcc-------HHHHHHHHHHHcCCEEEEEEecCCEEEEEEE
Confidence 79999999999999999988764 2346777765431 345599999999999963 46677766654
No 55
>PRK09591 celC cellobiose phosphotransferase system IIA component; Reviewed
Probab=34.97 E-value=1.2e+02 Score=27.03 Aligned_cols=53 Identities=17% Similarity=0.147 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 043016 372 HWNSMKSCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQKADEKASHDIFKARNKS 427 (511)
Q Consensus 372 ~~~~Rne~~~kAa~Ay~rGd~~~A~~Lseegr~~~~karean~~AA~~If~~rN~~ 427 (511)
|.-.-+.++-+|-++.+.||...|..+..+|+.....+..++ .+.|-..-+..
T Consensus 16 ~aG~Ars~~~eAl~~ak~gdf~~A~~~l~eA~~~l~~AH~~q---t~liq~Ea~g~ 68 (104)
T PRK09591 16 HSGNARTEVHEAFAAMREGNFDLAEQKLNQSNEELLEAHHAQ---TKLLQEYASGT 68 (104)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhCCC
Confidence 333444577889999999999999999999999877776666 34554444443
No 56
>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=34.70 E-value=1.3e+02 Score=26.55 Aligned_cols=48 Identities=19% Similarity=0.174 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 043016 377 KSCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQKADEKASHDIFKARNKS 427 (511)
Q Consensus 377 ne~~~kAa~Ay~rGd~~~A~~Lseegr~~~~karean~~AA~~If~~rN~~ 427 (511)
+.++-+|-++.+.||...|..+..+|++...++...+ .+.|-..-+.+
T Consensus 16 rs~~~eAl~~a~~g~fe~A~~~l~ea~~~l~~AH~~q---t~liq~ea~g~ 63 (97)
T cd00215 16 RSKALEALKAAKEGDFAEAEELLEEANDSLNEAHHAQ---TKLLQQEASGE 63 (97)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhcCC
Confidence 4577889999999999999999999999887776666 34555554443
No 57
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=33.36 E-value=59 Score=24.98 Aligned_cols=27 Identities=11% Similarity=0.279 Sum_probs=22.1
Q ss_pred hHHHHHHHHHhCCCceeeCCCcEEEEE
Q 043016 480 LKQSVIELVENEGLHWSEENRGTVLIK 506 (511)
Q Consensus 480 LKpAV~~~Lek~gi~~~e~n~G~IlV~ 506 (511)
.+.+..+||.++||.|.....|..+|.
T Consensus 16 ~~~~Q~~~L~~~Gi~~~~~~~G~p~V~ 42 (47)
T PF13986_consen 16 RPSKQIRWLRRNGIPFVVRADGRPIVT 42 (47)
T ss_pred CHHHHHHHHHHCCCeeEECCCCCEEee
Confidence 566789999999999988778876664
No 58
>PF14164 YqzH: YqzH-like protein
Probab=30.32 E-value=26 Score=29.01 Aligned_cols=20 Identities=40% Similarity=0.702 Sum_probs=15.8
Q ss_pred HHHHHHhhccccccchHHHHHHHhhcCCcHH
Q 043016 182 EQFLYSMLGDECQFSMAVVRDVLCQCGYNVE 212 (511)
Q Consensus 182 E~FL~sMLGdgfqL~~~vIrdVL~~cGyDv~ 212 (511)
|.||-+| |+.+|.|+|||++
T Consensus 3 ek~I~Km-----------i~~~l~QYg~d~~ 22 (64)
T PF14164_consen 3 EKLIEKM-----------IINCLRQYGYDVE 22 (64)
T ss_pred HHHHHHH-----------HHHHHHHhCCccc
Confidence 5666666 6789999999975
No 59
>COG2250 Uncharacterized conserved protein related to C-terminal domain of eukaryotic chaperone, SACSIN [Function unknown]
Probab=30.16 E-value=1.9e+02 Score=26.57 Aligned_cols=40 Identities=18% Similarity=0.263 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHH
Q 043016 366 RKDAKQHWNSMKSCYQKASAAYSKGEWGYAAHLSEQGKSL 405 (511)
Q Consensus 366 R~~A~e~~~~Rne~~~kAa~Ay~rGd~~~A~~Lseegr~~ 405 (511)
|..+..+.+.-...+..|...+..|+...|-++++|+-++
T Consensus 3 ~~~~~~~~~rA~~~l~~A~~~le~G~y~~a~f~aqQAvel 42 (132)
T COG2250 3 REEAEKWLRRAERDLKLAKRDLELGDYDLACFHAQQAVEL 42 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHH
Confidence 5677778888888999999999999999999999985443
No 60
>PF09507 CDC27: DNA polymerase subunit Cdc27; InterPro: IPR019038 This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterised by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. ; GO: 0006260 DNA replication, 0005634 nucleus; PDB: 1U76_B 3E0J_B.
Probab=30.01 E-value=58 Score=34.46 Aligned_cols=38 Identities=18% Similarity=0.155 Sum_probs=28.2
Q ss_pred CCChHHHHHHHHHHHHHHHhc--CCCceEEEEEccCCCCC
Q 043016 438 GQHVKPAMKLLKLHLVMVSYA--QSVQTLRVITGCGSHGV 475 (511)
Q Consensus 438 GL~V~EAl~~Lk~~L~~~~~~--~s~~~L~VITG~G~HS~ 475 (511)
++||..|-++|.+|+...... ..+.-.|||||.-.+..
T Consensus 13 ~ihvn~AK~~L~ef~~~~~~k~~~~l~atYlvsG~~k~~~ 52 (430)
T PF09507_consen 13 GIHVNQAKQMLYEFHEKQNAKKPGSLHATYLVSGWLKDNG 52 (430)
T ss_dssp T--HHHHHHHHHHHHHHHHHHHS-S-EEEEEEEEEEESSS
T ss_pred CCCHHHHHHHHHHHHHhccccCCCceEEEEEEEEEeCCCC
Confidence 578999999999999877532 46788999999987755
No 61
>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=29.77 E-value=1.8e+02 Score=25.50 Aligned_cols=47 Identities=19% Similarity=0.140 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 043016 377 KSCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQKADEKASHDIFKARNK 426 (511)
Q Consensus 377 ne~~~kAa~Ay~rGd~~~A~~Lseegr~~~~karean~~AA~~If~~rN~ 426 (511)
+.++-+|-++.+.||...|..+..+|+....++...+- +.|-..-+.
T Consensus 15 rs~~~eAl~~a~~~~fe~A~~~l~~a~~~l~~AH~~qt---~llq~ea~g 61 (96)
T PF02255_consen 15 RSLAMEALKAAREGDFEEAEELLKEADEELLKAHKIQT---ELLQQEANG 61 (96)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHTT
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHhcc
Confidence 34677888889999999999999999988877766654 444444443
No 62
>PF04858 TH1: TH1 protein; InterPro: IPR006942 TH1 is a highly conserved but uncharacterised metazoan protein. No homologue has been identified in Caenorhabditis elegans []. TH1 binds specifically to A-Raf kinase [].; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=26.99 E-value=1.3e+02 Score=34.63 Aligned_cols=43 Identities=16% Similarity=0.387 Sum_probs=35.6
Q ss_pred cchhHHHHHHHHHhhCC---C---CHHHHHHHHHHhcCChhHHHHHHHh
Q 043016 40 NDTKNQIIHSLTEAFGS---V---SLEEATSAFCEANGDVNKAEELLTA 82 (511)
Q Consensus 40 ~~~~~k~l~~LleaFgs---~---Sl~~ia~Ay~~A~~d~~~A~eiL~~ 82 (511)
+++..+.|+..+..|.. + ++-+.-..|.+|||+++.+-+.|.+
T Consensus 31 ~~~~~~~~~~~~~~l~~~D~Imep~i~~~i~~y~~~gG~p~~vv~~Ls~ 79 (584)
T PF04858_consen 31 DEEPEEVLEECLRRLSQPDAIMEPSIFDTIKRYFRAGGDPEEVVELLSE 79 (584)
T ss_pred CCChHHHHHHHHHhcCCCCeeeCchHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 44566888888888874 2 7888889999999999999999985
No 63
>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=26.70 E-value=28 Score=35.07 Aligned_cols=27 Identities=22% Similarity=0.357 Sum_probs=23.3
Q ss_pred HHHHHHHHHhhccccccchHHHHHHHh
Q 043016 179 EEMEQFLYSMLGDECQFSMAVVRDVLC 205 (511)
Q Consensus 179 ~d~E~FL~sMLGdgfqL~~~vIrdVL~ 205 (511)
++-|+|=..+|+++|.+|-++||.||.
T Consensus 25 ~~p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 25 EDPEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred hCccccCHHHHHhhCCCCHHHHHHHHh
Confidence 444567889999999999999999995
No 64
>PF03948 Ribosomal_L9_C: Ribosomal protein L9, C-terminal domain; InterPro: IPR020069 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L9 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L9 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins grouped on the basis of sequence similarities [, ]. The crystal structure of Bacillus stearothermophilus L9 shows the 149-residue protein comprises two globular domains connected by a rigid linker []. Each domain contains an rRNA binding site, and the protein functions as a structural protein in the large subunit of the ribosome. The C-terminal domain consists of two loops, an alpha-helix and a three-stranded mixed parallel, anti-parallel beta-sheet packed against the central alpha-helix. The long central alpha-helix is exposed to solvent in the middle and participates in the hydrophobic cores of the two domains at both ends. ; PDB: 3D5B_I 3PYV_H 3F1H_I 3PYR_H 3MRZ_H 1VSP_G 3MS1_H 1VSA_G 3PYT_H 2WH4_I ....
Probab=24.57 E-value=41 Score=28.78 Aligned_cols=24 Identities=29% Similarity=0.458 Sum_probs=20.6
Q ss_pred hhCCCCHHHHHHHHHHh-cCChhHH
Q 043016 53 AFGSVSLEEATSAFCEA-NGDVNKA 76 (511)
Q Consensus 53 aFgs~Sl~~ia~Ay~~A-~~d~~~A 76 (511)
-|||++-.||+.+..+. |-++|+.
T Consensus 28 lfGSVt~~dIa~~l~~~~g~~Idk~ 52 (87)
T PF03948_consen 28 LFGSVTSKDIAKALKEQTGIEIDKK 52 (87)
T ss_dssp BSSEBSHHHHHHHHHHCCSSSSSSS
T ss_pred eecCcCHHHHHHHHHHhhCCeEecc
Confidence 39999999999999999 7777653
No 65
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=24.11 E-value=2.5e+02 Score=25.49 Aligned_cols=39 Identities=10% Similarity=0.121 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHH
Q 043016 371 QHWNSMKSCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQ 410 (511)
Q Consensus 371 e~~~~Rne~~~kAa~Ay~rGd~~~A~~Lseegr~~~~kar 410 (511)
.+..--+.+|+.|..+|+.| ...|..|.+.++....+++
T Consensus 9 ia~eRi~~L~~lA~~~~~~~-~~laRrYv~la~~Is~K~r 47 (105)
T COG2023 9 IAAERIDYLYSLAEETFRTG-PDLARRYVKLARRISMKYR 47 (105)
T ss_pred HHHHHHHHHHHHHHHHHhcC-cHHHHHHHHHHHHHHHhhc
Confidence 34444567899999999999 7888777777666655543
No 66
>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=23.80 E-value=3.3e+02 Score=23.55 Aligned_cols=61 Identities=11% Similarity=0.131 Sum_probs=47.5
Q ss_pred hhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043016 355 LCAKGDEYQVFRKDAKQHWNSMKSCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQKADEKAS 417 (511)
Q Consensus 355 ~~~~~~~Y~~lR~~A~e~~~~Rne~~~kAa~Ay~rGd~~~A~~Lseegr~~~~karean~~AA 417 (511)
....+..|..+..+.......||.+-.+-..+...| ..+..|..+++...........+..
T Consensus 31 i~~ld~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~--~~~~~l~~e~~~lk~~i~~le~~~~ 91 (108)
T PF02403_consen 31 IIELDQERRELQQELEELRAERNELSKEIGKLKKAG--EDAEELKAEVKELKEEIKELEEQLK 91 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTT--CCTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhCc--ccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345778888888999999999999999999999888 5666677777777776666555443
No 67
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=23.67 E-value=1.2e+02 Score=26.42 Aligned_cols=30 Identities=13% Similarity=0.170 Sum_probs=23.5
Q ss_pred cchHHHHHHHhhcCCcHHHHHHHHHcccCCC
Q 043016 195 FSMAVVRDVLCQCGYNVEKAMDVLLDLSAPS 225 (511)
Q Consensus 195 L~~~vIrdVL~~cGyDv~ks~d~LLd~S~~~ 225 (511)
+...+|+++|.+||+++.++. .+|.+|-.+
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AA-r~LGIsRsT 84 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAA-LMLGINRGT 84 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHH-HHhCCCHHH
Confidence 346789999999999999986 566666554
No 68
>KOG3837 consensus Uncharacterized conserved protein, contains DM14 and C2 domains [General function prediction only]
Probab=23.31 E-value=2e+02 Score=32.08 Aligned_cols=36 Identities=22% Similarity=0.078 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHH
Q 043016 378 SCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQKAD 413 (511)
Q Consensus 378 e~~~kAa~Ay~rGd~~~A~~Lseegr~~~~karean 413 (511)
+|-..|.+|-++||...|+.|....+.|....+.+.
T Consensus 214 qyq~AAiqAKs~gD~eqAK~ylri~Kgfd~~I~aa~ 249 (523)
T KOG3837|consen 214 QYQVAAIQAKSKGDQEQAKMYLRIVKGFDDAIRAAK 249 (523)
T ss_pred HHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHh
Confidence 366677899999999999999999999988776553
No 69
>smart00380 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs.
Probab=23.01 E-value=65 Score=25.62 Aligned_cols=16 Identities=38% Similarity=0.576 Sum_probs=13.8
Q ss_pred hCCC-CHHHHHHHHHHh
Q 043016 54 FGSV-SLEEATSAFCEA 69 (511)
Q Consensus 54 Fgs~-Sl~~ia~Ay~~A 69 (511)
+|.| |++|++.||..|
T Consensus 28 lG~f~t~eeAa~Ayd~a 44 (64)
T smart00380 28 LGTFDTAEEAARAYDRA 44 (64)
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 5887 999999999775
No 70
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=21.96 E-value=1.2e+02 Score=19.86 Aligned_cols=28 Identities=21% Similarity=0.321 Sum_probs=22.2
Q ss_pred CHHHHHHHHHHhcCChhHHHHHHHhhcCC
Q 043016 58 SLEEATSAFCEANGDVNKAEELLTALTEG 86 (511)
Q Consensus 58 Sl~~ia~Ay~~A~~d~~~A~eiL~~~~~~ 86 (511)
+..-+..||++ .||++.|-++|..|...
T Consensus 3 ty~~ll~a~~~-~g~~~~a~~~~~~M~~~ 30 (34)
T PF13812_consen 3 TYNALLRACAK-AGDPDAALQLFDEMKEQ 30 (34)
T ss_pred HHHHHHHHHHH-CCCHHHHHHHHHHHHHh
Confidence 34557788888 78899999999999653
No 71
>PRK10454 PTS system N,N'-diacetylchitobiose-specific transporter subunit IIA; Provisional
Probab=21.50 E-value=5.7e+02 Score=23.36 Aligned_cols=65 Identities=15% Similarity=0.110 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHHHHcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcceeecCCC
Q 043016 372 HWNSMKSCYQKASAAYSKGEWGYAAHLSEQGKSLTKLAQKADEKASHDIFKARNKSFENVITIDLHGQ 439 (511)
Q Consensus 372 ~~~~Rne~~~kAa~Ay~rGd~~~A~~Lseegr~~~~karean~~AA~~If~~rN~~~~~~~~IDLHGL 439 (511)
|.-.-+.++-+|-++.+.||...|..+..+|++...++-..+ .+-|-..-+........|=.|..
T Consensus 27 ~aG~ArS~~~eAl~~Ak~gdfe~A~~~l~eA~e~l~~AH~~q---t~Liq~Ea~Ge~~~~slLlvHAQ 91 (115)
T PRK10454 27 NSGQARSLAYAALKQAKQGDFAAAKAMMDQSRMALNEAHLVQ---TKLIEGDQGEGKMKVSLVLVHAQ 91 (115)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHhcCCCCCcceeeehHH
Confidence 333344577789999999999999999999999877766665 45555555544322334444443
No 72
>cd00018 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies.
Probab=21.34 E-value=75 Score=24.87 Aligned_cols=16 Identities=38% Similarity=0.576 Sum_probs=13.9
Q ss_pred hCCC-CHHHHHHHHHHh
Q 043016 54 FGSV-SLEEATSAFCEA 69 (511)
Q Consensus 54 Fgs~-Sl~~ia~Ay~~A 69 (511)
+|.| |++|++.||..|
T Consensus 29 lG~f~t~eeAa~Ayd~a 45 (61)
T cd00018 29 LGTFDTAEEAARAYDRA 45 (61)
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 5887 999999999876
No 73
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=20.97 E-value=1.5e+02 Score=24.40 Aligned_cols=47 Identities=19% Similarity=0.317 Sum_probs=37.8
Q ss_pred cHHHHHHHHHHhhccccccchHHHHHHHhhcCCcHHHHHHHHHcccCC
Q 043016 177 DKEEMEQFLYSMLGDECQFSMAVVRDVLCQCGYNVEKAMDVLLDLSAP 224 (511)
Q Consensus 177 ~~~d~E~FL~sMLGdgfqL~~~vIrdVL~~cGyDv~ks~d~LLd~S~~ 224 (511)
.++++++++-.|+-..|.--+..|.+++.. ||...-=+..|.+.--.
T Consensus 4 ~~~~i~~i~~~~~~~~~~~~~~~~~~l~~~-G~s~~~Il~~l~~~l~~ 50 (89)
T PF08542_consen 4 PPEVIEEILESCLNGDFKEARKKLYELLVE-GYSASDILKQLHEVLVE 50 (89)
T ss_dssp -HHHHHHHHHHHHHTCHHHHHHHHHHHHHT-T--HHHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHHhCCHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHH
Confidence 478999999999999999999999999999 99988777777655433
No 74
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=20.84 E-value=99 Score=26.41 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=23.5
Q ss_pred cchhHHHHHHHHHhhCC--CCHHHHHHHHHH
Q 043016 40 NDTKNQIIHSLTEAFGS--VSLEEATSAFCE 68 (511)
Q Consensus 40 ~~~~~k~l~~LleaFgs--~Sl~~ia~Ay~~ 68 (511)
+..+++-|+.|.+.|+. +.|+-||+|--+
T Consensus 7 d~~D~~yL~~l~~~f~ggPvGl~tlA~~l~e 37 (76)
T PF05491_consen 7 DELDRRYLKTLIENFKGGPVGLDTLAAALGE 37 (76)
T ss_dssp BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS
T ss_pred CHHHHHHHHHHHHHcCCCCeeHHHHHHHHCC
Confidence 45678999999999995 799999988544
Done!