Query psy1643
Match_columns 962
No_of_seqs 116 out of 148
Neff 1.7
Searched_HMMs 46136
Date Fri Aug 16 21:05:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1643.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1643hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1510|consensus 100.0 1.1E-37 2.3E-42 292.3 16.4 135 825-961 1-137 (139)
2 PF11221 Med21: Subunit 21 of 100.0 4.3E-38 9.4E-43 289.7 10.6 128 825-954 1-143 (144)
3 PF07544 Med9: RNA polymerase 95.4 0.065 1.4E-06 47.1 7.4 55 882-936 26-80 (83)
4 PF05731 TROVE: TROVE domain; 94.6 0.024 5.2E-07 60.7 2.9 260 296-608 89-382 (385)
5 PF11315 Med30: Mediator compl 69.5 19 0.00041 35.9 7.4 115 815-961 33-149 (150)
6 PRK08147 flgK flagellar hook-a 61.2 18 0.00039 40.6 6.3 136 802-954 66-211 (547)
7 KOG1853|consensus 58.3 24 0.00052 38.5 6.3 71 879-949 76-146 (333)
8 TIGR02492 flgK_ends flagellar 57.4 22 0.00047 37.5 5.8 135 803-954 65-209 (322)
9 PF04999 FtsL: Cell division p 54.3 62 0.0013 28.4 7.2 47 915-961 35-86 (97)
10 PRK07739 flgK flagellar hook-a 52.7 32 0.00068 38.6 6.4 136 802-954 76-220 (507)
11 smart00150 SPEC Spectrin repea 51.4 1.3E+02 0.0028 24.2 8.4 35 910-944 33-67 (101)
12 PF03233 Cauli_AT: Aphid trans 50.2 54 0.0012 33.5 6.9 54 895-952 102-161 (163)
13 TIGR02209 ftsL_broad cell divi 48.7 96 0.0021 26.3 7.3 43 917-961 33-75 (85)
14 PF04977 DivIC: Septum formati 48.3 91 0.002 25.7 6.9 46 914-959 16-67 (80)
15 PF01865 PhoU_div: Protein of 46.2 2.4E+02 0.0052 27.4 10.5 119 819-955 71-200 (214)
16 PRK11797 D-ribose pyranase; Pr 45.8 20 0.00043 34.8 3.1 91 669-776 37-132 (139)
17 PF04111 APG6: Autophagy prote 45.5 34 0.00074 36.6 5.0 42 909-950 58-99 (314)
18 PRK07521 flgK flagellar hook-a 45.1 27 0.00058 38.9 4.4 135 803-954 59-203 (483)
19 PRK06665 flgK flagellar hook-a 44.4 44 0.00095 38.8 6.0 135 803-954 77-220 (627)
20 KOG4465|consensus 43.1 11 0.00024 42.6 1.1 232 331-608 170-425 (598)
21 PRK05683 flgK flagellar hook-a 41.9 47 0.001 39.2 5.8 136 802-954 65-208 (676)
22 PRK10884 SH3 domain-containing 39.0 1.4E+02 0.0029 30.8 7.9 36 916-951 133-168 (206)
23 PRK08871 flgK flagellar hook-a 38.7 25 0.00054 40.9 3.0 136 802-954 67-208 (626)
24 smart00502 BBC B-Box C-termina 38.2 2.2E+02 0.0048 24.4 8.0 44 910-953 56-99 (127)
25 PF12329 TMF_DNA_bd: TATA elem 37.5 1.3E+02 0.0028 26.6 6.5 63 885-947 3-65 (74)
26 PF06103 DUF948: Bacterial pro 36.8 1.7E+02 0.0036 25.5 7.1 39 914-952 32-70 (90)
27 KOG4304|consensus 35.3 68 0.0015 33.9 5.2 45 879-925 102-146 (250)
28 PRK07191 flgK flagellar hook-a 34.1 71 0.0015 35.4 5.4 135 803-954 66-208 (456)
29 PF06103 DUF948: Bacterial pro 33.7 1.6E+02 0.0035 25.6 6.5 38 916-953 27-64 (90)
30 TIGR01069 mutS2 MutS2 family p 33.0 1.2E+02 0.0025 36.4 7.2 13 894-906 511-523 (771)
31 PF04678 DUF607: Protein of un 32.9 2.2E+02 0.0047 28.3 8.0 51 896-946 38-88 (180)
32 PRK06799 flgK flagellar hook-a 31.7 70 0.0015 35.4 4.9 135 803-954 70-211 (431)
33 PRK00888 ftsB cell division pr 31.5 1.6E+02 0.0034 27.4 6.4 47 912-959 31-77 (105)
34 PF13801 Metal_resist: Heavy-m 30.8 2.6E+02 0.0057 23.5 7.2 26 911-936 44-69 (125)
35 PF00215 OMPdecase: Orotidine 30.7 13 0.00028 36.7 -0.7 77 467-543 25-107 (226)
36 COG1422 Predicted membrane pro 30.5 1.1E+02 0.0024 32.2 5.7 46 914-959 71-117 (201)
37 TIGR00996 Mtu_fam_mce virulenc 30.2 1.3E+02 0.0029 30.5 6.2 69 881-949 175-250 (291)
38 PF11887 DUF3407: Protein of u 29.7 2.8E+02 0.0061 29.1 8.6 72 881-952 60-131 (267)
39 PF00015 MCPsignal: Methyl-acc 28.2 2.5E+02 0.0054 26.3 7.2 27 879-905 81-107 (213)
40 KOG4031|consensus 27.7 1.5E+02 0.0034 31.5 6.3 41 910-950 112-153 (216)
41 COG4451 RbcS Ribulose bisphosp 27.5 1.9E+02 0.0041 28.8 6.4 97 577-686 14-112 (127)
42 PRK11637 AmiB activator; Provi 26.5 2.7E+02 0.0058 30.5 8.1 20 917-936 98-117 (428)
43 PF00435 Spectrin: Spectrin re 26.4 3.4E+02 0.0074 21.8 7.2 50 895-944 19-70 (105)
44 PRK13729 conjugal transfer pil 26.1 1.9E+02 0.0041 33.6 7.1 19 931-949 102-120 (475)
45 PF11471 Sugarporin_N: Maltopo 25.9 1.3E+02 0.0028 26.1 4.5 27 914-940 31-57 (60)
46 TIGR00606 rad50 rad50. This fa 25.9 5.3E+02 0.011 32.4 11.3 73 885-957 797-874 (1311)
47 PRK12714 flgK flagellar hook-a 25.9 83 0.0018 36.6 4.4 31 825-855 87-122 (624)
48 PF12290 DUF3802: Protein of u 25.8 1.4E+02 0.003 29.3 5.1 26 929-954 60-85 (113)
49 TIGR02132 phaR_Bmeg polyhydrox 24.8 3.1E+02 0.0068 28.8 7.7 68 879-946 71-138 (189)
50 PRK12715 flgK flagellar hook-a 24.8 96 0.0021 36.5 4.7 135 802-954 65-204 (649)
51 cd04776 HTH_GnyR Helix-Turn-He 24.5 4.5E+02 0.0097 24.4 8.1 36 894-929 59-94 (118)
52 PRK00409 recombination and DNA 23.6 1.8E+02 0.004 34.8 6.7 9 895-903 517-525 (782)
53 COG1463 Ttg2C ABC-type transpo 23.3 1.9E+02 0.0042 31.0 6.2 29 881-909 184-212 (359)
54 KOG1017|consensus 23.2 44 0.00094 35.7 1.4 46 792-841 66-113 (267)
55 PRK06945 flgK flagellar hook-a 23.2 1.3E+02 0.0027 35.5 5.2 136 802-954 66-210 (651)
56 PF13851 GAS: Growth-arrest sp 23.2 3.1E+02 0.0068 27.8 7.3 43 912-954 97-139 (201)
57 PRK11677 hypothetical protein; 23.1 2.9E+02 0.0063 27.2 6.8 37 917-953 31-67 (134)
58 PHA03162 hypothetical protein; 23.1 3.9E+02 0.0084 27.0 7.7 54 904-957 9-75 (135)
59 PF10018 Med4: Vitamin-D-recep 23.0 6.9E+02 0.015 24.9 9.5 60 884-949 2-63 (188)
60 COG2919 Septum formation initi 22.6 2.5E+02 0.0055 26.3 6.1 40 912-959 61-100 (117)
61 PF11336 DUF3138: Protein of u 22.4 1.2E+02 0.0025 35.4 4.6 38 892-930 2-40 (514)
62 PF04156 IncA: IncA protein; 22.4 6.2E+02 0.014 24.3 8.9 20 916-935 131-150 (191)
63 PF04201 TPD52: Tumour protein 22.3 2.4E+02 0.0053 28.9 6.3 40 906-949 24-66 (162)
64 PF10168 Nup88: Nuclear pore c 22.2 2.2E+02 0.0048 34.1 7.0 42 911-952 575-623 (717)
65 PF08614 ATG16: Autophagy prot 22.1 3.7E+02 0.0081 26.6 7.5 55 895-949 96-153 (194)
66 PF06295 DUF1043: Protein of u 21.7 3.2E+02 0.0069 26.0 6.6 35 918-952 28-69 (128)
67 PF12998 ING: Inhibitor of gro 21.6 5.4E+02 0.012 22.3 9.9 63 890-952 36-98 (105)
68 PF15254 CCDC14: Coiled-coil d 21.4 5E+02 0.011 32.3 9.5 37 891-927 360-413 (861)
69 PF05812 Herpes_BLRF2: Herpesv 21.3 2E+02 0.0044 28.2 5.3 50 909-958 4-66 (118)
70 KOG4552|consensus 21.2 2.5E+02 0.0054 30.4 6.4 56 890-948 66-121 (272)
71 KOG0425|consensus 20.7 34 0.00073 35.1 0.1 20 876-895 143-162 (171)
72 KOG2751|consensus 20.5 2.4E+02 0.0053 32.7 6.5 52 900-951 182-233 (447)
73 PF12729 4HB_MCP_1: Four helix 20.3 5.8E+02 0.013 22.2 7.7 47 880-927 75-121 (181)
74 PRK10780 periplasmic chaperone 20.2 8E+02 0.017 23.8 10.2 72 884-955 54-135 (165)
75 PRK10636 putative ABC transpor 20.0 4.1E+02 0.0089 30.7 8.3 67 882-948 565-631 (638)
76 KOG0994|consensus 20.0 5.9E+02 0.013 33.3 9.9 82 874-955 1486-1606(1758)
No 1
>KOG1510|consensus
Probab=100.00 E-value=1.1e-37 Score=292.33 Aligned_cols=135 Identities=39% Similarity=0.604 Sum_probs=129.0
Q ss_pred CCCcchHHHhhhCHHHHHHHHHHHHhhhccccCCCCCCCCCCCCCCC--CCCCCcchHHHHHHHHHHHHHHhhHHHHHHh
Q psy1643 825 KLKAKTPIQQLLSSAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQT--PQQQTQQEDYAHLFATLISRCARDIDALIES 902 (962)
Q Consensus 825 mADRLTQLQDCLD~aQLAEQFcNSIGYLQRdAPPSsFsPndKIsSpd--PqQqqp~EDnpQEFATDIIrKAKQIE~LIDS 902 (962)
||||||||||+|| +||+||||+|||||++|||+.|+++.+..+.+ |.+.+|+++++++||++|++++||||.||||
T Consensus 1 MaDRlTQLQd~vn--~~A~qf~naig~Lq~~~pp~~l~~~e~~~~~~~~~~pa~p~~~~~~~laa~i~~~akqId~LIds 78 (139)
T KOG1510|consen 1 MADRLTQLQDTVN--EMAEQFCNAIGVLQQTHPPVPLPNNEPESPDKVNPIPAEPFEEYAQLLAADIAKKAKQIDTLIDS 78 (139)
T ss_pred CchHHHHHHHHHH--HHHHHHHHHHHHHHhcCCcccCCCCCCCCCCCCCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 8999999999999 99999999999999999999999999875433 4567889999999999999999999999999
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccC
Q psy1643 903 LPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIAQSQLETNG 961 (962)
Q Consensus 903 LPGIDSSEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEALrdIAQSQLnTRp 961 (962)
|||+++++++|+++|.+|++||++++.||+++|.++|.||++|+.+|.+||+.||+|++
T Consensus 79 LP~~~~~~e~Ql~~i~kLq~en~e~~~el~~~v~~~e~Ll~~vq~~le~~a~~~l~~k~ 137 (139)
T KOG1510|consen 79 LPGEEGSAEAQLEKIKKLQEENEEVALELEELVSKGEKLLEQVQSLLEDIADLQLNSKK 137 (139)
T ss_pred CCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 99999999999999999999999999999999999999999999999999999999985
No 2
>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.
Probab=100.00 E-value=4.3e-38 Score=289.72 Aligned_cols=128 Identities=37% Similarity=0.523 Sum_probs=106.0
Q ss_pred CCCcchHHHhhhCHHHHHHHHHHHHhhhccccCCCCCCCCC-CCCCCCCC--------------CCCcchHHHHHHHHHH
Q psy1643 825 KLKAKTPIQQLLSSAEQADNFCNSVGILQQTAIPSKFSGFD-RGGSQTPQ--------------QQTQQEDYAHLFATLI 889 (962)
Q Consensus 825 mADRLTQLQDCLD~aQLAEQFcNSIGYLQRdAPPSsFsPnd-KIsSpdPq--------------Qqqp~EDnpQEFATDI 889 (962)
||||||||||||| ||+++||||||||+++|||+.|++++ .+.+..|+ ++.++++++++||+||
T Consensus 1 M~DrlTQLQd~ld--qL~~~f~~si~~l~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~elA~dI 78 (144)
T PF11221_consen 1 MADRLTQLQDCLD--QLAEQFCNSIGYLQRDAPPSPLSPNDPSISDPKPQAPPQQQQQAEPAPDPPEEFEENIKELATDI 78 (144)
T ss_dssp --HHHHHHHHHHH--HHHHHHHHHHHHHHHTTGGGG-----------------------------HHHHHHHHHHHHHHH
T ss_pred CCcHHHHHHHHHH--HHHHHHHHHHhhhccCCCCCCCCCCcccccCccccchhhhhhhhcccCCChhhHHHHHHHHHHHH
Confidence 8999999999999 99999999999999999999999998 33222111 1235678999999999
Q ss_pred HHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 890 SRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIAQ 954 (962)
Q Consensus 890 IrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEALrdIAQ 954 (962)
++|+||||+|||||||+++||++|+++|++|++||+++++||+++|+++|++|++|+++|+.||+
T Consensus 79 i~kakqIe~LIdsLPg~~~see~Q~~~i~~L~~E~~~~~~el~~~v~e~e~ll~~v~~~i~~ia~ 143 (144)
T PF11221_consen 79 IRKAKQIEYLIDSLPGIEVSEEEQLKRIKELEEENEEAEEELQEAVKEAEELLKQVQELIREIAR 143 (144)
T ss_dssp HHHHHHHHHHHHHSTTSSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--
T ss_pred HHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999986
No 3
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=95.42 E-value=0.065 Score=47.10 Aligned_cols=55 Identities=20% Similarity=0.189 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 882 AHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVR 936 (962)
Q Consensus 882 pQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVK 936 (962)
...-+..|-.+-+..-.+|.+|||++.|.|+|.+.|+.|+++++...+-|.+.-+
T Consensus 26 ~~~~~~~lk~Klq~ar~~i~~lpgi~~s~eeq~~~i~~Le~~i~~k~~~L~~~~~ 80 (83)
T PF07544_consen 26 LDTATGSLKHKLQKARAAIRELPGIDRSVEEQEEEIEELEEQIRKKREVLQKFKE 80 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCccCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344667777888888999999999999999999999999999777666655443
No 4
>PF05731 TROVE: TROVE domain; InterPro: IPR008858 The TROVE (Telomerase, Ro and Vault) domain is a module of ~300-500 residues that is found in TEP1 and Ro60 the protein components of three ribonucleoprotein particles. The TROVE domain is also found in bacterial ribonucleoproteins suggesting an ancient origin of these ribonucleoproteins. The TROVE domain can be found associated with other domains, such as the VWFA domain, the TEP1 N-terminal domain, the NACHT-NTPase domain, and WD-40 repeats. The TROVE domain may be involved in binding the RNA components of the three RNPs, which are telomerase RNA, Y RNA and vault RNA []. The TROVE domain contains a few absolutely conserved residues. As none of these conserved residues are the polar type of amino acids found in active sites, it seems unlikely that this region has an enzymatic function [].; GO: 0003723 RNA binding, 0030529 ribonucleoprotein complex; PDB: 2NVO_A 2I91_B 1YVP_A 1YVR_A.
Probab=94.58 E-value=0.024 Score=60.73 Aligned_cols=260 Identities=23% Similarity=0.241 Sum_probs=125.1
Q ss_pred hhhhhhhhhhccccCchhHHHHHHH----H-hcCCCCCCCchHHHHHHHHHhcccCCCcEEEEEEeecccccccccchhe
Q psy1643 296 TKVLELAVDRVAGQNSERFLMFVLY----M-LNFSPKSLRPDAVRKQLQKWYMGKESDQLVVLVAKCSVYQGLSHANVLK 370 (962)
Q Consensus 296 ~~~~~~~~~~~~~~~~~~~~~~~~~----~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 370 (962)
...+..++.+|. ++..-++.|+-| + -.-.-..-=|-++||.+++||-.+..-| ++|+..-.|-||..+++
T Consensus 89 r~~~~~~~~~Vv-r~p~dl~ef~~~~q~~~~~~~~~~~~lg~~lRkav~~wf~~~d~yq----LaKY~~r~~~s~rD~lr 163 (385)
T PF05731_consen 89 RPAARRYFPRVV-RRPSDLFEFVQYYQSLARKGVRGRRGLGRALRKAVADWFNQFDAYQ----LAKYKQRNGWSHRDVLR 163 (385)
T ss_dssp HHHHHHHHHHH---SHHHHHHHHHH--HHHHHHHTTT-S-SHHHHHHHHHHHHCS-HHH----HHH-SEETTEEHHHHHH
T ss_pred HHHHHHHHHHHH-cCcchHHHHHHHHHHHHhccccCCCCcCHHHHHHHHHHHhcCCHHH----HHHhhccCCCChhhhhh
Confidence 345556677766 455567778877 1 1111122247899999999999988555 46888889999999999
Q ss_pred eeeeeccccCCccchhHHHhhhhhhhhhhhhccccc-ccCCCCCCcccCcchhhhcccchhhhcceeeEEEecCch----
Q psy1643 371 LIHFDVFHQSPDKKLALYAIAFGFAYVSHRLISGKF-LATPRVPPFVTSDDCFDKASDKVKTIVKDVAVVRCNTSH---- 445 (962)
Q Consensus 371 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---- 445 (962)
+.|-..-. .+. .-..-|.|+..+.. +| -+...+|+-+....=-.|....--.+.....+|.|-..+
T Consensus 164 l~Hpkp~~----~~~---~~~~l~~~l~~~~~--~~~~~~~~l~~~~~~~~~~~k~~~~~~~~~~~~~~v~~l~~~~~~k 234 (385)
T PF05731_consen 164 LVHPKPKD----ERP---EQEALFKYLIKGRH--KFEEEYKALPEKKRKWKFTLKKLIEKLHIEEPAEHVMALLGFEKLK 234 (385)
T ss_dssp HCT---SS----H-----HHHHHHHHHHC--------------------HHHHHHHTTT----HHHCCHHHHHHHHHHCT
T ss_pred ccCCCCCc----chh---hHHHHHHHHHcCCc--ccccccchhhhhhhhhHHHHHHHhcccccccchHHHHHHHHHHHHH
Confidence 98864322 111 11122334433311 11 122234433321110000000000011111112221111
Q ss_pred ----hHHHHHhhhcccc-------------------ccccccchhhhhcccchhhhcc-hhhhhhHHHhhhhccccccCC
Q psy1643 446 ----QKVVAAAVKTHSL-------------------GIESVCPKFAKSFKVNTACLEG-MTQRGLLQSMHRLRKDNVLSS 501 (962)
Q Consensus 446 ----~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~ 501 (962)
..-++..++.|-| ..|.+-....++=.|=.+-+.. |.-..||..+-+|-.-+|+..
T Consensus 235 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~rm~l~~p~twE~~~s~~~~~~~vW~~Li~~~mp~~allrNL~~l~~~Gv~~~ 314 (385)
T PF05731_consen 235 HLIRYPSAAELIERSRLPGGWDYPRAGKRMKLPRPETWERLLSALGNSKEVWEALIPSKMPFMALLRNLRNLTRAGVLEP 314 (385)
T ss_dssp T--SHHHHHHHHHHHT-------------------G-GGGCSTCGGG-HHHHHHHHTT---HHHHHHCHHHHHHTTTT-T
T ss_pred hhcchHHHHHHHHHhccccccccccccccccccccccHHHHcCCcCCCHHHHHHHHHhhccHHHHHHHHHHHHHcCCChh
Confidence 1224556677777 6777777777766677777777 888899998888888888653
Q ss_pred CCceecccCcccchhhhhcCCCCCCCCCCChHHHHHHhhhhhhhcccccccccccccCCCCCCCCCCccccccccCCCcc
Q psy1643 502 EDHAIVDESTTCGTYVKQLGASPVTEPPLHPAEVLAAYAEYVLAPVTKMASFQKKAVKPPPSEGGGGDQAQEKSEDETPV 581 (962)
Q Consensus 502 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 581 (962)
.|..|=+--+.-.- |...-.||..+|+||-.|--. .+.....
T Consensus 315 -~~~~v~~rL~d~~~--------v~~sr~~P~~~l~A~~~~~~~--------------------~~~~~~~--------- 356 (385)
T PF05731_consen 315 -HHEKVLERLTDPEA--------VRKSRQHPFRFLSAYRVYESG--------------------RPQLRGK--------- 356 (385)
T ss_dssp -T-HHHHHHHT-HHH--------HHHTT--HHHHHHHHHHHHCS--------------------B-S-TT----------
T ss_pred -HHHHHHHHhcCHHH--------HHHcccCHHHHHHHHHHHHhc--------------------Ccccccc---------
Confidence 33322222222222 334568999999999887311 0000000
Q ss_pred eeccCCchHHHHHHHHHHHhhcccccc
Q psy1643 582 LTAKAPEPAIVSALQELYKSSFSNLKT 608 (962)
Q Consensus 582 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 608 (962)
..-.|.+.|+.||++-+.-||.|+..
T Consensus 357 -~~~~~~~~i~~ALe~A~~~s~~nv~p 382 (385)
T PF05731_consen 357 -LKWEPDPEIVDALEEAFYLSFHNVPP 382 (385)
T ss_dssp --B----HHHHHHHHHHHHHCCGG---
T ss_pred -ccCCChHHHHHHHHHHHHHHHhcCCC
Confidence 33458899999999999999999853
No 5
>PF11315 Med30: Mediator complex subunit 30; InterPro: IPR021019 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med30 is a metazoan-specific subunit of Mediator [], having no homologues in yeasts.
Probab=69.45 E-value=19 Score=35.91 Aligned_cols=115 Identities=14% Similarity=0.209 Sum_probs=68.7
Q ss_pred CCCCCCcCCCCCCcchHHHhhhCHHHHHHHHHHHHhhhccccCCCCCCCCCCCCCCCCCCCCcchHHHHHHHHHHHHHHh
Q psy1643 815 TNSSHLKYMPKLKAKTPIQQLLSSAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQTQQEDYAHLFATLISRCAR 894 (962)
Q Consensus 815 ~~s~~~~~~PmADRLTQLQDCLD~aQLAEQFcNSIGYLQRdAPPSsFsPndKIsSpdPqQqqp~EDnpQEFATDIIrKAK 894 (962)
||.+--.+.-..||++-|||.++ .....|-.++.+-..-.-.. .+ .+|.
T Consensus 33 Png~t~~~~~aqdr~~kl~e~lr---~i~~LFkkLRlIYekCne~~-~~------l~~~--------------------- 81 (150)
T PF11315_consen 33 PNGSTQQQNMAQDRRNKLQEQLR---TIKVLFKKLRLIYEKCNENC-QG------LEPT--------------------- 81 (150)
T ss_pred CCCccchhhhhhhHHHHHHHHHH---HHHHHHHHHHHHHHHHHHhc-cC------CCCC---------------------
Confidence 33333334455688888888888 55555566676654310000 00 0010
Q ss_pred hHHHHHHhCCCCCCCHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccC
Q psy1643 895 DIDALIESLPNEDSTTELQ--LASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIAQSQLETNG 961 (962)
Q Consensus 895 QIE~LIDSLPGIDSSEEEQ--LERIRELEEENKEAEQELQEAVKEAEELLEQVQEALrdIAQSQLnTRp 961 (962)
+||.||=.-=......++. -+..+.+.+|++++-+.+.+.-++-..++++++..+-+|.. .|.||+
T Consensus 82 ~iEsLIP~~~~~~~k~e~~~~s~~~~~~~~er~el~e~v~~KN~qLk~iid~lR~~iweIN~-ml~~r~ 149 (150)
T PF11315_consen 82 PIESLIPYKEEPRNKEEERDSSEEYRQLLEERKELIEQVKQKNQQLKEIIDQLRNIIWEINT-MLAMRR 149 (150)
T ss_pred CHHHhccccCCccccccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHccc
Confidence 4555554444444444443 23566788888888888888888888888888888877755 476664
No 6
>PRK08147 flgK flagellar hook-associated protein FlgK; Validated
Probab=61.18 E-value=18 Score=40.57 Aligned_cols=136 Identities=10% Similarity=0.158 Sum_probs=69.0
Q ss_pred HHHHHHHHhhccCCCCCCCcCCCCCCcchHHHhhhC-----HHHHHHHHHHHHhhhccccCCCCCCCCCCCCCCCCCCCC
Q psy1643 802 IFAEYMEKTKRKNTNSSHLKYMPKLKAKTPIQQLLS-----SAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQT 876 (962)
Q Consensus 802 ~~~~~~ek~krk~~~s~~~~~~PmADRLTQLQDCLD-----~aQLAEQFcNSIGYLQRdAPPSsFsPndKIsSpdPqQqq 876 (962)
++-+|++.+-|. .+++.+-+-...+.|.||++.++ +...++.||+++.-|..+ | .+. ....
T Consensus 66 ~~D~fl~~q~r~-~~s~~~~~~~~~~~l~~le~~~~~~~~gl~~~l~~ff~a~~~ls~~--P-----~~~------~~r~ 131 (547)
T PRK08147 66 EYDAFITNQLRA-AQTQSSGLTTRYEQMSKIDNLLSDSTNSLSTTMQDFFTSLQTLVSN--A-----EDP------AARQ 131 (547)
T ss_pred HHHHHHHHHHHH-HHhhhhHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHHHhC--C-----CCH------HHHH
Confidence 344555544432 22333333444566777776653 457888999999988754 1 110 0001
Q ss_pred cchHHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHH
Q psy1643 877 QQEDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVR-----RGELLLEQIQAALTD 951 (962)
Q Consensus 877 p~EDnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVK-----EAEELLEQVQEALrd 951 (962)
..-...+.|+..+=....+++.+-... +..-+.+..+|-.|-+++.++.++....-. .+-.|+.+-+.+|++
T Consensus 132 ~vl~~a~~l~~~~n~~~~~L~~~~~~~---~~~i~~~V~~iN~l~~~Ia~LN~~I~~~~~~~~g~~~ndL~DqRD~ll~e 208 (547)
T PRK08147 132 ALIGKAEGLVNQFKTTDQYLRDQDKGV---NTAIGSSVDQINNYAKQIASLNDQITRLTGVGAGASPNDLLDQRDQLVSE 208 (547)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCcchhHHHHHHHHHH
Confidence 112244455554444444444433321 122334455566666666655555544321 233566666666666
Q ss_pred HHH
Q psy1643 952 IAQ 954 (962)
Q Consensus 952 IAQ 954 (962)
+++
T Consensus 209 LS~ 211 (547)
T PRK08147 209 LNQ 211 (547)
T ss_pred HHh
Confidence 654
No 7
>KOG1853|consensus
Probab=58.28 E-value=24 Score=38.47 Aligned_cols=71 Identities=17% Similarity=0.128 Sum_probs=44.4
Q ss_pred hHHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 879 EDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAAL 949 (962)
Q Consensus 879 EDnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEAL 949 (962)
+.+.+.|-..-++-.|||+.|=|-|--...--|.|.++|++||+-|..++.-.+..+--++.+=..++.+|
T Consensus 76 e~~Kek~e~q~~q~y~q~s~Leddlsqt~aikeql~kyiReLEQaNDdLErakRati~sleDfeqrLnqAI 146 (333)
T KOG1853|consen 76 ERNKEKQEDQRVQFYQQESQLEDDLSQTHAIKEQLRKYIRELEQANDDLERAKRATIYSLEDFEQRLNQAI 146 (333)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHhhhhhhhhHHHHHHHHHHHH
Confidence 44555566666777888888888876655555666788999988777665544333333333333333333
No 8
>TIGR02492 flgK_ends flagellar hook-associated protein FlgK. The flagellar hook-associated protein FlgK of bacterial flagella has conserved N- and C-terminal domains. The central region is highly variable in length and sequence, and often contains substantial runs of low-complexity sequence. This model is built from an alignment of FlgK sequences with the central region excised. Note that several other proteins of the flagellar apparatus also are homologous in the N- and C-terminal regions to FlgK, but are excluded from this model.
Probab=57.35 E-value=22 Score=37.46 Aligned_cols=135 Identities=16% Similarity=0.245 Sum_probs=71.0
Q ss_pred HHHHHHHhhccCCCCCCCcCCCCCCcchHHHhhhC------HHHHHHHHHHHHhhhccccCCCCCCCCCCCCCCCCCCCC
Q psy1643 803 FAEYMEKTKRKNTNSSHLKYMPKLKAKTPIQQLLS------SAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQT 876 (962)
Q Consensus 803 ~~~~~ek~krk~~~s~~~~~~PmADRLTQLQDCLD------~aQLAEQFcNSIGYLQRdAPPSsFsPndKIsSpdPqQqq 876 (962)
+-+|+.++.|+ .++....+-...+-|.||+..++ +...+..||+++.-|..+ | .+. ....
T Consensus 65 ~d~~l~~q~r~-~~s~~~~~~~~~~~l~~le~~~~~~~~~gl~~~l~~ff~a~~~ls~~--P-----~~~------~~r~ 130 (322)
T TIGR02492 65 QDQFLDNQYRR-ANSSAGYADSRASALSQIENLFNDLDESGLSTYLNNFFNALQELAKN--P-----DSE------ALRQ 130 (322)
T ss_pred hhHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhCCCCcCcHHHHHHHHHHHHHHHHhC--C-----CCH------HHHH
Confidence 34444444333 23333444555666777776554 236788999999877754 1 110 0001
Q ss_pred cchHHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHH
Q psy1643 877 QQEDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVR----RGELLLEQIQAALTDI 952 (962)
Q Consensus 877 p~EDnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVK----EAEELLEQVQEALrdI 952 (962)
..-...+.|+..+=....+|+.+-... +..-+.+...|-.|-+++.++.++....-. ..-.|+.+-+.+|+++
T Consensus 131 ~vl~~a~~l~~~~n~~~~~L~~~~~~~---~~~i~~~V~~iN~ll~~Ia~lN~~I~~~~~~~g~~~n~L~DqRD~ll~~L 207 (322)
T TIGR02492 131 AVLESAQALANSFNQTSNELQDLRKGI---NAEIKSAVTEINSLLKQIASLNKEIQQVEAKSGQDANDLLDQRDLLLKEL 207 (322)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCchHhHHHHHHHHHHH
Confidence 122345555555555555555444332 223344556666666666666655544221 2345777777777766
Q ss_pred HH
Q psy1643 953 AQ 954 (962)
Q Consensus 953 AQ 954 (962)
++
T Consensus 208 S~ 209 (322)
T TIGR02492 208 SQ 209 (322)
T ss_pred Hh
Confidence 65
No 9
>PF04999 FtsL: Cell division protein FtsL; InterPro: IPR007082 In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein IPR007060 from INTERPRO [], however this interaction may be indirect [].; GO: 0007049 cell cycle, 0016021 integral to membrane
Probab=54.32 E-value=62 Score=28.44 Aligned_cols=47 Identities=19% Similarity=0.176 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHhhhhccC
Q psy1643 915 ASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAA-----LTDIAQSQLETNG 961 (962)
Q Consensus 915 ERIRELEEENKEAEQELQEAVKEAEELLEQVQEA-----LrdIAQSQLnTRp 961 (962)
...+.+..|+..++++..+.-.+-+.|.-++..+ |+.||..+|.|++
T Consensus 35 ~~~~~~~~~l~~l~~~~~~l~~e~~~L~lE~~~l~~~~rIe~iA~~~LgM~~ 86 (97)
T PF04999_consen 35 HQSRQLFYELQQLEKEIDQLQEENERLRLEIATLSSPSRIERIAREKLGMVP 86 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHcCCCCC
Confidence 3455666666666666666666666666666544 7999999999975
No 10
>PRK07739 flgK flagellar hook-associated protein FlgK; Validated
Probab=52.74 E-value=32 Score=38.63 Aligned_cols=136 Identities=13% Similarity=0.205 Sum_probs=73.6
Q ss_pred HHHHHHHHhhccCCCCCCCcCCCCCCcchHHHhhhC------HHHHHHHHHHHHhhhccccCCCCCCCCCCCCCCCCCCC
Q psy1643 802 IFAEYMEKTKRKNTNSSHLKYMPKLKAKTPIQQLLS------SAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQ 875 (962)
Q Consensus 802 ~~~~~~ek~krk~~~s~~~~~~PmADRLTQLQDCLD------~aQLAEQFcNSIGYLQRdAPPSsFsPndKIsSpdPqQq 875 (962)
++-+|+.++-|. .++..+.+-..++.|.||+..++ +...+..||+++.-|-.+ |.+ +...
T Consensus 76 ~~D~fl~~q~r~-~~s~~~~~~~~~~~l~~le~~f~~~~~~gl~~~l~~ff~a~~~la~~-------P~~------~~~r 141 (507)
T PRK07739 76 IRDQFLDIQYRR-ENNKLGYWETKADALSQMEDIMNEPSDTGLNKVLDQFWNSLQELSKN-------PEN------LGAR 141 (507)
T ss_pred hHHHHHHHHHHH-HHhhhhhHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHHHHhC-------cCC------HHHH
Confidence 344555444333 23344445555677777776664 246788999999887754 111 0001
Q ss_pred CcchHHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHH
Q psy1643 876 TQQEDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVR---RGELLLEQIQAALTDI 952 (962)
Q Consensus 876 qp~EDnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVK---EAEELLEQVQEALrdI 952 (962)
...-...+.|+..|=..+.+++.+-..+ +..-+.+...|-.|-+++.++.++...+-. ..-.|+.+-+.+|+++
T Consensus 142 ~~vl~~a~~La~~~n~~~~~L~~~~~~~---~~~i~~~V~~iN~ll~~Ia~LN~~I~~~~~~g~~~ndLlDqRD~ll~~L 218 (507)
T PRK07739 142 SVVRQRAQALAETFNYLSQSLTDIQNDL---KSEIDVTVKEINSLASQISDLNKQIAKVEPNGYLPNDLYDQRDLLLDEL 218 (507)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHHH
Confidence 1122355666666655555555554432 222345556666666666666666554322 1335677777777666
Q ss_pred HH
Q psy1643 953 AQ 954 (962)
Q Consensus 953 AQ 954 (962)
++
T Consensus 219 S~ 220 (507)
T PRK07739 219 SK 220 (507)
T ss_pred Hh
Confidence 64
No 11
>smart00150 SPEC Spectrin repeats.
Probab=51.35 E-value=1.3e+02 Score=24.24 Aligned_cols=35 Identities=31% Similarity=0.381 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 910 TELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQ 944 (962)
Q Consensus 910 EEEQLERIRELEEENKEAEQELQEAVKEAEELLEQ 944 (962)
-+.|++..+.++.|+......+..+...++.|+..
T Consensus 33 ~~~~~~~~~~~~~e~~~~~~~v~~~~~~~~~L~~~ 67 (101)
T smart00150 33 VEALLKKHEALEAELEAHEERVEALNELGEQLIEE 67 (101)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHc
Confidence 35677888999999999999999999999888874
No 12
>PF03233 Cauli_AT: Aphid transmission protein; InterPro: IPR004917 This protein is found in various caulimoviruses. It codes for an 18 kDa protein (PII), which is dispensable for infection but which is required for aphid transmission of the virus []. This protein interacts with the PIII protein []. ; GO: 0019089 transmission of virus
Probab=50.23 E-value=54 Score=33.46 Aligned_cols=54 Identities=22% Similarity=0.358 Sum_probs=38.4
Q ss_pred hHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 895 DIDALIESLPNEDSTTELQLASLRKLEQDNQGAA------ERLEDTVRRGELLLEQIQAALTDI 952 (962)
Q Consensus 895 QIE~LIDSLPGIDSSEEEQLERIRELEEENKEAE------QELQEAVKEAEELLEQVQEALrdI 952 (962)
+++..++-+|.+ +|.|- +|++|+++.+.++ .++.+.|+.-|+-|..|++-+..|
T Consensus 102 d~~k~~~~l~~L---~e~sn-ki~kLe~~~k~L~d~Iv~~~~i~e~IKd~de~L~~I~d~iK~I 161 (163)
T PF03233_consen 102 DKQKQLKLLPTL---EEISN-KIRKLETEVKKLKDNIVTEKLIEELIKDFDERLKEIRDKIKKI 161 (163)
T ss_pred chhhHHHHHHHH---HHHHH-HHHHHHHHHHhHhhhccccHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 344444444444 22332 8899998888774 478889999999999999988776
No 13
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=48.75 E-value=96 Score=26.31 Aligned_cols=43 Identities=21% Similarity=0.174 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccC
Q psy1643 917 LRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIAQSQLETNG 961 (962)
Q Consensus 917 IRELEEENKEAEQELQEAVKEAEELLEQVQEALrdIAQSQLnTRp 961 (962)
+.+++.++++...|-.+...|...|-. .+.|..+|...|.|.+
T Consensus 33 ~~~~~~~~~~l~~en~~L~~ei~~l~~--~~rIe~~Ar~~lgM~~ 75 (85)
T TIGR02209 33 LQKLQLEIDKLQKEWRDLQLEVAELSR--HERIEKIAKKQLGMKL 75 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcC--HHHHHHHHHHhcCCCC
Confidence 444444444444444444444443333 4558999999998865
No 14
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=48.33 E-value=91 Score=25.65 Aligned_cols=46 Identities=20% Similarity=0.315 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHhhhhc
Q psy1643 914 LASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAA------LTDIAQSQLET 959 (962)
Q Consensus 914 LERIRELEEENKEAEQELQEAVKEAEELLEQVQEA------LrdIAQSQLnT 959 (962)
..++.+++.|..+..+++.+.-.+-+.|-.+++.+ |..+|...|.|
T Consensus 16 ~~~~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~~~~ie~~AR~~lgm 67 (80)
T PF04977_consen 16 YSRYYQLNQEIAELQKEIEELKKENEELKEEIERLKNDPDYIEKVAREKLGM 67 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcCC
Confidence 34445555555555555555555555555555444 67778777765
No 15
>PF01865 PhoU_div: Protein of unknown function DUF47; InterPro: IPR018445 This family includes prokaryotic proteins of unknown function, as well as a protein annotated as the pit accessory protein from Rhizobium meliloti (Sinorhizobium meliloti) (O30498 from SWISSPROT). However, the function of this protein is also unknown (Pit stands for Phosphate transport) [].; PDB: 2OLT_C 2IIU_C 3L39_A.
Probab=46.22 E-value=2.4e+02 Score=27.41 Aligned_cols=119 Identities=18% Similarity=0.211 Sum_probs=74.8
Q ss_pred CCcCCCCCCcchHHHhhhCHHHHHHHHHHHHhhhccccCCCCCCCCCCCCCCCCCCCCcchHHHHHHHHHHHHHHhhHHH
Q psy1643 819 HLKYMPKLKAKTPIQQLLSSAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQTQQEDYAHLFATLISRCARDIDA 898 (962)
Q Consensus 819 ~~~~~PmADRLTQLQDCLD~aQLAEQFcNSIGYLQRdAPPSsFsPndKIsSpdPqQqqp~EDnpQEFATDIIrKAKQIE~ 898 (962)
-.+.++-.|++. |=..+| ..++..-.+...+.-...+ + +.+..+...+|+..++...+-+..
T Consensus 71 fitP~dRedi~~-L~~~lD--~I~d~i~~~a~~l~~~~~~--~-------------~~~~~~~~~~l~~~~~~~~~~l~~ 132 (214)
T PF01865_consen 71 FITPFDREDILR-LISSLD--DIADYIEDAAKRLSLYKVE--I-------------PEELREEFQELAEIVVEAIEELVE 132 (214)
T ss_dssp SS-SS-HHHHHH-HHHHHH--HHHHHHHHHHHHHHHHT-------------------CCGHHHHHHHHHHHHHHHHHHHH
T ss_pred ccCCCcHHHHHH-HHHHHH--HHHHHHHHHHHHHHHhccC--C-------------CcchhHHHHHHHHHHHHHHHHHHH
Confidence 334444445443 555566 5666666666555544311 0 123455788899999999999999
Q ss_pred HHHhCCCC-CCCHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHh
Q psy1643 899 LIESLPNE-DSTTE--LQLASLRKLEQDNQGAAERLEDTVRRGEL--------LLEQIQAALTDIAQS 955 (962)
Q Consensus 899 LIDSLPGI-DSSEE--EQLERIRELEEENKEAEQELQEAVKEAEE--------LLEQVQEALrdIAQS 955 (962)
.|..|... +++-+ +....|+.+|.+-..+..++...+-+-+. .+..|-+.|..++|.
T Consensus 133 ~i~~l~~~~~~~~~~~~~~~~I~~~E~~~D~l~~~~~~~lf~~~~~~d~~~~~~~~ei~~~le~~~D~ 200 (214)
T PF01865_consen 133 AIEELKSILESSFEEKELIKEINKLEEEADKLYRRLIKKLFSNEDEMDPIEIIKLKEIYEHLEDIADK 200 (214)
T ss_dssp HHCCCCCCCCS-HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 99999974 34444 58889999999999998888777776332 233444455555554
No 16
>PRK11797 D-ribose pyranase; Provisional
Probab=45.82 E-value=20 Score=34.80 Aligned_cols=91 Identities=25% Similarity=0.235 Sum_probs=58.9
Q ss_pred ccceeeecccCCCCcccCchhHHhhhhhcccCCCchhhhhhhcCCCchhHHHHhHHHHHHHHHhhcCCc-----cccchh
Q psy1643 669 VRPIVRLKTHNCDDNLEGLDDLVDELATVKLEDAPEAEKEEESGKDSADSIIKNYEKIWRYYKRQIPKA-----RGITIH 743 (962)
Q Consensus 669 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~ 743 (962)
++.|.+.-+++-.+-++-|+.++.++. .|.+- --+|...+ |. .+|+.|+..++++ ++++++
T Consensus 37 ~~~idla~~~g~p~f~~vl~aIL~~~~---Ve~~~---~~~e~~~~-------~p-~~~~~~~~~l~~~~~~~~~~~~~~ 102 (139)
T PRK11797 37 VERIDLALTKGVPSFLDVLDVVLSEMQ---VEKAI---LAEEIKEH-------NP-ELHEALLTQLEQLEQHQGNTIEIE 102 (139)
T ss_pred CceEEeccCCCCCCHHHHHHHHHHhcC---cchHH---Hhhhcccc-------CH-HHHHHHHHHHHHhhhccCCCccee
Confidence 455666666665544455555555554 33322 12222222 33 4999999999873 357899
Q ss_pred hhhhhhhcccccccEEEEEeccccccccccccc
Q psy1643 744 KLLSWSIKQMWHPDVYVVICSQENLSLYKTNVI 776 (962)
Q Consensus 744 ~~~~~~~~~~~~~~~~~~~c~~~~~sl~~~~vi 776 (962)
.+-.|..+++=. +.|.|+...|. .+|+ |+|
T Consensus 103 ~i~r~~Fy~~a~-~a~avVrTGE~-~~Ya-NiI 132 (139)
T PRK11797 103 YVSHEEFKQLTA-ESKAVIRTGEC-TPYA-NII 132 (139)
T ss_pred EECHHHHHHHHh-cceEEEECCCC-CCee-EEE
Confidence 888899999766 89999988875 5565 655
No 17
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=45.48 E-value=34 Score=36.57 Aligned_cols=42 Identities=24% Similarity=0.222 Sum_probs=22.2
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 909 TTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALT 950 (962)
Q Consensus 909 SEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEALr 950 (962)
-|++-.+.|.+|+.|.+++.+|+.+.-++.+.+-..-....+
T Consensus 58 Ee~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE~~~~~ 99 (314)
T PF04111_consen 58 EEEELLQELEELEKEREELDQELEELEEELEELDEEEEEYWR 99 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445556666666666666655555555554444433333
No 18
>PRK07521 flgK flagellar hook-associated protein FlgK; Validated
Probab=45.06 E-value=27 Score=38.87 Aligned_cols=135 Identities=11% Similarity=0.088 Sum_probs=67.3
Q ss_pred HHHHHHHhhccCCCCCCCcCCCCCCcchHHHhhhC-------HHHHHHHHHHHHhhhccccCCCCCCCCCCCCCCCCCCC
Q psy1643 803 FAEYMEKTKRKNTNSSHLKYMPKLKAKTPIQQLLS-------SAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQ 875 (962)
Q Consensus 803 ~~~~~ek~krk~~~s~~~~~~PmADRLTQLQDCLD-------~aQLAEQFcNSIGYLQRdAPPSsFsPndKIsSpdPqQq 875 (962)
+-+|+.++-|+ .++..+.+-...+-|.||+..++ +...+..||+++.-|..+ | .+. ...
T Consensus 59 ~D~fl~~q~r~-~~s~~~~~~~~~~~l~~le~~~~e~~~~~gl~~~l~~ff~a~~~la~~--P-----~~~------~~R 124 (483)
T PRK07521 59 QDPALLAQRLL-ATSAAAAQDTLADGLERLASTVGDNDYEGSPSARLSDFQAALQTAASS--P-----DNT------TLA 124 (483)
T ss_pred cCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHHhC--C-----CCH------HHH
Confidence 34555544433 34445555566677778777555 347788999999988754 1 110 000
Q ss_pred CcchHHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHH
Q psy1643 876 TQQEDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVR---RGELLLEQIQAALTDI 952 (962)
Q Consensus 876 qp~EDnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVK---EAEELLEQVQEALrdI 952 (962)
...-...+.|+..+=....+++.+=+.+ +..-+.+..+|-.|-+++.++.++....-- .+-.|+.+=+.+|+++
T Consensus 125 ~~vl~~a~~L~~~~n~~~~~L~~~~~~~---~~~i~~~V~~iN~l~~~Ia~LN~~I~~~~~~g~~~ndL~DqRD~ll~~L 201 (483)
T PRK07521 125 QAAVDAAQDLANSLNDASDAVQSARADA---DAEIADSVDTLNDLLAQFEDANNAVVSGTATGRDASDALDQRDKLLKQI 201 (483)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCchhhHHHHHHHHHHH
Confidence 1112244455554444444444443322 112223344455555555555444433211 1235666666666666
Q ss_pred HH
Q psy1643 953 AQ 954 (962)
Q Consensus 953 AQ 954 (962)
++
T Consensus 202 S~ 203 (483)
T PRK07521 202 SQ 203 (483)
T ss_pred Hh
Confidence 54
No 19
>PRK06665 flgK flagellar hook-associated protein FlgK; Validated
Probab=44.37 E-value=44 Score=38.75 Aligned_cols=135 Identities=12% Similarity=0.145 Sum_probs=70.0
Q ss_pred HHHHHHHhhccCCCCCCCcCCCCCCcchHHHhhhC------HHHHHHHHHHHHhhhccccCCCCCCCCCCCCCCCCCCCC
Q psy1643 803 FAEYMEKTKRKNTNSSHLKYMPKLKAKTPIQQLLS------SAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQT 876 (962)
Q Consensus 803 ~~~~~ek~krk~~~s~~~~~~PmADRLTQLQDCLD------~aQLAEQFcNSIGYLQRdAPPSsFsPndKIsSpdPqQqq 876 (962)
+-+|+.++-| +.++..+.+--..+.|.||+..++ +...++.||+++.-|..+ | .+. ....
T Consensus 77 ~D~fl~~q~r-~~~s~~~~~~~~~~~l~~le~if~e~~~~gl~~~l~~ff~al~~ls~~--P-----~~~------a~R~ 142 (627)
T PRK06665 77 RDELLDSRII-EESGRLGYWKTKDKYLSQLEQVYNEPEDQSLRTRLDDFWDSWQDLSNY--P-----EGL------AERQ 142 (627)
T ss_pred hhHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHHhC--C-----CCH------HHHH
Confidence 4445543332 233444445555666777776654 235788999999988754 1 110 0001
Q ss_pred cchHHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHH
Q psy1643 877 QQEDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVR---RGELLLEQIQAALTDIA 953 (962)
Q Consensus 877 p~EDnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVK---EAEELLEQVQEALrdIA 953 (962)
..-...+.|+..+=....+++.+-+.+ +..-+.+..+|-.|-+++.++.++....-. ..-.|+.+=+.+|++++
T Consensus 143 ~vl~~A~~La~~~n~~~~~L~~~~~~~---~~~i~~~V~~iN~ll~qIa~LN~qI~~~~~~g~~~ndLlDqRD~ll~eLS 219 (627)
T PRK06665 143 VVLERAQSLGERIHDRYRSLERIRDMA---NDEIEITVEEINNILRNIADLNEQIVKSQAMGDNPNDLLDRRDLLVDKLS 219 (627)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchhhHHHHHHHHHHHH
Confidence 112245555555555555554444432 223334456666666666666655544321 13356666666666665
Q ss_pred H
Q psy1643 954 Q 954 (962)
Q Consensus 954 Q 954 (962)
+
T Consensus 220 ~ 220 (627)
T PRK06665 220 S 220 (627)
T ss_pred h
Confidence 4
No 20
>KOG4465|consensus
Probab=43.11 E-value=11 Score=42.58 Aligned_cols=232 Identities=25% Similarity=0.417 Sum_probs=137.2
Q ss_pred chHHHHHHHHHhcccCCCcEEEEEEeecccccccccchheeeeeecc-----ccCCccchhHHHhhhhhhhhh-------
Q psy1643 331 PDAVRKQLQKWYMGKESDQLVVLVAKCSVYQGLSHANVLKLIHFDVF-----HQSPDKKLALYAIAFGFAYVS------- 398 (962)
Q Consensus 331 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~------- 398 (962)
-.++||.+.+||-.|....|..++.|-.--.|.||..++.|-|-..- .||.|. |- .+|.|-|+.-.
T Consensus 170 gralr~aia~wy~~k~~e~lal~ltky~qregwshkdlfrlahpnl~~srs~gqsedr-le-~~~l~kfa~kgdlvkrkr 247 (598)
T KOG4465|consen 170 GRALRKAIADWYNEKGGEALALALTKYKQREGWSHKDLFRLAHPNLKDSRSEGQSEDR-LE-LAILFKFATKGDLVKRKR 247 (598)
T ss_pred HHHHHHHHHHHHhccchHHHHHHHhhcccccCCchHhHHHhcCCccCCccccCccchh-HH-HHHHHHHHhccchhhhhh
Confidence 46899999999999999999999999999999999999999996543 345443 33 46777776432
Q ss_pred ----------hhhcccccccCCCCCCcccCcchhhh-cccchhhhcceeeEEEecCchhHHHHHhhhccccccccccchh
Q psy1643 399 ----------HRLISGKFLATPRVPPFVTSDDCFDK-ASDKVKTIVKDVAVVRCNTSHQKVVAAAVKTHSLGIESVCPKF 467 (962)
Q Consensus 399 ----------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 467 (962)
|.|..-|-|..|. ...=.-| -....-..+.-|--+ -|+....++-+|++.|.|--|..--.-
T Consensus 248 kmsvee~aeve~l~d~kalkl~~------teeklikeeqsralnllea~~kl-knek~e~~iiaai~~h~lvrehl~t~~ 320 (598)
T KOG4465|consen 248 KMSVEEVAEVEELWDEKALKLET------TEEKLIKEEQSRALNLLEAVEKL-KNEKDEEEIIAAIEEHGLVREHLLTNH 320 (598)
T ss_pred hccHHHHHHHHHHHHhhhcCCCc------hHHHHHHHHHHHHHHHHHHHHHH-hccccHHHHHHHHHHhhhHHHhccccc
Confidence 3344444433221 1110000 000000011111111 256667788889999999888776666
Q ss_pred hhhcccchhhhc-chhhhhhHHHhhhhccccccCCCCceecccCcccchhhhhcCCCCCCCCCCChHHHHHHhhhhhhhc
Q psy1643 468 AKSFKVNTACLE-GMTQRGLLQSMHRLRKDNVLSSEDHAIVDESTTCGTYVKQLGASPVTEPPLHPAEVLAAYAEYVLAP 546 (962)
Q Consensus 468 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 546 (962)
-||-.|-.+-+. .|.-..|+..+-.+--..+|..... -|| ..|-....| .-....-.||-.+|-|.+-|-
T Consensus 321 l~sk~vwealfdv~mpltalirnlakmt~~galdegnk-~vd--~i~~kl~de---e~lkkarihp~~il~a~a~ya--- 391 (598)
T KOG4465|consen 321 LKSKEVWEALFDVEMPLTALIRNLAKMTANGALDEGNK-EVD--LICEKLCDE---EELKKARIHPFHILIALATYA--- 391 (598)
T ss_pred cchHHHHHHHHhccCcHHHHHHHHHhhhhhcccCcccc-HHH--HHHHHhcCH---HHHHhhcCCchHHHHHHHHHH---
Confidence 677666666555 5665566666555555555533211 111 123222111 111234578888888877773
Q ss_pred ccccccccccccCCCCCCCCCCccccccccCCCcceeccCCchHHHHHHHHHHHhhcccccc
Q psy1643 547 VTKMASFQKKAVKPPPSEGGGGDQAQEKSEDETPVLTAKAPEPAIVSALQELYKSSFSNLKT 608 (962)
Q Consensus 547 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 608 (962)
.|-||...-+- -|...|..||..-|-..|.|...
T Consensus 392 ------------------qg~g~kg~l~w----------epde~i~dalda~fykaf~na~p 425 (598)
T KOG4465|consen 392 ------------------QGHGDKGKLKW----------EPDEEICDALDAAFYKAFKNAEP 425 (598)
T ss_pred ------------------ccCCccccccc----------CCcHHHHHHHHHHHHHHhccCCC
Confidence 13444333222 36678999999887778887654
No 21
>PRK05683 flgK flagellar hook-associated protein FlgK; Validated
Probab=41.88 E-value=47 Score=39.15 Aligned_cols=136 Identities=12% Similarity=0.161 Sum_probs=72.0
Q ss_pred HHHHHHHHhhccCCCCCCCcCCCCCCcchHHHhhhC-----HHHHHHHHHHHHhhhccccCCCCCCCCCCCCCCCCCCCC
Q psy1643 802 IFAEYMEKTKRKNTNSSHLKYMPKLKAKTPIQQLLS-----SAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQT 876 (962)
Q Consensus 802 ~~~~~~ek~krk~~~s~~~~~~PmADRLTQLQDCLD-----~aQLAEQFcNSIGYLQRdAPPSsFsPndKIsSpdPqQqq 876 (962)
++-+|+..+-|... +....+-...|.|+||...+. +...++.||+++.-|..+. .+ +...+
T Consensus 65 ~~D~fl~~q~r~~~-s~~~~~~~~~~~l~~ld~ll~~~~~gls~~L~~Ff~alq~la~~P-------~s------~aaRq 130 (676)
T PRK05683 65 IYNSFLDTQLRTAT-SLNSDASAYLGQISQLDKLLSDSTTGISPALQRFFTALQTAAANP-------TD------TAARQ 130 (676)
T ss_pred hHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHhhcCCCCccHHHHHHHHHHHHHHHHHCC-------CC------HHHHH
Confidence 34455555544331 122222334566777766543 3367889999998887651 11 00001
Q ss_pred cchHHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHH
Q psy1643 877 QQEDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVR---RGELLLEQIQAALTDIA 953 (962)
Q Consensus 877 p~EDnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVK---EAEELLEQVQEALrdIA 953 (962)
..-...+.|+..+-....+++.+-+.+ +..-+.+..+|-.|-+++.++.++...+-. ..-.||.+-+.+|++++
T Consensus 131 ~vl~~A~~La~~fn~~~~~L~~l~~~v---n~qI~~~V~~IN~l~~qIA~LN~qI~~~~~~G~~~NdLlDqRD~Ll~eLS 207 (676)
T PRK05683 131 LLLTQAQGLSKRFNSLSSQLNQQNSNI---NSQLSAMTDQVNNLTTSIASYNKQIAQASASGATPNDLLDARDEAVRQLN 207 (676)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHhHHHHHHHHHHHH
Confidence 122355666666655555555555443 222344456666666666666666544321 23467777777777776
Q ss_pred H
Q psy1643 954 Q 954 (962)
Q Consensus 954 Q 954 (962)
+
T Consensus 208 ~ 208 (676)
T PRK05683 208 E 208 (676)
T ss_pred h
Confidence 5
No 22
>PRK10884 SH3 domain-containing protein; Provisional
Probab=38.98 E-value=1.4e+02 Score=30.84 Aligned_cols=36 Identities=14% Similarity=0.139 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 916 SLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTD 951 (962)
Q Consensus 916 RIRELEEENKEAEQELQEAVKEAEELLEQVQEALrd 951 (962)
.+.+|++||+++.+|++++-.+.+.+-.++++.=+.
T Consensus 133 ~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~~~ 168 (206)
T PRK10884 133 VINGLKEENQKLKNQLIVAQKKVDAANLQLDDKQRT 168 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355688888888888888888877766665555433
No 23
>PRK08871 flgK flagellar hook-associated protein FlgK; Validated
Probab=38.68 E-value=25 Score=40.93 Aligned_cols=136 Identities=10% Similarity=0.145 Sum_probs=64.5
Q ss_pred HHHHHHHHhhccCCCCCCCcCCCCCCcchHHHhhhC------HHHHHHHHHHHHhhhccccCCCCCCCCCCCCCCCCCCC
Q psy1643 802 IFAEYMEKTKRKNTNSSHLKYMPKLKAKTPIQQLLS------SAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQ 875 (962)
Q Consensus 802 ~~~~~~ek~krk~~~s~~~~~~PmADRLTQLQDCLD------~aQLAEQFcNSIGYLQRdAPPSsFsPndKIsSpdPqQq 875 (962)
++-+|+.++-|... +...-+-...+.|+||+..+. +...++.||+++.-|..+. .+ +...
T Consensus 67 ~~D~fl~~q~r~~~-s~~~~~~~~~~~l~~ld~l~~~~~~~gls~~L~~Ff~alq~la~~P-------~~------~aaR 132 (626)
T PRK08871 67 SWDQFAVNELNLST-TNLANKTDTEANLDMLSSMLSSVASKKIPENLNEWFDAVKTLADSP-------ND------LGAR 132 (626)
T ss_pred chhHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHHhCC-------CC------HHHH
Confidence 34555555433321 111222223445666666555 1245889999998887541 11 0000
Q ss_pred CcchHHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 876 TQQEDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIAQ 954 (962)
Q Consensus 876 qp~EDnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEALrdIAQ 954 (962)
+..-...+.|+..+=....+++.+-+.+ +..-+.+..+|-.|-+++.++.++....-...-.||.+-+.+|+++++
T Consensus 133 q~vl~~A~~La~~fn~~~~~L~~~~~~v---n~qi~~~V~~IN~l~~qIA~LN~qI~~~~g~pNdLlDqRD~ll~eLS~ 208 (626)
T PRK08871 133 KVVLEKAKLISQTLNDFHETVRQQKDVT---NKKLDLGVERINQIALEIRDIHRLMMRTPGPHNDLMDQHEKLVKELSQ 208 (626)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCchhhHHHHHHHHHHHHh
Confidence 1112244445544444444444433321 112223345555555555555555543212244677777777776664
No 24
>smart00502 BBC B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains
Probab=38.19 E-value=2.2e+02 Score=24.43 Aligned_cols=44 Identities=16% Similarity=0.160 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 910 TELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIA 953 (962)
Q Consensus 910 EEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEALrdIA 953 (962)
++.....+.+|+.+.++....+...+...+..+..+..++..+-
T Consensus 56 ~~~e~~ll~~l~~~~~~~~~~l~~q~~~l~~~l~~l~~~~~~~e 99 (127)
T smart00502 56 NKRKKQLLEDLEEQKENKLKVLEQQLESLTQKQEKLSHAINFTE 99 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44556668888888888888888888888888888877776553
No 25
>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.
Probab=37.50 E-value=1.3e+02 Score=26.59 Aligned_cols=63 Identities=11% Similarity=0.159 Sum_probs=41.7
Q ss_pred HHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 885 FATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQA 947 (962)
Q Consensus 885 FATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQE 947 (962)
+...|..|--+|..|..-.=.+...+-.+...|+.|-.++.+.+.++.+.-++.+.+...+..
T Consensus 3 l~~~l~EKDe~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~~~~~l~~~~~~~e~~~~~ 65 (74)
T PF12329_consen 3 LEKKLAEKDEQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEKQIKELKKKLEELEKELES 65 (74)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455677788888888876555555555566778888888877777666555544444444443
No 26
>PF06103 DUF948: Bacterial protein of unknown function (DUF948); InterPro: IPR009293 This family consists of bacterial sequences several of which are thought to be general stress proteins.
Probab=36.84 E-value=1.7e+02 Score=25.52 Aligned_cols=39 Identities=15% Similarity=0.324 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 914 LASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDI 952 (962)
Q Consensus 914 LERIRELEEENKEAEQELQEAVKEAEELLEQVQEALrdI 952 (962)
.+.++.|+++......|..+.+.+...+++.+++....+
T Consensus 32 ~~ti~~l~~~~~~i~~e~~~ll~~~n~l~~dv~~k~~~v 70 (90)
T PF06103_consen 32 NKTIDTLQEQVDPITKEINDLLHNTNELLEDVNEKLEKV 70 (90)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 345666677777777777777777777666666655443
No 27
>KOG4304|consensus
Probab=35.30 E-value=68 Score=33.92 Aligned_cols=45 Identities=16% Similarity=0.191 Sum_probs=33.4
Q ss_pred hHHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHH
Q psy1643 879 EDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQ 925 (962)
Q Consensus 879 EDnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENK 925 (962)
....+-|...-+.++..+-.....+||.+. +...+-+.-|..-..
T Consensus 102 ~~~~d~f~~Gf~ec~~EVsr~ls~~~~~~~--~~~~~L~~HL~~~~~ 146 (250)
T KOG4304|consen 102 ALPVDSFRAGFRECAAEVSRYLSICPGMDA--AKGTRLLTHLQAHLA 146 (250)
T ss_pred cccchhhhccHHHHHHHHHHHHhhCCCCCh--HHHhHHHHHHHHHhh
Confidence 346778999999999999999999999987 444444555544443
No 28
>PRK07191 flgK flagellar hook-associated protein FlgK; Validated
Probab=34.09 E-value=71 Score=35.42 Aligned_cols=135 Identities=13% Similarity=0.107 Sum_probs=65.7
Q ss_pred HHHHHHHhhccCCCCCCCcCCCCCCcchHHHhhhC-----HHHHHHHHHHHHhhhccccCCCCCCCCCCCCCCCCCCCCc
Q psy1643 803 FAEYMEKTKRKNTNSSHLKYMPKLKAKTPIQQLLS-----SAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQTQ 877 (962)
Q Consensus 803 ~~~~~ek~krk~~~s~~~~~~PmADRLTQLQDCLD-----~aQLAEQFcNSIGYLQRdAPPSsFsPndKIsSpdPqQqqp 877 (962)
+-+|+.++-|. .++..+.+-...+.|.||+..++ +...+..||+++.-|..+. .+. .....
T Consensus 66 ~D~~l~~~~~~-~~s~~~~~~~~~~~l~~le~~~~~~~~gl~~~l~~ff~a~~~la~~P-------~~~------~~r~~ 131 (456)
T PRK07191 66 SQQYVVMQEWQ-ANSQQGYYDAGEQYFNALELVVGNKSTSLATGLNNFFSALSAATQLP-------DSP------PMRQQ 131 (456)
T ss_pred HhHHHHHHHHH-HHhHhHHHHHHHHHHHHHHHHhCCCCCchHHHHHHHHHHHHHHHhCC-------CCH------HHHHH
Confidence 34444443332 23334444445666677766653 3467889999998887641 110 00011
Q ss_pred chHHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH
Q psy1643 878 QEDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVR---RGELLLEQIQAALTDIAQ 954 (962)
Q Consensus 878 ~EDnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVK---EAEELLEQVQEALrdIAQ 954 (962)
.-+..+.|+..+=....+++.+-+.+- ..-+.+..+|-.|-+++.++.++....-. ..-.|+.+=+.+|+++++
T Consensus 132 vl~~a~~la~~~n~~~~~l~~~~~~~~---~~i~~~V~~iN~ll~~Ia~LN~~I~~~~~~g~~~ndL~DqRD~ll~eLS~ 208 (456)
T PRK07191 132 VIESANAMALRFNNVNNFIVQQKKSIG---QQRDATVKQINSLTRSIADYNQKILKNRSDGNNISDLLDQRDLQIKKLSG 208 (456)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCchhHHHHHHHHHHHHh
Confidence 122344444444444433333333221 11234556666666666666555543221 123566666666666554
No 29
>PF06103 DUF948: Bacterial protein of unknown function (DUF948); InterPro: IPR009293 This family consists of bacterial sequences several of which are thought to be general stress proteins.
Probab=33.68 E-value=1.6e+02 Score=25.62 Aligned_cols=38 Identities=16% Similarity=0.260 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 916 SLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIA 953 (962)
Q Consensus 916 RIRELEEENKEAEQELQEAVKEAEELLEQVQEALrdIA 953 (962)
.++++++-.+..+++.....+|.+.++...++.+.++.
T Consensus 27 ~l~~~~~ti~~l~~~~~~i~~e~~~ll~~~n~l~~dv~ 64 (90)
T PF06103_consen 27 TLDEVNKTIDTLQEQVDPITKEINDLLHNTNELLEDVN 64 (90)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35555555666666666666666666666666655543
No 30
>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=33.03 E-value=1.2e+02 Score=36.37 Aligned_cols=13 Identities=38% Similarity=0.575 Sum_probs=8.5
Q ss_pred hhHHHHHHhCCCC
Q psy1643 894 RDIDALIESLPNE 906 (962)
Q Consensus 894 KQIE~LIDSLPGI 906 (962)
.+++.||+.|=..
T Consensus 511 ~~~~~li~~L~~~ 523 (771)
T TIGR01069 511 EEINVLIEKLSAL 523 (771)
T ss_pred HHHHHHHHHHHHH
Confidence 3777777777443
No 31
>PF04678 DUF607: Protein of unknown function, DUF607; InterPro: IPR006769 This entry represents the C-terminal domain of coiled-coil domain containing protein 109.
Probab=32.92 E-value=2.2e+02 Score=28.28 Aligned_cols=51 Identities=14% Similarity=0.100 Sum_probs=27.7
Q ss_pred HHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 896 IDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQ 946 (962)
Q Consensus 896 IE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQ 946 (962)
|..+|.++=.....++.|..+.+.|.+++.++++|++..-+++.++-+..+
T Consensus 38 v~~~v~~~~~~~~~~~~~~~~~~~l~~~l~~~~~el~~le~~k~~id~~A~ 88 (180)
T PF04678_consen 38 VKEAVHRLLPLLNVEEYQNSRERQLRKRLEELRQELAPLEKIKQEIDEKAE 88 (180)
T ss_pred HHHHHHHHhccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333333333355666666666777776666666655555554444433
No 32
>PRK06799 flgK flagellar hook-associated protein FlgK; Validated
Probab=31.66 E-value=70 Score=35.42 Aligned_cols=135 Identities=16% Similarity=0.181 Sum_probs=65.7
Q ss_pred HHHHHHHhhccCCCCCCCcCCCCCCcchHHHhhhC------HHHHHHHHHHHHhhhccccCCCCCCCCCCCCCCCCCCCC
Q psy1643 803 FAEYMEKTKRKNTNSSHLKYMPKLKAKTPIQQLLS------SAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQT 876 (962)
Q Consensus 803 ~~~~~ek~krk~~~s~~~~~~PmADRLTQLQDCLD------~aQLAEQFcNSIGYLQRdAPPSsFsPndKIsSpdPqQqq 876 (962)
+-+|+.++.|. .+++-+.+-...+-|+||+..++ +...+..||+++.-|..+ | .+. ....
T Consensus 70 ~D~~l~~q~~~-~~s~~~~~~~~~~~l~~le~~~~~~~~~gl~~~l~~ff~a~~~ls~~--P-----~~~------~~r~ 135 (431)
T PRK06799 70 TDEVKTKQYND-QLSQLSYYNYMNSALSRVESMVGTTGKNSLSSLMDGFFNAFREVAKN--P-----EQA------NYYD 135 (431)
T ss_pred HhHHHHHHHHH-HHHHHhHHHHHHHHHHHHHHHhCCCCcCchHHHHHHHHHHHHHHHhC--c-----CCH------HHHH
Confidence 44555544332 33444444455666777776654 236778999999988764 1 110 0001
Q ss_pred cchHHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Q psy1643 877 QQEDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVR-RGELLLEQIQAALTDIAQ 954 (962)
Q Consensus 877 p~EDnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVK-EAEELLEQVQEALrdIAQ 954 (962)
..-...+.|+..|=....+++.+-... +..-+.+..+|-.|-+++.++.++....-. .+-.|+.+=+.+|+++++
T Consensus 136 ~vl~~a~~l~~~~n~~~~~L~~~~~~~---~~~i~~~V~~iN~ll~~Ia~LN~~I~~~~~~~~ndL~DqRD~ll~eLS~ 211 (431)
T PRK06799 136 TLISETGKFTSQLNRLAKGLDELEAQT---TEDIEAHVNEFNRLAKSLAEANKKIGQAGTQVPNQLLDERDRILTEMSK 211 (431)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCchhhHHHHHHHHHHHHh
Confidence 111234445444444444443333221 112234455555555555555555443211 123566666666666654
No 33
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=31.49 E-value=1.6e+02 Score=27.41 Aligned_cols=47 Identities=17% Similarity=0.095 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q psy1643 912 LQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIAQSQLET 959 (962)
Q Consensus 912 EQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEALrdIAQSQLnT 959 (962)
++.+++.++++|++++.++-++.-++.+.|-.. .+.+..+|...|.+
T Consensus 31 ~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~-~dyiEe~AR~~Lg~ 77 (105)
T PRK00888 31 RVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGG-QEAIEERARNELGM 77 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCc-HHHHHHHHHHHcCC
Confidence 344455666666655555544444444433321 25778888888765
No 34
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=30.78 E-value=2.6e+02 Score=23.51 Aligned_cols=26 Identities=27% Similarity=0.289 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 911 ELQLASLRKLEQDNQGAAERLEDTVR 936 (962)
Q Consensus 911 EEQLERIRELEEENKEAEQELQEAVK 936 (962)
++|.+.|+++.++.......++..+.
T Consensus 44 ~eQ~~~l~~~~~~~~~~~~~~r~~~~ 69 (125)
T PF13801_consen 44 PEQQAKLRALMDEFRQEMRALRQELR 69 (125)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666665555444444443333
No 35
>PF00215 OMPdecase: Orotidine 5'-phosphate decarboxylase / HUMPS family; InterPro: IPR001754 Orotidine 5'-phosphate decarboxylase (OMPdecase) [, ] catalyses the last step in the de novo biosynthesis of pyrimidines, the decarboxylation of OMP into UMP. In higher eukaryotes OMPdecase is part, with orotate phosphoribosyltransferase, of a bifunctional enzyme, while the prokaryotic and fungal OMPdecases are monofunctional protein. Some parts of the sequence of OMPdecase are well conserved across species. The best conserved region is located in the N-terminal half of OMPdecases and is centred around a lysine residue which is essential for the catalytic function of the enzyme. This entry also includes enzymes such as 3-hexulose-6-phosphate synthase 4.1.2.43 from EC and 3-keto-L-gulonate-6-phosphate decarboxylase 4.1.1.85 from EC.; GO: 0004590 orotidine-5'-phosphate decarboxylase activity, 0006207 'de novo' pyrimidine base biosynthetic process; PDB: 2YYT_D 2YYU_B 3RU6_D 2CZE_B 2CZ5_B 2CZF_A 2CZD_A 3R89_A 2ZCG_A 2ZA1_A ....
Probab=30.68 E-value=13 Score=36.71 Aligned_cols=77 Identities=22% Similarity=0.244 Sum_probs=63.6
Q ss_pred hhhhcccchhhhcchhhhhhHHHhhhhccccccCCCCceecccCcccchhh------hhcCCCCCCCCCCChHHHHHHhh
Q psy1643 467 FAKSFKVNTACLEGMTQRGLLQSMHRLRKDNVLSSEDHAIVDESTTCGTYV------KQLGASPVTEPPLHPAEVLAAYA 540 (962)
Q Consensus 467 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~ 540 (962)
....+|+++..+.......|.+.++.||+.+..--.|.-+.|...|...|+ ..+||.-+|--|.-..+.+.+..
T Consensus 25 ~v~~iKvG~~l~~~~G~~~l~~~i~~l~~~~~~I~~D~K~~Dig~t~~~~~~~~~~~~~~gaD~vTv~~~~G~~tl~~~~ 104 (226)
T PF00215_consen 25 YVDIIKVGTPLFLAYGLEALPEIIEELKERGKPIFLDLKLGDIGNTVARYAEAGFAAFELGADAVTVHPFAGDDTLEAAV 104 (226)
T ss_dssp GSSEEEEEHHHHHHHCHHHHHHHHHHHHHTTSEEEEEEEE-SSHHHHHHHHHSCHHHHTTTESEEEEEGTTHHHHHHHHH
T ss_pred cceEEEEChHHHhcCChhhHHHHHHHHHHhcCCEeeeeeecccchHHHHHHHHhhhhhcCCCcEEEEeccCCHHHHHHHH
Confidence 566789999887654444688889999999877788999999999999999 59999999999998888888877
Q ss_pred hhh
Q psy1643 541 EYV 543 (962)
Q Consensus 541 ~~~ 543 (962)
+..
T Consensus 105 ~~a 107 (226)
T PF00215_consen 105 KAA 107 (226)
T ss_dssp HHH
T ss_pred HHH
Confidence 654
No 36
>COG1422 Predicted membrane protein [Function unknown]
Probab=30.53 E-value=1.1e+02 Score=32.17 Aligned_cols=46 Identities=13% Similarity=0.254 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHhhhhc
Q psy1643 914 LASLRKLEQDNQGAAERLEDTVRRGE-LLLEQIQAALTDIAQSQLET 959 (962)
Q Consensus 914 LERIRELEEENKEAEQELQEAVKEAE-ELLEQVQEALrdIAQSQLnT 959 (962)
.+++++++++.+|..+|.+++-+++| .-|+++|+.=.++.+.|.++
T Consensus 71 ~ekm~~~qk~m~efq~e~~eA~~~~d~~~lkkLq~~qmem~~~Q~el 117 (201)
T COG1422 71 QEKMKELQKMMKEFQKEFREAQESGDMKKLKKLQEKQMEMMDDQREL 117 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHH
Confidence 47788888888888888888877654 56788888888888777654
No 37
>TIGR00996 Mtu_fam_mce virulence factor Mce family protein. Members of this paralogous family are found as six tandem homologous proteins in the same orientation per cassette, in four separate cassettes in Mycobacterium tuberculosis. The six members of each cassette represent six subfamilies. One subfamily includes the protein mce (mycobacterial cell entry), a virulence protein required for invasion of non-phagocytic cells.
Probab=30.18 E-value=1.3e+02 Score=30.52 Aligned_cols=69 Identities=17% Similarity=0.132 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 881 YAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQG-------AAERLEDTVRRGELLLEQIQAAL 949 (962)
Q Consensus 881 npQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKE-------AEQELQEAVKEAEELLEQVQEAL 949 (962)
+...++..+.....+|..+|+.+=.+-.+-+++.+.|.++-+.... ...++.+++......+..++..|
T Consensus 175 ~l~~l~~~l~~~~~~i~~ll~~l~~l~~~l~~~~~~l~~~v~~l~~~~~~l~~~~~~l~~~l~~l~~~~~~~~~~l 250 (291)
T TIGR00996 175 GLAQLTAALNARDGDIGALIDNLNRVLDVLADRSDQLDRLLDNLATLTAQLADRDDALDDALAALSGASAQVRDLL 250 (291)
T ss_pred HHHHHHHHHHhcchhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555555566666655544333333333334433333222 33344444444444444433333
No 38
>PF11887 DUF3407: Protein of unknown function (DUF3407); InterPro: IPR024516 This entry represents a domain of unknown function found at the C terminus of many proteins in the mammalian cell entry family.
Probab=29.69 E-value=2.8e+02 Score=29.07 Aligned_cols=72 Identities=18% Similarity=0.064 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 881 YAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDI 952 (962)
Q Consensus 881 npQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEALrdI 952 (962)
....++..+...+.||...++.+.-.-.+=.+|.+.|..|-.....+..+..+.+.+.+.-|..+=+.++-+
T Consensus 60 ~l~~v~~~~a~aapdL~~~l~~~~~~s~tL~~~~~~L~~lL~~~~~~a~~~~~~l~~n~~~L~~~~~~L~p~ 131 (267)
T PF11887_consen 60 NLADVADTYADAAPDLLDALDNLTTTSRTLVDQRQQLDALLLSATGLADTGTDFLADNRDNLIRALDDLRPT 131 (267)
T ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 455567777888888888888888877777777788888877777777777777776655554444444333
No 39
>PF00015 MCPsignal: Methyl-accepting chemotaxis protein (MCP) signalling domain; InterPro: IPR004089 Methyl-accepting chemotaxis proteins (MCPs) are a family of bacterial receptors that mediate chemotaxis to diverse signals, responding to changes in the concentration of attractants and repellents in the environment by altering swimming behaviour []. Environmental diversity gives rise to diversity in bacterial signalling receptors, and consequently there are many genes encoding MCPs []. For example, there are four well-characterised MCPs found in Escherichia coli: Tar (taxis towards aspartate and maltose, away from nickel and cobalt), Tsr (taxis towards serine, away from leucine, indole and weak acids), Trg (taxis towards galactose and ribose) and Tap (taxis towards dipeptides). MCPs share similar topology and signalling mechanisms. MCPs either bind ligands directly or interact with ligand-binding proteins, transducing the signal to downstream signalling proteins in the cytoplasm. MCPs undergo two covalent modifications: deamidation and reversible methylation at a number of glutamate residues. Attractants increase the level of methylation, while repellents decrease it. The methyl groups are added by the methyl-transferase cheR and are removed by the methylesterase cheB. Most MCPs are homodimers that contain the following organisation: an N-terminal signal sequence that acts as a transmembrane domain in the mature protein; a poorly-conserved periplasmic receptor (ligand-binding) domain; a second transmembrane domain; and a highly-conserved C-terminal cytoplasmic domain that interacts with downstream signalling components. The C-terminal domain contains the glycosylated glutamate residues. This entry represents the signalling domain found in several methyl-accepting chemotaxis proteins. This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs.; GO: 0004871 signal transducer activity, 0007165 signal transduction, 0016020 membrane; PDB: 2CH7_A 3ZX6_B 1QU7_A 3G6B_B 3UR1_C 3G67_B.
Probab=28.24 E-value=2.5e+02 Score=26.25 Aligned_cols=27 Identities=26% Similarity=0.383 Sum_probs=20.9
Q ss_pred hHHHHHHHHHHHHHHhhHHHHHHhCCC
Q psy1643 879 EDYAHLFATLISRCARDIDALIESLPN 905 (962)
Q Consensus 879 EDnpQEFATDIIrKAKQIE~LIDSLPG 905 (962)
-+.++.||...-..+++|..+|+.+-.
T Consensus 81 A~eir~LA~~t~~~~~~I~~~i~~i~~ 107 (213)
T PF00015_consen 81 ADEIRKLAEQTSESAKEISEIIEEIQE 107 (213)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhhhhhhhHHHHHHHHHhhhhh
Confidence 346788888888888888888887643
No 40
>KOG4031|consensus
Probab=27.74 E-value=1.5e+02 Score=31.48 Aligned_cols=41 Identities=17% Similarity=0.218 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Q psy1643 910 TELQLASLRKLEQDNQGAAERLE-DTVRRGELLLEQIQAALT 950 (962)
Q Consensus 910 EEEQLERIRELEEENKEAEQELQ-EAVKEAEELLEQVQEALr 950 (962)
-++|++||.++.+.-+...+|++ +++++-|.+..+..+.+.
T Consensus 112 keeQ~~rl~ekD~~sek~k~ElrekAkKelddwy~~~~ek~~ 153 (216)
T KOG4031|consen 112 KEEQMKRLQEKDEASEKLKEELREKAKKELDDWYDQQNEKLE 153 (216)
T ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36899999999888888777765 577888888888877763
No 41
>COG4451 RbcS Ribulose bisphosphate carboxylase small subunit [Energy production and conversion]
Probab=27.48 E-value=1.9e+02 Score=28.84 Aligned_cols=97 Identities=27% Similarity=0.317 Sum_probs=69.6
Q ss_pred CCCcceeccCCchHHHHHHHHHHHhhcccccccCceeeEEeecCCccccCCCCCCC-CCCCCCchhHHHHHHHHH-hhhc
Q psy1643 577 DETPVLTAKAPEPAIVSALQELYKSSFSNLKTHDSLKISVCLDLQPRFESQPCRDY-RPLSGSHVAVLVLESLLR-MVDY 654 (962)
Q Consensus 577 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~-~~~~ 654 (962)
.-+|.||. -.|..-+|-|. |...||.|=.--+|||+..----+ -|+-|.|-+-=||..|-+ ..||
T Consensus 14 s~lp~Ltd----~qi~~QVrylL---------~QGykigvE~~d~rrprtgsWt~wg~p~f~~~~~~evlaele~Cr~dh 80 (127)
T COG4451 14 SSLPPLTD----EQIAEQVRYLL---------SQGYKIGVEYVDDRRPRTGSWTMWGTPMFGAKTAGEVLAELEACRADH 80 (127)
T ss_pred ecCCcCcH----HHHHHHHHHHH---------hCCcccceeecccCCcccceeeecCCccccccchHHHHHHHHHHHHhC
Confidence 34666665 34555555554 456789998888999987543333 367888887766666554 4799
Q ss_pred cccceEEeeccCCcccceeeecccCCCCcccC
Q psy1643 655 KMDNIRLVGFKDAKVRPIVRLKTHNCDDNLEG 686 (962)
Q Consensus 655 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 686 (962)
--+-|||+||...+-|-++..-.|-=+.|-.|
T Consensus 81 p~eYIRliGfDp~gkrrv~sfIVhRPng~~~~ 112 (127)
T COG4451 81 PGEYIRLIGFDPKGKRRVVSFIVHRPNGNPSG 112 (127)
T ss_pred CCCeEEEEEecCCCceEEEEEEEECCCCCCCC
Confidence 99999999999999999988888876665544
No 42
>PRK11637 AmiB activator; Provisional
Probab=26.53 E-value=2.7e+02 Score=30.46 Aligned_cols=20 Identities=10% Similarity=0.174 Sum_probs=7.9
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy1643 917 LRKLEQDNQGAAERLEDTVR 936 (962)
Q Consensus 917 IRELEEENKEAEQELQEAVK 936 (962)
|..+++++..+++++.+.-+
T Consensus 98 i~~~~~ei~~l~~eI~~~q~ 117 (428)
T PRK11637 98 LNQLNKQIDELNASIAKLEQ 117 (428)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44444444433333333333
No 43
>PF00435 Spectrin: Spectrin repeat; InterPro: IPR002017 Spectrin repeats [] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [, ], alpha-actinin [] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.; GO: 0005515 protein binding; PDB: 1HCI_A 1QUU_A 3FB2_B 1S35_A 1U5P_A 1U4Q_A 1CUN_B 1YDI_B 3EDV_A 1AJ3_A ....
Probab=26.38 E-value=3.4e+02 Score=21.75 Aligned_cols=50 Identities=22% Similarity=0.316 Sum_probs=32.8
Q ss_pred hHHHHHHhCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 895 DIDALIESLPN--EDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQ 944 (962)
Q Consensus 895 QIE~LIDSLPG--IDSSEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQ 944 (962)
+.+..+.+.+. --..-+.+++.++.+++++...+.++..+...++.|+..
T Consensus 19 ~~e~~l~~~~~~~~~~~~~~~~~~~~~~~~ei~~~~~~l~~l~~~~~~L~~~ 70 (105)
T PF00435_consen 19 ETEAKLSSSEPGSDLEELEEQLKKHKELQEEIESRQERLESLNEQAQQLIDS 70 (105)
T ss_dssp HHHHHHCSCTHSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHhCCCCCCCHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHc
Confidence 44444444443 222344566778888888888888888888888888443
No 44
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=26.14 E-value=1.9e+02 Score=33.62 Aligned_cols=19 Identities=0% Similarity=-0.109 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy1643 931 LEDTVRRGELLLEQIQAAL 949 (962)
Q Consensus 931 LQEAVKEAEELLEQVQEAL 949 (962)
+++.|++.|..++++++-+
T Consensus 102 le~KIkeLEaE~~~Lk~Ql 120 (475)
T PRK13729 102 DQRRIEKLGQDNAALAEQV 120 (475)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444333
No 45
>PF11471 Sugarporin_N: Maltoporin periplasmic N-terminal extension; InterPro: IPR021570 This N-terminal domain is found in members of the sugar porin family 1.B.3 from TC, They are related to LamB - the well characterised maltoporin of Escherichia coli for which the three-dimensional structures with and without its substrate have been obtained by X-ray diffraction. The protein consists of an 18 beta-stranded beta-barrel in contrast to proteins of the general bacterial porin family (GBP) and the Rhodobacter PorCa Porin (RPP) family which consist of 16 beta-stranded beta-barrels. Although maltoporin contains a wider beta-barrel than the porins of the GBP and RPP families (1.B.1 from TC and 1.B.7 from TC), it exhibits a narrower channel, showing only 5% of the ionic conductance of the latter porins.
Probab=25.93 E-value=1.3e+02 Score=26.09 Aligned_cols=27 Identities=30% Similarity=0.272 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 914 LASLRKLEQDNQGAAERLEDTVRRGEL 940 (962)
Q Consensus 914 LERIRELEEENKEAEQELQEAVKEAEE 940 (962)
.+||..||+++++++++.+.+-.++..
T Consensus 31 EqRLa~LE~rL~~ae~ra~~ae~~~~~ 57 (60)
T PF11471_consen 31 EQRLAALEQRLQAAEQRAQAAEARAKQ 57 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999988877666543
No 46
>TIGR00606 rad50 rad50. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.86 E-value=5.3e+02 Score=32.42 Aligned_cols=73 Identities=15% Similarity=0.146 Sum_probs=48.0
Q ss_pred HHHHHHHHHhhHHHHHHhCCCCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHhhh
Q psy1643 885 FATLISRCARDIDALIESLPNEDST--TELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAA---LTDIAQSQL 957 (962)
Q Consensus 885 FATDIIrKAKQIE~LIDSLPGIDSS--EEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEA---LrdIAQSQL 957 (962)
+..++....++|+.|-..+++-+.+ -++=.+.|..++.++..+..++.....+.+.+-.+|+.+ +..+.+..+
T Consensus 797 ~~~ei~~l~~qie~l~~~l~~~~~~~s~~ele~ei~~~~~el~~l~~~~e~l~~e~e~~~~eI~~Lq~ki~el~~~kl 874 (1311)
T TIGR00606 797 FQMELKDVERKIAQQAAKLQGSDLDRTVQQVNQEKQEKQHELDTVVSKIELNRKLIQDQQEQIQHLKSKTNELKSEKL 874 (1311)
T ss_pred HHHHHHHHHHHHHHHHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677788888999999999976542 222233466666666666666666677777766666666 655544433
No 47
>PRK12714 flgK flagellar hook-associated protein FlgK; Provisional
Probab=25.86 E-value=83 Score=36.56 Aligned_cols=31 Identities=23% Similarity=0.208 Sum_probs=21.9
Q ss_pred CCCcchHHHhhhC-----HHHHHHHHHHHHhhhccc
Q psy1643 825 KLKAKTPIQQLLS-----SAEQADNFCNSVGILQQT 855 (962)
Q Consensus 825 mADRLTQLQDCLD-----~aQLAEQFcNSIGYLQRd 855 (962)
..+.|+||++.+. +...++.||+++.-|-.+
T Consensus 87 ~~~~l~~le~ll~~~~~gls~~l~~ff~alq~la~~ 122 (624)
T PRK12714 87 LSSLSNRVDALYSNTATNVAGLWSNFFDSTSALSSN 122 (624)
T ss_pred HHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHHHHhC
Confidence 3566666666654 346788999999888754
No 48
>PF12290 DUF3802: Protein of unknown function (DUF3802); InterPro: IPR020979 This family of proteins is found in bacteria and are typically between 114 and 143 amino acids in length. There is a conserved KNLFD sequence motif. The annotation with this family suggests that it may be the B subunit of bacterial type IIA DNA topoisomerase but there is no evidence to support this annotation.
Probab=25.82 E-value=1.4e+02 Score=29.28 Aligned_cols=26 Identities=8% Similarity=0.243 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 929 ERLEDTVRRGELLLEQIQAALTDIAQ 954 (962)
Q Consensus 929 QELQEAVKEAEELLEQVQEALrdIAQ 954 (962)
..|-+.++|+|.++.-+++.|..+..
T Consensus 60 ~~R~~iirE~Daiv~DLeEVLa~V~~ 85 (113)
T PF12290_consen 60 SQRFQIIREADAIVYDLEEVLASVWN 85 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 35566778888888888888776643
No 49
>TIGR02132 phaR_Bmeg polyhydroxyalkanoic acid synthase, PhaR subunit. This model describes a protein, PhaR, localized to polyhydroxyalkanoic acid (PHA) inclusion granules in Bacillus cereus and related species. PhaR is required for PHA biosynthesis along with PhaC and may be a regulatory subunit.
Probab=24.81 E-value=3.1e+02 Score=28.85 Aligned_cols=68 Identities=15% Similarity=0.181 Sum_probs=35.5
Q ss_pred hHHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 879 EDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQ 946 (962)
Q Consensus 879 EDnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQ 946 (962)
.+.+..||..++.-+-.||.|=..+-..-..-++|.+.-..|..+...+++.+...=++.|.+|..++
T Consensus 71 r~DiarvA~lvinlE~kvD~lee~fdd~~d~l~~q~eq~~~~~~~v~~~~q~~~~l~~K~D~~L~llE 138 (189)
T TIGR02132 71 KEDIANVASLVINLEEKVDLIEEFFDDKFDELEAQQEQAPALKKDVTKLKQDIKSLDKKLDKILELLE 138 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCchHHhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45677787777654443333211111100111255555556666666666666666666666666655
No 50
>PRK12715 flgK flagellar hook-associated protein FlgK; Provisional
Probab=24.79 E-value=96 Score=36.49 Aligned_cols=135 Identities=14% Similarity=0.177 Sum_probs=63.8
Q ss_pred HHHHHHHHhhccCCCCCCCcCCCCCCcchHHHhhhC-----HHHHHHHHHHHHhhhccccCCCCCCCCCCCCCCCCCCCC
Q psy1643 802 IFAEYMEKTKRKNTNSSHLKYMPKLKAKTPIQQLLS-----SAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQT 876 (962)
Q Consensus 802 ~~~~~~ek~krk~~~s~~~~~~PmADRLTQLQDCLD-----~aQLAEQFcNSIGYLQRdAPPSsFsPndKIsSpdPqQqq 876 (962)
++-+|+.++-|.. .+....+-...+.|+||+..+. +...++.||+++.-|-.+ | .+. ...+
T Consensus 65 ~~d~fl~~q~r~~-~s~~~~~~~~~~~l~~i~~ll~~~~~gls~~l~~ff~a~q~la~~--P-----~~~------~~Rq 130 (649)
T PRK12715 65 NVDQFANAQVRST-LSYRTQYDAFYNQAIQIDKLLSQDGSSISVPLQTFFDSIGQLNST--P-----DNI------ATRG 130 (649)
T ss_pred hHhHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHHHHHC--C-----CCH------HHHH
Confidence 3445555444432 2222233333455666665443 347788999999888754 1 110 0001
Q ss_pred cchHHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 877 QQEDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIAQ 954 (962)
Q Consensus 877 p~EDnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEALrdIAQ 954 (962)
..-...+.|+..+-....+++.+=+.+ +..-+.+..+|-.|-+++.++.++.... ...-.||.+-+.+|+++++
T Consensus 131 ~vl~~A~~L~~~fn~~~~~L~~~~~~~---n~~I~~~V~~iN~l~~qIA~LN~qI~~~-~~~ndLlDqRD~ll~eLS~ 204 (649)
T PRK12715 131 VVLKQSQLLAQQFNSLQTKLEEYERNS---TLQVTESVKIINRITKELAEVNGKLLGN-NNIPELLDHRDELLKQLSG 204 (649)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCchHhHHHHHHHHHHHHh
Confidence 112244445444444444443333221 1122333455555555555555554321 1123577777777776664
No 51
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=24.53 E-value=4.5e+02 Score=24.40 Aligned_cols=36 Identities=14% Similarity=0.199 Sum_probs=17.3
Q ss_pred hhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q psy1643 894 RDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAE 929 (962)
Q Consensus 894 KQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQ 929 (962)
.+|-.+++....-+.+.+.-.+.+..|+++.+++++
T Consensus 59 ~~I~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~ 94 (118)
T cd04776 59 EEIRELLDLYDPPGGNRKQLEKMLEKIEKRRAELEQ 94 (118)
T ss_pred HHHHHHHHhhccCCchHHHHHHHHHHHHHHHHHHHH
Confidence 477777776543333332223344455555544433
No 52
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=23.61 E-value=1.8e+02 Score=34.81 Aligned_cols=9 Identities=44% Similarity=0.730 Sum_probs=5.9
Q ss_pred hHHHHHHhC
Q psy1643 895 DIDALIESL 903 (962)
Q Consensus 895 QIE~LIDSL 903 (962)
+++.||+.|
T Consensus 517 ~~~~li~~l 525 (782)
T PRK00409 517 KLNELIASL 525 (782)
T ss_pred HHHHHHHHH
Confidence 666666666
No 53
>COG1463 Ttg2C ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=23.29 E-value=1.9e+02 Score=31.05 Aligned_cols=29 Identities=24% Similarity=0.233 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHhhHHHHHHhCCCCCCC
Q psy1643 881 YAHLFATLISRCARDIDALIESLPNEDST 909 (962)
Q Consensus 881 npQEFATDIIrKAKQIE~LIDSLPGIDSS 909 (962)
+.+.|+..+-....+|..+|++|.-+-.+
T Consensus 184 ~l~~~~~~ln~~~~~i~~~i~~l~~~~~~ 212 (359)
T COG1463 184 NLAQFTDALNARDGDIGALIANLNQLLDS 212 (359)
T ss_pred HHHHHHHHHHhcchhHHHHHHHHHHHHHH
Confidence 56666666666666777777666654433
No 54
>KOG1017|consensus
Probab=23.23 E-value=44 Score=35.72 Aligned_cols=46 Identities=22% Similarity=0.287 Sum_probs=36.1
Q ss_pred ccccccchhhHHHHHHHHhhccCCCCCCCcCCCCCCcchHH--HhhhCHHHH
Q psy1643 792 ENLSLYKTNVIFAEYMEKTKRKNTNSSHLKYMPKLKAKTPI--QQLLSSAEQ 841 (962)
Q Consensus 792 ~~~~~~~~~~~~~~~~ek~krk~~~s~~~~~~PmADRLTQL--QDCLD~aQL 841 (962)
.||.|...|-+|+|+.-+-|.|+++ |..++=.||||-.| .+||| ||
T Consensus 66 ~~lkll~~n~q~~el~ti~Rdkst~--rsDF~F~ADRLiRLViEE~LN--qL 113 (267)
T KOG1017|consen 66 SNLKLLECNSQVAELLTILRDKSTN--RSDFVFNADRLIRLVIEECLN--QL 113 (267)
T ss_pred cccchhhhHHHHHHHHHHHhhccCc--ccceeecHHHHHHHHHHHHhh--cC
Confidence 4667778899999999888877765 55677789999887 57777 65
No 55
>PRK06945 flgK flagellar hook-associated protein FlgK; Validated
Probab=23.22 E-value=1.3e+02 Score=35.47 Aligned_cols=136 Identities=10% Similarity=0.230 Sum_probs=68.6
Q ss_pred HHHHHHHHhhccCCCCCCCcCCCCCCcchHHHhhhC-----HHHHHHHHHHHHhhhccccCCCCCCCCCCCCCCCCCCCC
Q psy1643 802 IFAEYMEKTKRKNTNSSHLKYMPKLKAKTPIQQLLS-----SAEQADNFCNSVGILQQTAIPSKFSGFDRGGSQTPQQQT 876 (962)
Q Consensus 802 ~~~~~~ek~krk~~~s~~~~~~PmADRLTQLQDCLD-----~aQLAEQFcNSIGYLQRdAPPSsFsPndKIsSpdPqQqq 876 (962)
++-+|+..+-|+.. +.-..+--..+.|.||++.+. +...+..||+++.-|-.+ | .+ +...+
T Consensus 66 ~~d~fl~~q~r~~~-s~~~~~~~~~~~l~~le~l~~~~~~gls~~L~~Ff~alq~la~~--P-----~~------~~~Rq 131 (651)
T PRK06945 66 QYSQYLSAQLNNAQ-AASSSLSTYYSQISQLNNYLADPTAGLSPAITSFFTGLQNVANN--P-----SD------PSARQ 131 (651)
T ss_pred HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHHHHhC--C-----CC------HHHHH
Confidence 45566666555442 222233344566777776544 236788999999888754 1 11 00001
Q ss_pred cchHHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHH
Q psy1643 877 QQEDYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTV----RRGELLLEQIQAALTDI 952 (962)
Q Consensus 877 p~EDnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAV----KEAEELLEQVQEALrdI 952 (962)
..-...+.|+..+=....+++.+-+.. +..-+.+.++|-.|-+++.++.++...+. ...-.||.+-+.+|+++
T Consensus 132 ~vl~~a~~La~~fn~~~~~L~~~~~~~---n~~I~~~V~~IN~l~~qIA~LN~~I~~~~~~~g~~~ndLlDqRD~ll~eL 208 (651)
T PRK06945 132 TMLSNAQTLASQFNAAGQQLDQLRQSV---NTQLTSSVTQINSYTKQIAQLNDQIAKAESSQGQPPNDLLDQRDQLVSEL 208 (651)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCcchhHHHHHHHHHHH
Confidence 112244445544444444444333321 12223345556666666655555554431 12335777777777777
Q ss_pred HH
Q psy1643 953 AQ 954 (962)
Q Consensus 953 AQ 954 (962)
++
T Consensus 209 S~ 210 (651)
T PRK06945 209 SK 210 (651)
T ss_pred Hh
Confidence 65
No 56
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=23.18 E-value=3.1e+02 Score=27.85 Aligned_cols=43 Identities=16% Similarity=0.286 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 912 LQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIAQ 954 (962)
Q Consensus 912 EQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEALrdIAQ 954 (962)
...+.|+.|.-|++..+++..++.++.++|......+|.++-+
T Consensus 97 ~~ek~l~~Lk~e~evL~qr~~kle~ErdeL~~kf~~~i~evqQ 139 (201)
T PF13851_consen 97 ELEKELKDLKWEHEVLEQRFEKLEQERDELYRKFESAIQEVQQ 139 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456788888899999999999999999999998888877755
No 57
>PRK11677 hypothetical protein; Provisional
Probab=23.15 E-value=2.9e+02 Score=27.23 Aligned_cols=37 Identities=14% Similarity=0.099 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 917 LRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIA 953 (962)
Q Consensus 917 IRELEEENKEAEQELQEAVKEAEELLEQVQEALrdIA 953 (962)
.++|++|++++..||++--.+...-..+--+++..++
T Consensus 31 q~~le~eLe~~k~ele~YkqeV~~HFa~TA~Ll~~L~ 67 (134)
T PRK11677 31 QQALQYELEKNKAELEEYRQELVSHFARSAELLDTMA 67 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666666666665555555544444444444333
No 58
>PHA03162 hypothetical protein; Provisional
Probab=23.10 E-value=3.9e+02 Score=27.00 Aligned_cols=54 Identities=24% Similarity=0.339 Sum_probs=33.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHhhh
Q psy1643 904 PNEDSTTELQLASLRKLEQDNQGAAERLEDT-------------VRRGELLLEQIQAALTDIAQSQL 957 (962)
Q Consensus 904 PGIDSSEEEQLERIRELEEENKEAEQELQEA-------------VKEAEELLEQVQEALrdIAQSQL 957 (962)
|+-+-+.|+=.++|.+|+-||+.+.+++.+- =.++|.++...-..|...|.-.+
T Consensus 9 pk~~~tmEeLaaeL~kLqmENK~LKkkl~~~~~~~~~p~d~~LTp~qKea~I~s~v~~Lts~A~kKI 75 (135)
T PHA03162 9 PKAQPTMEDLAAEIAKLQLENKALKKKIKEGTDDDPLPGDPILTPAAKEAMIGAATAALTRQAAKKI 75 (135)
T ss_pred CccCCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5666677777777777777777776666433 24556666666666655554433
No 59
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=23.01 E-value=6.9e+02 Score=24.89 Aligned_cols=60 Identities=15% Similarity=0.239 Sum_probs=42.0
Q ss_pred HHHHHHHHHHhhHHHHHHhCCCCCCCHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 884 LFATLISRCARDIDALIESLPNEDSTTELQ--LASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAAL 949 (962)
Q Consensus 884 EFATDIIrKAKQIE~LIDSLPGIDSSEEEQ--LERIRELEEENKEAEQELQEAVKEAEELLEQVQEAL 949 (962)
+.+.+|+.+-+.+..+++.|. +.| .++|..|.+|......+..+.+++....-..+..++
T Consensus 2 ~~~~~L~~~d~~L~~~L~~l~------~hq~~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~ 63 (188)
T PF10018_consen 2 ELAEDLIEADDELSSALEELQ------EHQENQARIQQLRAEIEELDEQIRDILKQLKEARKELRTLP 63 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 357788888888888888773 222 356888888888887777777766655555555555
No 60
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=22.61 E-value=2.5e+02 Score=26.28 Aligned_cols=40 Identities=28% Similarity=0.351 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q psy1643 912 LQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIAQSQLET 959 (962)
Q Consensus 912 EQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEALrdIAQSQLnT 959 (962)
.|.+.++.|.+++...++|... |=.. .+.|.+.|...|.|
T Consensus 61 ~~~~e~~~L~~~~~~l~~ei~~-------L~dg-~~~i~e~AR~~l~~ 100 (117)
T COG2919 61 AQQAELEKLSARNTALEAEIKD-------LKDG-RDYIEERARSELGM 100 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-------hccc-HHHHHHHHHHHhCC
Confidence 4455555555555555444433 3333 77788888877764
No 61
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=22.44 E-value=1.2e+02 Score=35.42 Aligned_cols=38 Identities=18% Similarity=0.291 Sum_probs=28.6
Q ss_pred HHhhHHHHHH-hCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q psy1643 892 CARDIDALIE-SLPNEDSTTELQLASLRKLEQDNQGAAER 930 (962)
Q Consensus 892 KAKQIE~LID-SLPGIDSSEEEQLERIRELEEENKEAEQE 930 (962)
|-|.|-.||- +|||+-. ...+..+|+.|++|++++.+|
T Consensus 2 k~~~~~alv~~al~~~a~-a~a~a~~i~~L~~ql~aLq~~ 40 (514)
T PF11336_consen 2 KKKLITALVAGALPGAAM-AAATADQIKALQAQLQALQDQ 40 (514)
T ss_pred chhHHHHHHHhhcccccc-ccCCHHHHHHHHHHHHHHHHH
Confidence 4578889999 9999753 666777788888888666554
No 62
>PF04156 IncA: IncA protein; InterPro: IPR007285 Chlamydia trachomatis is an obligate intracellular bacterium that develops within a parasitophorous vacuole termed an inclusion. The inclusion is nonfusogenic with lysosomes but intercepts lipids from a host cell exocytic pathway. Initiation of chlamydial development is concurrent with modification of the inclusion membrane by a set of C. trachomatis-encoded proteins collectively designated Incs. One of these Incs, IncA (Inclusion membrane protein A), is functionally associated with the homotypic fusion of inclusions [].
Probab=22.43 E-value=6.2e+02 Score=24.33 Aligned_cols=20 Identities=10% Similarity=0.233 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy1643 916 SLRKLEQDNQGAAERLEDTV 935 (962)
Q Consensus 916 RIRELEEENKEAEQELQEAV 935 (962)
++..++++.+...++..+..
T Consensus 131 ~l~~l~~~~~~~~~e~~~l~ 150 (191)
T PF04156_consen 131 RLDSLDESIKELEKEIRELQ 150 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444444
No 63
>PF04201 TPD52: Tumour protein D52 family; InterPro: IPR007327 The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family []. These proteins have an N-terminal coiled-coil that allows members to form homo- and heterodimers with each other [].
Probab=22.27 E-value=2.4e+02 Score=28.88 Aligned_cols=40 Identities=18% Similarity=0.185 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHH
Q psy1643 906 EDSTTELQLASLRKLEQDNQGAAE---RLEDTVRRGELLLEQIQAAL 949 (962)
Q Consensus 906 IDSSEEEQLERIRELEEENKEAEQ---ELQEAVKEAEELLEQVQEAL 949 (962)
.+-+|++|. +|..||..+++ -|++++..+|.....++..|
T Consensus 24 ~~LsEeE~e----eLr~EL~KvEeEI~TLrqvL~aKer~~~eLKrkL 66 (162)
T PF04201_consen 24 EGLSEEERE----ELRSELAKVEEEIQTLRQVLAAKERHCAELKRKL 66 (162)
T ss_pred ccCCHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 345677765 34444444444 47788888888888777765
No 64
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=22.21 E-value=2.2e+02 Score=34.09 Aligned_cols=42 Identities=29% Similarity=0.484 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 911 ELQLASLRKLEQDNQGA-------AERLEDTVRRGELLLEQIQAALTDI 952 (962)
Q Consensus 911 EEQLERIRELEEENKEA-------EQELQEAVKEAEELLEQVQEALrdI 952 (962)
+.|+++|++|+++.+.+ +++++++.++=|.|.++++.+++.+
T Consensus 575 e~Ql~~L~~l~e~~~~l~~~ae~LaeR~e~a~d~Qe~L~~R~~~vl~~l 623 (717)
T PF10168_consen 575 EQQLKELQELQEERKSLRESAEKLAERYEEAKDKQEKLMKRVDRVLQLL 623 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46777777777666555 4445555555555666666666544
No 65
>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.
Probab=22.06 E-value=3.7e+02 Score=26.63 Aligned_cols=55 Identities=20% Similarity=0.218 Sum_probs=24.9
Q ss_pred hHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHH
Q psy1643 895 DIDALIESLPNEDSTTELQLASLRKLEQDNQGAAE---RLEDTVRRGELLLEQIQAAL 949 (962)
Q Consensus 895 QIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQ---ELQEAVKEAEELLEQVQEAL 949 (962)
++-.+-+.|=..+..-.++..+|..|+.++..... .+.+.+++.+..++.+++-+
T Consensus 96 ~L~~~~~~l~~l~~~~~~~~~~l~~l~~~~~~L~~~~~~l~~~l~ek~k~~e~l~DE~ 153 (194)
T PF08614_consen 96 QLVELNDELQELEKELSEKERRLAELEAELAQLEEKIKDLEEELKEKNKANEILQDEL 153 (194)
T ss_dssp ------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cccccccccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444444455555566677777777665544 56667777777777666655
No 66
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=21.69 E-value=3.2e+02 Score=26.03 Aligned_cols=35 Identities=26% Similarity=0.333 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHH
Q psy1643 918 RKLEQDNQGAAERLEDTVRRGEL-------LLEQIQAALTDI 952 (962)
Q Consensus 918 RELEEENKEAEQELQEAVKEAEE-------LLEQVQEALrdI 952 (962)
++|++|++++.+|+.+--.+... ||..+.+-.+.+
T Consensus 28 ~~l~~eL~~~k~el~~yk~~V~~HF~~ta~Ll~~l~~~Y~~l 69 (128)
T PF06295_consen 28 AKLEQELEQAKQELEQYKQEVNDHFAQTAELLDNLTQDYQKL 69 (128)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555555555555555555444 555555444443
No 67
>PF12998 ING: Inhibitor of growth proteins N-terminal histone-binding; InterPro: IPR024610 Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterised C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. This entry represents the N-terminal histone binding domain found in inhibitor proteins.; PDB: 4AFL_A.
Probab=21.58 E-value=5.4e+02 Score=22.30 Aligned_cols=63 Identities=11% Similarity=0.215 Sum_probs=40.9
Q ss_pred HHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 890 SRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDI 952 (962)
Q Consensus 890 IrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEALrdI 952 (962)
-...+.+..++...+.-..++++-.+.+++++++..++..-..+.|.-+....+.|+.-++.+
T Consensus 36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~~~~~~~l~deKv~lA~~~~d~v~~hi~rL 98 (105)
T PF12998_consen 36 EELDQQIQKFIKNHGSPSLSPEKRRELLKEIQEEYERALELSDEKVALAQQAYDLVDRHIRRL 98 (105)
T ss_dssp HHHHHHHHHHHTCTTS--S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhcccccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344557777777776633455555666777777777777777777777777777777766554
No 68
>PF15254 CCDC14: Coiled-coil domain-containing protein 14
Probab=21.44 E-value=5e+02 Score=32.33 Aligned_cols=37 Identities=30% Similarity=0.389 Sum_probs=26.7
Q ss_pred HHHhhHHHHHHhCCCCC----------------CCHHHHHHH-HHHHHHHHHHH
Q psy1643 891 RCARDIDALIESLPNED----------------STTELQLAS-LRKLEQDNQGA 927 (962)
Q Consensus 891 rKAKQIE~LIDSLPGID----------------SSEEEQLER-IRELEEENKEA 927 (962)
+--..+|..|+-||-+- .||..|++| |+-|+..++|-
T Consensus 360 RLitEvE~cislLPav~g~tniq~EIALA~QplrsENaqLrRrLrilnqqlreq 413 (861)
T PF15254_consen 360 RLITEVEACISLLPAVSGSTNIQVEIALAMQPLRSENAQLRRRLRILNQQLREQ 413 (861)
T ss_pred HHHHHHHHHHHhhhhhhccccchhhhHhhhhhhhhhhHHHHHHHHHHHHHHHHH
Confidence 34457888899999876 467777765 77777777664
No 69
>PF05812 Herpes_BLRF2: Herpesvirus BLRF2 protein; InterPro: IPR008642 This family consists of several herpes virus BLRF2 tegument proteins.; PDB: 2OA5_B 2H3R_D.
Probab=21.27 E-value=2e+02 Score=28.16 Aligned_cols=50 Identities=26% Similarity=0.385 Sum_probs=39.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHhhhh
Q psy1643 909 TTELQLASLRKLEQDNQGAAERLEDTVR-------------RGELLLEQIQAALTDIAQSQLE 958 (962)
Q Consensus 909 SEEEQLERIRELEEENKEAEQELQEAVK-------------EAEELLEQVQEALrdIAQSQLn 958 (962)
|-|+=.++|.+|+-||+.+.+++.+-.. ++|.++...-..|...|...+.
T Consensus 4 t~EeLaaeL~kLqmENk~LKkkl~~~~~p~~~p~~~~LTp~qKe~~I~s~~~~Lss~A~~KIe 66 (118)
T PF05812_consen 4 TMEELAAELQKLQMENKALKKKLRQSVGPGPSPDDEVLTPAQKEAMITSAVSKLSSQASKKIE 66 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTT---S-TT--B--HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCCccccChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566678899999999999999998884 7888888888888777765554
No 70
>KOG4552|consensus
Probab=21.18 E-value=2.5e+02 Score=30.38 Aligned_cols=56 Identities=16% Similarity=0.207 Sum_probs=39.4
Q ss_pred HHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 890 SRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAA 948 (962)
Q Consensus 890 IrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEA 948 (962)
+...+.++-+|+.|-- --|--.+.|++|+..+++++.-|-.++-.|.+-|+.|.++
T Consensus 66 a~eq~k~e~~m~~Lea---~VEkrD~~IQqLqk~LK~aE~iLtta~fqA~qKLksi~~A 121 (272)
T KOG4552|consen 66 APEQQKREQLMRTLEA---HVEKRDEVIQQLQKNLKSAEVILTTACFQANQKLKSIKEA 121 (272)
T ss_pred hHhHHHHHHHHHHHHH---HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444567777776622 1223334588888888888888888888888888888776
No 71
>KOG0425|consensus
Probab=20.70 E-value=34 Score=35.10 Aligned_cols=20 Identities=15% Similarity=0.418 Sum_probs=12.6
Q ss_pred CcchHHHHHHHHHHHHHHhh
Q psy1643 876 TQQEDYAHLFATLISRCARD 895 (962)
Q Consensus 876 qp~EDnpQEFATDIIrKAKQ 895 (962)
..+.++.+||..-+.++++.
T Consensus 143 ~~~Ren~~EykkkV~r~vr~ 162 (171)
T KOG0425|consen 143 KEWRENPEEYKKKVRRCVRR 162 (171)
T ss_pred HHHhhCHHHHHHHHHHHHHH
Confidence 34556777777776666553
No 72
>KOG2751|consensus
Probab=20.51 E-value=2.4e+02 Score=32.68 Aligned_cols=52 Identities=21% Similarity=0.262 Sum_probs=38.7
Q ss_pred HHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 900 IESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTD 951 (962)
Q Consensus 900 IDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEALrd 951 (962)
...|-.+.-.|+.+++.|.+|+++..++..++.+.-.+++++.++-....+.
T Consensus 182 ~~e~~~l~~eE~~L~q~lk~le~~~~~l~~~l~e~~~~~~~~~e~~~~~~~e 233 (447)
T KOG2751|consen 182 LKELKNLKEEEERLLQQLEELEKEEAELDHQLKELEFKAERLNEEEDQYWRE 233 (447)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333344456777888899999999999888888888888888876665543
No 73
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=20.28 E-value=5.8e+02 Score=22.20 Aligned_cols=47 Identities=13% Similarity=0.121 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHH
Q psy1643 880 DYAHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGA 927 (962)
Q Consensus 880 DnpQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEA 927 (962)
+..+++...+-...++|+.+++.+-....+++++ +.+.++.+..+..
T Consensus 75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~y 121 (181)
T PF12729_consen 75 EERQEIEKEIDEARAEIDEALEEYEKLILSPEEK-QLLEEFKEAWKAY 121 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHH-HHHHHHHHHHHHH
Confidence 3566677777777788888888877765555542 2444444433333
No 74
>PRK10780 periplasmic chaperone; Provisional
Probab=20.23 E-value=8e+02 Score=23.77 Aligned_cols=72 Identities=19% Similarity=0.203 Sum_probs=37.5
Q ss_pred HHHHHHHHHHhhHHHHHHhCC--CCCCCHHHHHHH---HHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHH
Q psy1643 884 LFATLISRCARDIDALIESLP--NEDSTTELQLAS---LRKLEQDNQGAAERLEDTVR-----RGELLLEQIQAALTDIA 953 (962)
Q Consensus 884 EFATDIIrKAKQIE~LIDSLP--GIDSSEEEQLER---IRELEEENKEAEQELQEAVK-----EAEELLEQVQEALrdIA 953 (962)
.+-..|-...+.|..+...|= +---|+++..++ |..++++.+...+.+++.+. .-..++..|++++..||
T Consensus 54 ~~q~el~~~~~elq~~~~~~q~~~~~ms~~~~~~~~~el~~~~~~~q~~~~~~qq~~~~~~~e~~~~i~~ki~~ai~~va 133 (165)
T PRK10780 54 GRASELQRMETDLQAKMQKLQRDGSTMKGSDRTKLEKDVMAQRQTFSQKAQAFEQDRRRRSNEERNKILTRIQTAVKSVA 133 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334566666677777777662 222344444433 33334444443333222211 12457788888888887
Q ss_pred Hh
Q psy1643 954 QS 955 (962)
Q Consensus 954 QS 955 (962)
..
T Consensus 134 k~ 135 (165)
T PRK10780 134 NK 135 (165)
T ss_pred HH
Confidence 64
No 75
>PRK10636 putative ABC transporter ATP-binding protein; Provisional
Probab=20.03 E-value=4.1e+02 Score=30.71 Aligned_cols=67 Identities=15% Similarity=0.075 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHhhHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy1643 882 AHLFATLISRCARDIDALIESLPNEDSTTELQLASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAA 948 (962)
Q Consensus 882 pQEFATDIIrKAKQIE~LIDSLPGIDSSEEEQLERIRELEEENKEAEQELQEAVKEAEELLEQVQEA 948 (962)
.+.+-..|...+++|+.|-..|...+.-.+...+++.+|.+|+.++++++++...+=++|-+++.++
T Consensus 565 ~~~~e~~i~~le~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~w~~l~~~~~~~ 631 (638)
T PRK10636 565 IARLEKEMEKLNAQLAQAEEKLGDSELYDQSRKAELTACLQQQASAKSGLEECEMAWLEAQEQLEQM 631 (638)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCchhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3446677778888888888888654322222234688888888888888887777777766655443
No 76
>KOG0994|consensus
Probab=20.00 E-value=5.9e+02 Score=33.29 Aligned_cols=82 Identities=18% Similarity=0.220 Sum_probs=0.0
Q ss_pred CCCcchHHHHHHH------------HHHHHHHhhHHHHHHhCCCCC---------------------------CCHHHHH
Q psy1643 874 QQTQQEDYAHLFA------------TLISRCARDIDALIESLPNED---------------------------STTELQL 914 (962)
Q Consensus 874 Qqqp~EDnpQEFA------------TDIIrKAKQIE~LIDSLPGID---------------------------SSEEEQL 914 (962)
++....+.++++| ..|-...-+|..-+.|||.+| ...+.|+
T Consensus 1486 ~~~adp~si~~vA~~vL~l~lp~tpeqi~~L~~~I~e~v~sL~nVd~IL~~T~~di~ra~~L~s~A~~a~~~A~~v~~~a 1565 (1758)
T KOG0994|consen 1486 QPDADPDSIEEVAEEVLALELPLTPEQIQQLTGEIQERVASLPNVDAILSRTKGDIARAENLQSEAERARSRAEDVKGQA 1565 (1758)
T ss_pred CCCCCHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHhcccHHHHHHhhhhhHHHHHHHHHHHHHHHhHHHHHHHHH
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy1643 915 ASLRKLEQDNQGAAERLEDTVRRGELLLEQIQAALTDIAQS 955 (962)
Q Consensus 915 ERIRELEEENKEAEQELQEAVKEAEELLEQVQEALrdIAQS 955 (962)
+.+.+--+|-.++..+-+.+|+.++.-+...++.|..|-+.
T Consensus 1566 e~V~eaL~~Ad~Aq~~a~~ai~~a~~~~~~a~~~l~kv~~~ 1606 (1758)
T KOG0994|consen 1566 EDVVEALEEADVAQGEAQDAIQGADRDIRLAQQLLAKVQEE 1606 (1758)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Done!