Query 034224
Match_columns 101
No_of_seqs 106 out of 111
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 11:08:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034224.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034224hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00093 geranylgeranyl diphos 99.9 1E-26 2.2E-31 189.2 10.1 95 3-98 355-449 (450)
2 TIGR02023 BchP-ChlP geranylger 99.9 7E-22 1.5E-26 153.6 9.2 82 4-86 307-388 (388)
3 TIGR02028 ChlP geranylgeranyl 99.8 8.3E-20 1.8E-24 144.5 9.6 84 2-86 315-398 (398)
4 PF15300 INT_SG_DDX_CT_C: INTS 82.6 1.2 2.6E-05 29.5 2.3 35 10-48 13-47 (65)
5 PRK09639 RNA polymerase sigma 70.1 7.8 0.00017 26.4 3.7 57 3-62 1-57 (166)
6 PF08990 Docking: Erythronolid 65.1 3.9 8.5E-05 23.0 1.1 16 1-17 1-16 (27)
7 KOG0429 Ubiquitin-conjugating 64.8 6.2 0.00013 32.4 2.6 33 4-37 103-135 (258)
8 PHA01632 hypothetical protein 57.1 14 0.00031 24.7 2.9 21 2-23 28-48 (64)
9 PF05669 Med31: SOH1; InterPr 51.5 6.6 0.00014 28.1 0.6 46 18-65 55-100 (101)
10 KOG4624 Uncharacterized conser 50.7 4.8 0.0001 29.2 -0.2 14 41-54 73-86 (104)
11 PTZ00059 dynein light chain; P 49.2 10 0.00022 25.6 1.2 20 3-23 35-55 (90)
12 PF00621 RhoGEF: RhoGEF domain 49.1 64 0.0014 21.6 5.2 55 25-86 97-152 (180)
13 PRK12526 RNA polymerase sigma 48.8 46 0.00099 24.2 4.7 36 37-73 67-105 (206)
14 PF07539 DRIM: Down-regulated 45.0 16 0.00036 26.5 1.9 32 31-62 10-43 (141)
15 PF13072 DUF3936: Protein of u 42.5 27 0.00059 21.3 2.3 19 6-25 18-36 (38)
16 PRK12534 RNA polymerase sigma 40.7 68 0.0015 22.4 4.4 53 7-62 27-82 (187)
17 PLN03058 dynein light chain ty 40.5 19 0.00041 26.5 1.6 21 3-24 67-88 (128)
18 PF03015 Sterile: Male sterili 39.9 75 0.0016 20.6 4.3 53 12-64 20-83 (94)
19 KOG3430 Dynein light chain typ 37.1 24 0.00051 25.0 1.6 22 3-24 35-56 (90)
20 PF12345 DUF3641: Protein of u 33.9 29 0.00063 26.0 1.7 25 2-26 3-27 (134)
21 PRK11467 secY/secA suppressor 33.8 29 0.00062 25.8 1.7 25 37-61 12-41 (124)
22 PF07849 DUF1641: Protein of u 33.0 19 0.00041 21.4 0.5 12 43-54 16-27 (42)
23 cd00160 RhoGEF Guanine nucleot 32.0 1.2E+02 0.0026 20.7 4.5 47 36-86 111-157 (181)
24 PF13555 AAA_29: P-loop contai 31.9 43 0.00093 21.5 2.1 20 24-45 38-57 (62)
25 COG3073 RseA Negative regulato 31.3 27 0.00059 28.0 1.3 21 39-60 20-40 (213)
26 PF09450 DUF2019: Domain of un 31.2 1.1E+02 0.0023 22.0 4.2 50 13-65 25-74 (106)
27 PRK12516 RNA polymerase sigma 31.0 1.1E+02 0.0024 22.0 4.3 25 2-26 7-31 (187)
28 PF06099 Phenol_hyd_sub: Pheno 30.1 19 0.00042 23.7 0.2 17 40-56 42-58 (59)
29 PRK12540 RNA polymerase sigma 27.6 1.6E+02 0.0034 21.1 4.6 36 1-36 1-43 (182)
30 PF04078 Rcd1: Cell differenti 27.1 2.3E+02 0.0051 23.2 6.0 57 20-86 65-125 (262)
31 PRK06811 RNA polymerase factor 26.9 2.2E+02 0.0048 20.1 5.2 7 56-62 72-78 (189)
32 PF10892 DUF2688: Protein of u 26.3 53 0.0012 21.8 1.8 24 26-49 20-43 (60)
33 PRK09644 RNA polymerase sigma 24.4 1.6E+02 0.0035 20.1 4.1 39 27-75 30-68 (165)
34 PRK12541 RNA polymerase sigma 24.1 1.4E+02 0.003 20.4 3.6 56 3-62 3-60 (161)
35 PF02397 Bac_transf: Bacterial 24.1 1.2E+02 0.0026 23.1 3.7 33 53-88 153-185 (187)
36 PRK12537 RNA polymerase sigma 23.1 1.5E+02 0.0032 20.8 3.8 55 5-62 23-80 (182)
37 smart00025 Pumilio Pumilio-lik 23.0 45 0.00097 16.9 0.8 24 40-69 3-26 (36)
38 PRK12546 RNA polymerase sigma 22.9 1.7E+02 0.0036 21.2 4.1 58 3-63 5-64 (188)
39 cd03572 ENTH_epsin_related ENT 22.8 86 0.0019 22.6 2.5 29 58-87 40-68 (122)
40 cd05611 STKc_Rim15_like Cataly 21.9 47 0.001 23.4 1.0 35 24-58 223-260 (260)
41 PF11951 Fungal_trans_2: Funga 21.2 98 0.0021 22.3 2.5 30 10-39 333-363 (383)
42 PF12909 DUF3832: Protein of u 20.8 1.2E+02 0.0027 20.9 2.9 29 10-49 48-81 (89)
43 PF01221 Dynein_light: Dynein 20.7 1.1E+02 0.0024 20.0 2.5 21 2-23 33-54 (89)
44 PF08707 PriCT_2: Primase C te 20.1 2.5E+02 0.0053 17.8 4.6 43 18-60 16-63 (78)
No 1
>PLN00093 geranylgeranyl diphosphate reductase; Provisional
Probab=99.94 E-value=1e-26 Score=189.21 Aligned_cols=95 Identities=58% Similarity=1.056 Sum_probs=90.9
Q ss_pred CHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCchhHHHHHhhhCCcchhhhhhhhhhhhhhcCCChhHHHHHHHHHHH
Q 034224 3 SESDLKREYLRKWDDEYLMTYRFLDLLQRVFYGSNVGREALVELCGDEYVQRMTFDSYLYKKLAEGSRFQDVKMVMKTIG 82 (101)
Q Consensus 3 te~~l~~~Ylkrf~k~yg~tf~vL~iLQ~v~Y~sd~~RE~FVemC~D~dVQrlTfdSYlyK~lv~~~p~~~~ki~~k~i~ 82 (101)
++++|+ .|+++|+++||+.|+++..||++||+||+.+|+||++|+|++||++||+|||+|+|++++|+.|+|++|||||
T Consensus 355 s~~~L~-~Y~~~~~~~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~k~l~~~~~~~~~~~~~~~~~ 433 (450)
T PLN00093 355 DEADLR-EYLRKWDKKYWPTYKVLDILQKVFYRSNPAREAFVEMCADEYVQKMTFDSYLYKRVVPGNPLDDIKLLVNTIG 433 (450)
T ss_pred CHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHhhhhhHHHHhHHHHHHHHhhCCChHHHHHHHHHHHH
Confidence 577887 9999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhhhccccccchhhcc
Q 034224 83 SFMRCNIVGREMEAFK 98 (101)
Q Consensus 83 ~L~r~~al~~~~~~~~ 98 (101)
||+||+++++++..+.
T Consensus 434 ~~~~~~~~~~~~~~~~ 449 (450)
T PLN00093 434 SLVRANALRREMEKLS 449 (450)
T ss_pred HHHhccccCccccccC
Confidence 9999999999876553
No 2
>TIGR02023 BchP-ChlP geranylgeranyl reductase. This model represents a group of geranylgeranyl reductases specific for the biosyntheses of bacteriochlorophyll and chlorophyll. It is unclear whether the processes of isoprenoid ligation to the chlorin ring and reduction of the geranylgeranyl chain to a phytyl chain are necessarily ordered the same way in all species (see introduction to ).
Probab=99.86 E-value=7e-22 Score=153.60 Aligned_cols=82 Identities=45% Similarity=0.781 Sum_probs=79.4
Q ss_pred HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCchhHHHHHhhhCCcchhhhhhhhhhhhhhcCCChhHHHHHHHHHHHH
Q 034224 4 ESDLKREYLRKWDDEYLMTYRFLDLLQRVFYGSNVGREALVELCGDEYVQRMTFDSYLYKKLAEGSRFQDVKMVMKTIGS 83 (101)
Q Consensus 4 e~~l~~~Ylkrf~k~yg~tf~vL~iLQ~v~Y~sd~~RE~FVemC~D~dVQrlTfdSYlyK~lv~~~p~~~~ki~~k~i~~ 83 (101)
+++|. .|+++|++.+|+.|+.+.++|+++|.||..+|+|+++|+|+|||++|++|||+|+|++.+|++|+||++|||+|
T Consensus 307 ~~~L~-~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 385 (388)
T TIGR02023 307 ATDLR-HYERKFMKLYGTTFRVLRVLQMVYYRSDRRREVFVEMCRDKDVQRLTFDSYMYKQMAPAPWLAQLKIAAKNIGS 385 (388)
T ss_pred HHHHH-HHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHHhccccHHHhhHHHhhhhccccCChHHHHHHHHHHHHH
Confidence 45677 99999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhh
Q 034224 84 FMR 86 (101)
Q Consensus 84 L~r 86 (101)
|+|
T Consensus 386 ~~~ 388 (388)
T TIGR02023 386 LVR 388 (388)
T ss_pred hhC
Confidence 986
No 3
>TIGR02028 ChlP geranylgeranyl reductase. This model represents the reductase which acts reduces the geranylgeranyl group to the phytyl group in the side chain of chlorophyll. It is unclear whether the enzyme has a preference for acting before or after the attachment of the side chain to chlorophyllide a by chlorophyll synthase. This clade is restricted to plants and cyanobacteria to separate it from the homologues which act in the biosynthesis of bacteriochlorophyll.
Probab=99.81 E-value=8.3e-20 Score=144.47 Aligned_cols=84 Identities=61% Similarity=1.028 Sum_probs=81.3
Q ss_pred CCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCchhHHHHHhhhCCcchhhhhhhhhhhhhhcCCChhHHHHHHHHHH
Q 034224 2 ISESDLKREYLRKWDDEYLMTYRFLDLLQRVFYGSNVGREALVELCGDEYVQRMTFDSYLYKKLAEGSRFQDVKMVMKTI 81 (101)
Q Consensus 2 ~te~~l~~~Ylkrf~k~yg~tf~vL~iLQ~v~Y~sd~~RE~FVemC~D~dVQrlTfdSYlyK~lv~~~p~~~~ki~~k~i 81 (101)
++++.|+ .|+++|++.||..++....+|++||+||..+|+|+++|+|+|||+++++|||.|++++.+|+.++|.++|||
T Consensus 315 ~~~~~l~-~Y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 393 (398)
T TIGR02028 315 TEEGDLA-GYLRRWDKEYRPTYRVLDLLQRVFYRSNAGREAFVEMCADEHVQKRTFDSYLYKRVAPAEPLGDLKLLWRTI 393 (398)
T ss_pred CCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHhcCcchhhhhHHHhhhhhhhCCChHHHHHHHHHHH
Confidence 4677888 999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhh
Q 034224 82 GSFMR 86 (101)
Q Consensus 82 ~~L~r 86 (101)
|||+|
T Consensus 394 ~~~~~ 398 (398)
T TIGR02028 394 GSLVR 398 (398)
T ss_pred HHhhC
Confidence 99986
No 4
>PF15300 INT_SG_DDX_CT_C: INTS6/SAGE1/DDX26B/CT45 C-terminus
Probab=82.59 E-value=1.2 Score=29.45 Aligned_cols=35 Identities=23% Similarity=0.358 Sum_probs=30.3
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHHHhcCchhHHHHHhhhC
Q 034224 10 EYLRKWDDEYLMTYRFLDLLQRVFYGSNVGREALVELCG 48 (101)
Q Consensus 10 ~Ylkrf~k~yg~tf~vL~iLQ~v~Y~sd~~RE~FVemC~ 48 (101)
...+++-+.|..+|..|+-+| ||-+.|..||++|=
T Consensus 13 keIRrpGr~ye~iF~lL~~vq----G~~~~r~~fv~~~I 47 (65)
T PF15300_consen 13 KEIRRPGRNYEKIFKLLEQVQ----GPLEVRKQFVEMII 47 (65)
T ss_pred HHHHccCCcHHHHHHHHHHcc----CCHHHHHHHHHHHH
Confidence 466778888999999999888 89999999999983
No 5
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=70.15 E-value=7.8 Score=26.44 Aligned_cols=57 Identities=9% Similarity=0.191 Sum_probs=37.4
Q ss_pred CHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCchhHHHHHhhhCCcchhhhhhhhhhh
Q 034224 3 SESDLKREYLRKWDDEYLMTYRFLDLLQRVFYGSNVGREALVELCGDEYVQRMTFDSYLY 62 (101)
Q Consensus 3 te~~l~~~Ylkrf~k~yg~tf~vL~iLQ~v~Y~sd~~RE~FVemC~D~dVQrlTfdSYly 62 (101)
||..+...|.+-+...|+-+++.++ .-.-.-|-..|.|+.++....-+.-+|.+||+
T Consensus 1 ~~~~f~~l~~~y~~~l~~~~~~~~~---~~~~aeDlvQe~fi~~~~~~~~~~~~~~~wl~ 57 (166)
T PRK09639 1 SDETFEDLFEQYYPDVVQQIFYIVK---DRTQAEDLAQEVFLRLYRSDFKGIENEKGWLI 57 (166)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHhC---CHHHHHHHHHHHHHHHHHHhcccccchHHHHH
Confidence 3555666666667777776666654 33345677788888888773234557888886
No 6
>PF08990 Docking: Erythronolide synthase docking; InterPro: IPR015083 The N-terminal docking domain found in modular polyketide synthase assumes an alpha-helical structure, wherein two alpha-helices are connected by a short loop. Two such N-terminal domains dimerise to form amphipathic parallel alpha-helical coiled coils: dimerisation is essential for protein function []. ; GO: 0016740 transferase activity, 0048037 cofactor binding; PDB: 2HG4_E.
Probab=65.06 E-value=3.9 Score=22.99 Aligned_cols=16 Identities=31% Similarity=0.681 Sum_probs=10.6
Q ss_pred CCCHHHHHHHHHHHHHH
Q 034224 1 MISESDLKREYLRKWDD 17 (101)
Q Consensus 1 ~~te~~l~~~Ylkrf~k 17 (101)
|++|+.|+ .|||+-..
T Consensus 1 M~~e~kLr-~YLkr~t~ 16 (27)
T PF08990_consen 1 MANEDKLR-DYLKRVTA 16 (27)
T ss_dssp ---HCHHH-HHHHHHHH
T ss_pred CCcHHHHH-HHHHHHHH
Confidence 68899999 99997543
No 7
>KOG0429 consensus Ubiquitin-conjugating enzyme-related protein Ft1, involved in programmed cell death [Posttranslational modification, protein turnover, chaperones]
Probab=64.80 E-value=6.2 Score=32.44 Aligned_cols=33 Identities=36% Similarity=0.690 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCc
Q 034224 4 ESDLKREYLRKWDDEYLMTYRFLDLLQRVFYGSN 37 (101)
Q Consensus 4 e~~l~~~Ylkrf~k~yg~tf~vL~iLQ~v~Y~sd 37 (101)
|=||.+. .-+|.|.+--+..||-.||++||.-|
T Consensus 103 eLdl~ra-f~eWRk~ehhiwqvL~ylqriF~dpd 135 (258)
T KOG0429|consen 103 ELDLNRA-FPEWRKEEHHIWQVLVYLQRIFYDPD 135 (258)
T ss_pred ceeHhhh-hhhhhccccHHHHHHHHHHHHhcCcc
Confidence 3467744 45599999999999999999999765
No 8
>PHA01632 hypothetical protein
Probab=57.09 E-value=14 Score=24.67 Aligned_cols=21 Identities=24% Similarity=0.303 Sum_probs=18.4
Q ss_pred CCHHHHHHHHHHHHHHhhhhHH
Q 034224 2 ISESDLKREYLRKWDDEYLMTY 23 (101)
Q Consensus 2 ~te~~l~~~Ylkrf~k~yg~tf 23 (101)
|||++|| .-+-+-.+.|+++-
T Consensus 28 pteeelr-kvlpkilkdyanmi 48 (64)
T PHA01632 28 PTEEELR-KVLPKILKDYANMI 48 (64)
T ss_pred CCHHHHH-HHHHHHHHHHHHHH
Confidence 8999999 88888899998863
No 9
>PF05669 Med31: SOH1; InterPro: IPR008831 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 Med31 of the Mediator complex. It contains the Saccharomyces cerevisiae SOH1 homologues. SOH1 is responsible for the repression of temperature sensitive growth of the HPR1 mutant [] and has been found to be a component of the RNA polymerase II transcription complex. SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the SOH1 protein may serve to couple these two processes [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent, 0016592 mediator complex; PDB: 3FBI_D 3FBN_D.
Probab=51.52 E-value=6.6 Score=28.15 Aligned_cols=46 Identities=22% Similarity=0.371 Sum_probs=18.7
Q ss_pred hhhhHHHHHHHHHHHHhcCchhHHHHHhhhCCcchhhhhhhhhhhhhh
Q 034224 18 EYLMTYRFLDLLQRVFYGSNVGREALVELCGDEYVQRMTFDSYLYKKL 65 (101)
Q Consensus 18 ~yg~tf~vL~iLQ~v~Y~sd~~RE~FVemC~D~dVQrlTfdSYlyK~l 65 (101)
.|-++-.+|++||.=-.|++-.++.+++.+.| -|-..|..|..|++
T Consensus 55 ~YP~cL~~L~LLq~~~FR~~i~~~~~~~~i~~--q~~~~W~~~~~~r~ 100 (101)
T PF05669_consen 55 VYPHCLHFLELLQNEEFRQAIANPDFAKFIMD--QQFLHWQHYRRKRM 100 (101)
T ss_dssp SSTHHHHHHH-HHHHHHHH--B-TTS----------------------
T ss_pred cChHHHHHHHHHCcHHHHHHHhCCcccchhcc--cchhhhhccccccc
Confidence 35578899999999888999899998888855 46778988888875
No 10
>KOG4624 consensus Uncharacterized conserved protein [Function unknown]
Probab=50.66 E-value=4.8 Score=29.19 Aligned_cols=14 Identities=64% Similarity=1.039 Sum_probs=12.9
Q ss_pred HHHHhhhCCcchhh
Q 034224 41 EALVELCGDEYVQR 54 (101)
Q Consensus 41 E~FVemC~D~dVQr 54 (101)
|+|-|+|.|++||.
T Consensus 73 ~af~e~~rd~yv~E 86 (104)
T KOG4624|consen 73 EAFLEECRDEYVQE 86 (104)
T ss_pred HHHHHHHHHHHHHH
Confidence 68999999999996
No 11
>PTZ00059 dynein light chain; Provisional
Probab=49.23 E-value=10 Score=25.57 Aligned_cols=20 Identities=30% Similarity=0.708 Sum_probs=15.4
Q ss_pred CHHHHHHHHHH-HHHHhhhhHH
Q 034224 3 SESDLKREYLR-KWDDEYLMTY 23 (101)
Q Consensus 3 te~~l~~~Ylk-rf~k~yg~tf 23 (101)
+|.|+- .|+| .||++||+++
T Consensus 35 ~~kdiA-~~IK~~fD~~yg~~W 55 (90)
T PTZ00059 35 IEKDIA-AYIKKEFDKKYNPTW 55 (90)
T ss_pred chHHHH-HHHHHHHHhhcCCCC
Confidence 467775 6776 7899999875
No 12
>PF00621 RhoGEF: RhoGEF domain; InterPro: IPR000219 The Rho family GTPases Rho, Rac and CDC42 regulate a diverse array of cellular processes. Like all members of the Ras superfamily, the Rho proteins cycle between active GTP-bound and inactive GDP-bound conformational states. Activation of Rho proteins through release of bound GDP and subsequent binding of GTP, is catalysed by guanine nucleotide exchange factors (GEFs) in the Dbl family. The proteins encoded by members of the Dbl family share a common domain, presented in this entry, of about 200 residues (designated the Dbl homology or DH domain) that has been shown to encode a GEF activity specific for a number of Rho family members. In addition, all family members possess a second, shared domain designated the pleckstrin homology (PH) domain (IPR001849 from INTERPRO). Trio and its homologue UNC-73 are unique within the Dbl family insomuch as they encode two distinct DH/PH domain modules. The PH domain is invariably located immediately C-terminal to the DH domain and this invariant topography suggests a functional interdependence between these two structural modules. Biochemical data have established the role of the conserved DH domain in Rho GTPase interaction and activation, and the role of the tandem PH domain in intracellular targeting and/or regulation of DH domain function. The DH domain of Dbl has been shown to mediate oligomerisation that is mostly homophilic in nature. In addition to the tandem DH/PH domains Dbl family GEFs contain diverse structural motifs like serine/threonine kinase, RBD, PDZ, RGS, IQ, REM, Cdc25, RasGEF, CH, SH2, SH3, EF, spectrin or Ig. The DH domain is composed of three structurally conserved regions separated by more variable regions. It does not share significant sequence homology with other subtypes of small G-protein GEF motifs such as the Cdc25 domain and the Sec7 domain, which specifically interact with Ras and ARF family small GTPases, respectively, nor with other Rho protein interactive motifs, indicating that the Dbl family proteins are evolutionarily unique. The DH domain is composed of 11 alpha helices that are folded into a flattened, elongated alpha-helix bundle in which two of the three conserved regions, conserved region 1 (CR1) and conserved region 3 (CR3), are exposed near the centre of one surface. CR1 and CR3, together with a part of alpha-6 and the DH/PH junction site, constitute the Rho GTPase interacting pocket.; GO: 0005089 Rho guanyl-nucleotide exchange factor activity, 0035023 regulation of Rho protein signal transduction, 0005622 intracellular; PDB: 3MPX_A 2RGN_E 2Z0Q_A 3T06_A 3KZ1_A 1XCG_E 2KR9_A 1BY1_A 1RJ2_J 1KZG_C ....
Probab=49.09 E-value=64 Score=21.58 Aligned_cols=55 Identities=18% Similarity=0.230 Sum_probs=35.0
Q ss_pred HHHHHHHHHhcCchhHHHHHhhhCC-cchhhhhhhhhhhhhhcCCChhHHHHHHHHHHHHhhh
Q 034224 25 FLDLLQRVFYGSNVGREALVELCGD-EYVQRMTFDSYLYKKLAEGSRFQDVKMVMKTIGSFMR 86 (101)
Q Consensus 25 vL~iLQ~v~Y~sd~~RE~FVemC~D-~dVQrlTfdSYlyK~lv~~~p~~~~ki~~k~i~~L~r 86 (101)
.+..++. +...+..-..|++.|.. +..+++++.+||.+ |+.++.=+-..+..|++
T Consensus 97 ~~~~~~~-~~~~~~~~~~~l~~~~~~~~~~~~~l~~~l~~------Piqrl~rY~lll~~llk 152 (180)
T PF00621_consen 97 ALSLLEE-LRKKNSEFKKFLEEIENSPESKRLSLSSLLIK------PIQRLPRYPLLLKRLLK 152 (180)
T ss_dssp HHHHHHH-HHHHHHHHHHHHHHHHTSHHCTTSTHHHHTTH------HHHHHHHHHHHHHHHHH
T ss_pred hhhhhhH-HHhhccccccccccccccccccCCCHHHHHHH------hhhHHHHHHHHHHHHHH
Confidence 3445554 34555557778887765 78899999999997 55555444444444444
No 13
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=48.78 E-value=46 Score=24.21 Aligned_cols=36 Identities=8% Similarity=0.228 Sum_probs=17.6
Q ss_pred chhHHHHHhhhCCc---chhhhhhhhhhhhhhcCCChhHH
Q 034224 37 NVGREALVELCGDE---YVQRMTFDSYLYKKLAEGSRFQD 73 (101)
Q Consensus 37 d~~RE~FVemC~D~---dVQrlTfdSYlyK~lv~~~p~~~ 73 (101)
|.--|.|+.++... +.++-.|.+||+ ++++..-..+
T Consensus 67 DivQe~fl~l~~~~~~~~~~~~~~~~wl~-~I~rn~~~d~ 105 (206)
T PRK12526 67 ELVQETMSNVWRKAHLYNGDKGAATTWVY-TVMRNAAFDM 105 (206)
T ss_pred HHHHHHHHHHHHhHHhcCCcccchhHHHH-HHHHHHHHHH
Confidence 44555666665432 122335777776 4444443333
No 14
>PF07539 DRIM: Down-regulated in metastasis; InterPro: IPR011430 These eukaryotic proteins include DRIM (Down-Regulated In Metastasis) (O75691 from SWISSPROT), which is differentially expressed in metastatic and non-metastatic human breast carcinoma cells []. It is believed to be involved in processing of non-coding RNA [].
Probab=45.01 E-value=16 Score=26.51 Aligned_cols=32 Identities=28% Similarity=0.411 Sum_probs=27.3
Q ss_pred HHHhcCchhHHHHHhhhCC--cchhhhhhhhhhh
Q 034224 31 RVFYGSNVGREALVELCGD--EYVQRMTFDSYLY 62 (101)
Q Consensus 31 ~v~Y~sd~~RE~FVemC~D--~dVQrlTfdSYly 62 (101)
+..|+|+..++.|.+++.+ .+||++..|.-+.
T Consensus 10 k~l~~~~~l~~~~~~LL~~~d~~vQklAL~cll~ 43 (141)
T PF07539_consen 10 KSLYRSDELYDALLRLLSSRDPEVQKLALDCLLT 43 (141)
T ss_pred HHHhhHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 5679999999999999976 6799998887654
No 15
>PF13072 DUF3936: Protein of unknown function (DUF3936)
Probab=42.54 E-value=27 Score=21.26 Aligned_cols=19 Identities=5% Similarity=0.401 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHhhhhHHHH
Q 034224 6 DLKREYLRKWDDEYLMTYRF 25 (101)
Q Consensus 6 ~l~~~Ylkrf~k~yg~tf~v 25 (101)
+|| .+||.|-++|+.+...
T Consensus 18 eIr-~~Lkey~k~~~~v~ew 36 (38)
T PF13072_consen 18 EIR-AKLKEYGKQFGYVKEW 36 (38)
T ss_pred HHH-HHHHHHHHhhhhHHHh
Confidence 566 9999999999987654
No 16
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=40.67 E-value=68 Score=22.44 Aligned_cols=53 Identities=9% Similarity=0.050 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHhcCchhHHHHHhhhCCcch---hhhhhhhhhh
Q 034224 7 LKREYLRKWDDEYLMTYRFLDLLQRVFYGSNVGREALVELCGDEYV---QRMTFDSYLY 62 (101)
Q Consensus 7 l~~~Ylkrf~k~yg~tf~vL~iLQ~v~Y~sd~~RE~FVemC~D~dV---QrlTfdSYly 62 (101)
+...|.+-+...|+-+++.+ ..-.-..|-.-|.|+.++...+- ++-+|.+||+
T Consensus 27 ~~~l~~~y~~~l~~~~~~~~---~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~~~wl~ 82 (187)
T PRK12534 27 FEALYRQTSPKLFGVCLRMI---PQRAEAEEVLQDVFTLIWHKAGQFDPSRARGLTWLA 82 (187)
T ss_pred HHHHHHHhhHHHHHHHHHHh---cCHHHHHHHHHHHHHHHHhccccCCcccccHHHHHH
Confidence 33333333334444444333 22233345566777777766431 2345777777
No 17
>PLN03058 dynein light chain type 1 family protein; Provisional
Probab=40.54 E-value=19 Score=26.47 Aligned_cols=21 Identities=19% Similarity=0.352 Sum_probs=16.0
Q ss_pred CHHHHHHHHH-HHHHHhhhhHHH
Q 034224 3 SESDLKREYL-RKWDDEYLMTYR 24 (101)
Q Consensus 3 te~~l~~~Yl-krf~k~yg~tf~ 24 (101)
+|.|+- .|+ +.||++||+++-
T Consensus 67 ~ekdIA-~~IKk~fDkkYG~tWH 88 (128)
T PLN03058 67 DSKRLA-LALKKEFDSAYGPAWH 88 (128)
T ss_pred CHHHHH-HHHHHHHhhhhCCceE
Confidence 467776 777 568999999763
No 18
>PF03015 Sterile: Male sterility protein; InterPro: IPR004262 This family represents the C-terminal region of the male sterility protein in a number of organisms. The Arabidopsis thaliana male sterility 2 (MS2) protein is involved in male gametogenesis. The MS2 protein shows sequence similarity to a jojoba protein (also a member of this group) that converts wax fatty acids to fatty alcohols. It has been suggested that a possible function of the MS2 protein may be as a fatty acyl reductase in the formation of pollen wall substances [].; GO: 0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor, 0055114 oxidation-reduction process
Probab=39.87 E-value=75 Score=20.61 Aligned_cols=53 Identities=11% Similarity=0.241 Sum_probs=36.5
Q ss_pred HHHHHHhhhhHHHHHHHHHHHH-----hcCchhHHHHHhhhCCc------chhhhhhhhhhhhh
Q 034224 12 LRKWDDEYLMTYRFLDLLQRVF-----YGSNVGREALVELCGDE------YVQRMTFDSYLYKK 64 (101)
Q Consensus 12 lkrf~k~yg~tf~vL~iLQ~v~-----Y~sd~~RE~FVemC~D~------dVQrlTfdSYlyK~ 64 (101)
..++.|.|..++..++++|.|- +.||..++---.|..++ |+..+.|++|+..-
T Consensus 20 kp~~~k~~~ki~~~~~~~~~F~~~eW~F~~~n~~~L~~~l~~~D~~~F~fD~~~idW~~Y~~~~ 83 (94)
T PF03015_consen 20 KPRMVKIYRKIRKALEVLEYFTTNEWIFDNDNTRRLWERLSPEDREIFNFDIRSIDWEEYFRNY 83 (94)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHhCceeecchHHHHHHHhCchhcCceecCCCCCCCHHHHHHHH
Confidence 3567889999999999999874 34555554444444332 67778888888654
No 19
>KOG3430 consensus Dynein light chain type 1 [Cytoskeleton]
Probab=37.05 E-value=24 Score=25.02 Aligned_cols=22 Identities=23% Similarity=0.362 Sum_probs=16.3
Q ss_pred CHHHHHHHHHHHHHHhhhhHHH
Q 034224 3 SESDLKREYLRKWDDEYLMTYR 24 (101)
Q Consensus 3 te~~l~~~Ylkrf~k~yg~tf~ 24 (101)
.+.++-..--|.|||+||+++-
T Consensus 35 ~~k~iA~~iKkefDkkyG~~Wh 56 (90)
T KOG3430|consen 35 IEKDIAAFIKKEFDKKYGPTWH 56 (90)
T ss_pred ChHHHHHHHHHHHhhhcCCccE
Confidence 3566665556889999999863
No 20
>PF12345 DUF3641: Protein of unknown function (DUF3641) ; InterPro: IPR024521 This domain is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. It is found in association with an N-terminal radical_SAM domain (Pfam:PF04055 from PFAM).
Probab=33.86 E-value=29 Score=26.02 Aligned_cols=25 Identities=16% Similarity=0.411 Sum_probs=22.3
Q ss_pred CCHHHHHHHHHHHHHHhhhhHHHHH
Q 034224 2 ISESDLKREYLRKWDDEYLMTYRFL 26 (101)
Q Consensus 2 ~te~~l~~~Ylkrf~k~yg~tf~vL 26 (101)
|+++.|...|.+.-...||-+|-=|
T Consensus 3 P~Q~~LE~~Yk~~L~~~~GI~Fn~L 27 (134)
T PF12345_consen 3 PPQQALEADYKRELKERFGIVFNNL 27 (134)
T ss_pred CCHHHHHHHHHHHHHHhcCceecch
Confidence 8899999999999999999988544
No 21
>PRK11467 secY/secA suppressor protein; Provisional
Probab=33.79 E-value=29 Score=25.84 Aligned_cols=25 Identities=24% Similarity=0.453 Sum_probs=20.0
Q ss_pred chhHHHHHhhh-----CCcchhhhhhhhhh
Q 034224 37 NVGREALVELC-----GDEYVQRMTFDSYL 61 (101)
Q Consensus 37 d~~RE~FVemC-----~D~dVQrlTfdSYl 61 (101)
|++||.|.+-- .|+.||++.-+-|.
T Consensus 12 dAAREefla~~p~~d~~~a~v~q~nlQKYv 41 (124)
T PRK11467 12 DAAREEFLADNPGIDAEDANVQQFNLQKYV 41 (124)
T ss_pred HHHHHHHHhcCCCCCccchhHHHHhHHHHH
Confidence 78999998543 35669999998886
No 22
>PF07849 DUF1641: Protein of unknown function (DUF1641); InterPro: IPR012440 Archaeal and bacterial hypothetical proteins are found in this family, with the region in question being approximately 40 residues long.
Probab=33.01 E-value=19 Score=21.40 Aligned_cols=12 Identities=42% Similarity=0.409 Sum_probs=9.4
Q ss_pred HHhhhCCcchhh
Q 034224 43 LVELCGDEYVQR 54 (101)
Q Consensus 43 FVemC~D~dVQr 54 (101)
.+.+-.|||||+
T Consensus 16 l~~~l~Dpdvqr 27 (42)
T PF07849_consen 16 LLRALRDPDVQR 27 (42)
T ss_pred HHHHHcCHHHHH
Confidence 355678999997
No 23
>cd00160 RhoGEF Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Probab=31.97 E-value=1.2e+02 Score=20.73 Aligned_cols=47 Identities=17% Similarity=0.182 Sum_probs=31.5
Q ss_pred CchhHHHHHhhhCCcchhhhhhhhhhhhhhcCCChhHHHHHHHHHHHHhhh
Q 034224 36 SNVGREALVELCGDEYVQRMTFDSYLYKKLAEGSRFQDVKMVMKTIGSFMR 86 (101)
Q Consensus 36 sd~~RE~FVemC~D~dVQrlTfdSYlyK~lv~~~p~~~~ki~~k~i~~L~r 86 (101)
.++.=+.|++.|.. ..++++++|||.+ |-.-+..-+++++.|..-..
T Consensus 111 ~~~~f~~~~~~~~~-~~~~~~l~~~L~~---PvQRl~rY~lLL~~l~k~t~ 157 (181)
T cd00160 111 FNKFFQEFLEKAES-ECGRLKLESLLLK---PVQRLTKYPLLLKELLKHTP 157 (181)
T ss_pred ccHHHHHHHHHHHH-hcccCCHHHHhhh---hHHHhchHHHHHHHHHHhCC
Confidence 46666677777776 6789999999987 33334445666666655443
No 24
>PF13555 AAA_29: P-loop containing region of AAA domain
Probab=31.87 E-value=43 Score=21.53 Aligned_cols=20 Identities=35% Similarity=0.668 Sum_probs=16.5
Q ss_pred HHHHHHHHHHhcCchhHHHHHh
Q 034224 24 RFLDLLQRVFYGSNVGREALVE 45 (101)
Q Consensus 24 ~vL~iLQ~v~Y~sd~~RE~FVe 45 (101)
.+||.+|.+.|.++ |.+|=.
T Consensus 38 TllDAi~~~L~~~~--~~~fN~ 57 (62)
T PF13555_consen 38 TLLDAIQTVLYGNT--RRRFNA 57 (62)
T ss_pred HHHHHHHHHHcCCc--hhhhhh
Confidence 47999999999999 666644
No 25
>COG3073 RseA Negative regulator of sigma E activity [Signal transduction mechanisms]
Probab=31.25 E-value=27 Score=28.02 Aligned_cols=21 Identities=48% Similarity=0.657 Sum_probs=18.2
Q ss_pred hHHHHHhhhCCcchhhhhhhhh
Q 034224 39 GREALVELCGDEYVQRMTFDSY 60 (101)
Q Consensus 39 ~RE~FVemC~D~dVQrlTfdSY 60 (101)
.=|..+++|+|++.|. ||.||
T Consensus 20 ~~Ell~~L~~D~El~~-tW~~y 40 (213)
T COG3073 20 DSELLRELAHDEELQQ-TWESY 40 (213)
T ss_pred hHHHHHHHhcCHHHHH-HHHHH
Confidence 3477899999999987 99998
No 26
>PF09450 DUF2019: Domain of unknown function (DUF2019); InterPro: IPR018568 Protein of unknown function found in bacteria. ; PDB: 2I9C_A.
Probab=31.16 E-value=1.1e+02 Score=21.98 Aligned_cols=50 Identities=20% Similarity=0.159 Sum_probs=35.7
Q ss_pred HHHHHhhhhHHHHHHHHHHHHhcCchhHHHHHhhhCCcchhhhhhhhhhhhhh
Q 034224 13 RKWDDEYLMTYRFLDLLQRVFYGSNVGREALVELCGDEYVQRMTFDSYLYKKL 65 (101)
Q Consensus 13 krf~k~yg~tf~vL~iLQ~v~Y~sd~~RE~FVemC~D~dVQrlTfdSYlyK~l 65 (101)
+.+-|.|..+..+.+-|+. +++..|.+++.+-.+|+.|=-.|-+-.-=++
T Consensus 25 ~~~Nr~~~k~~~~~~eLk~---r~gd~r~aLl~LL~hpn~~VRl~AA~~~L~~ 74 (106)
T PF09450_consen 25 RTANRLYDKMIRIYDELKS---RGGDQRDALLPLLKHPNMQVRLWAAAHTLRY 74 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHH---STT-GGGGGGGGGGSS-HHHHHHHHHTTTTT
T ss_pred HHHHHHHHHHHHHHHHHHh---cCcchHHHHHHHHcCCChhHHHHHHHHHHHh
Confidence 5667777777777766665 7888999999999999999776666444333
No 27
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=31.01 E-value=1.1e+02 Score=22.01 Aligned_cols=25 Identities=16% Similarity=0.173 Sum_probs=16.4
Q ss_pred CCHHHHHHHHHHHHHHhhhhHHHHH
Q 034224 2 ISESDLKREYLRKWDDEYLMTYRFL 26 (101)
Q Consensus 2 ~te~~l~~~Ylkrf~k~yg~tf~vL 26 (101)
+++..+...|.+-+...|+-+++.+
T Consensus 7 ~~~~~f~~l~~~~~~~L~~~a~~~~ 31 (187)
T PRK12516 7 EGTPPFKRELLAALPSLRAFAVSLI 31 (187)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHc
Confidence 3556666667777777777666665
No 28
>PF06099 Phenol_hyd_sub: Phenol hydroxylase subunit; InterPro: IPR010353 This family consists of several bacterial phenol hydroxylase subunit proteins, which are part of a multicomponent phenol hydroxylase. Some bacteria can utilise phenol or some of its methylated derivatives as their sole source of carbon and energy. The first step in this process is the conversion of phenol into catechol. Catechol is then further metabolised via the meta-cleavage pathway into TCA cycle intermediates [].
Probab=30.12 E-value=19 Score=23.69 Aligned_cols=17 Identities=35% Similarity=0.647 Sum_probs=15.2
Q ss_pred HHHHHhhhCCcchhhhh
Q 034224 40 REALVELCGDEYVQRMT 56 (101)
Q Consensus 40 RE~FVemC~D~dVQrlT 56 (101)
+++|-+.|+--.||+||
T Consensus 42 ~~aF~~FC~~n~V~~l~ 58 (59)
T PF06099_consen 42 RAAFEEFCAANRVVRLD 58 (59)
T ss_pred HHHHHHHHHHCcEEeCC
Confidence 68999999999999886
No 29
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=27.57 E-value=1.6e+02 Score=21.08 Aligned_cols=36 Identities=17% Similarity=0.189 Sum_probs=20.0
Q ss_pred CCCHHHHHHHHHHHHHHhhhhHHHHH-------HHHHHHHhcC
Q 034224 1 MISESDLKREYLRKWDDEYLMTYRFL-------DLLQRVFYGS 36 (101)
Q Consensus 1 ~~te~~l~~~Ylkrf~k~yg~tf~vL-------~iLQ~v~Y~s 36 (101)
||--.+++..|...+...|+-.++.+ |++|.+|.+=
T Consensus 1 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl 43 (182)
T PRK12540 1 MPLTDSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRA 43 (182)
T ss_pred CCccHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence 45555566556555555555555544 4566555543
No 30
>PF04078 Rcd1: Cell differentiation family, Rcd1-like ; InterPro: IPR007216 Rcd1 (Required cell differentiation 1) -like proteins are found among a wide range of organisms []. Rcd1 was initially identified as an essential factor in nitrogen starvation-invoked differentiation in fission yeast. This results largely from a defect in nitrogen starvation-invoked induction of ste11+, a key transcriptional factor gene required for the onset of sexual development. It is one of the most conserved proteins in eukaryotes, and its mammalian homologue is expressed in a variety of differentiating tissues [, ]. The mammalian Rcd1 is a novel transcriptional cofactor and is critical for retinoic acid-induced differentiation of F9 mouse teratocarcinoma cells, at least in part, via forming complexes with retinoic acid receptor and activation transcription factor-2 (ATF-2) []. Two of the members in this family have been characterised as being involved in regulation of Ste11 regulated sex genes [, ].; PDB: 2FV2_B.
Probab=27.12 E-value=2.3e+02 Score=23.22 Aligned_cols=57 Identities=21% Similarity=0.310 Sum_probs=42.2
Q ss_pred hhHHHHHHHHHHHHhcCchhHHHHHhhhCCcchhhhhhhhhhh---hhhcCCChhHHHHHHH-HHHHHhhh
Q 034224 20 LMTYRFLDLLQRVFYGSNVGREALVELCGDEYVQRMTFDSYLY---KKLAEGSRFQDVKMVM-KTIGSFMR 86 (101)
Q Consensus 20 g~tf~vL~iLQ~v~Y~sd~~RE~FVemC~D~dVQrlTfdSYly---K~lv~~~p~~~~ki~~-k~i~~L~r 86 (101)
-++..+|.+||-+-. .+..|..|+.- -+-.||| ++....+|.+++|++. .-||+|++
T Consensus 65 nRVcnaLaLlQ~vAs-hpetr~~Fl~a---------~iplyLyPfL~tt~k~r~~E~LRLtsLGVIgaLvK 125 (262)
T PF04078_consen 65 NRVCNALALLQCVAS-HPETRMPFLKA---------HIPLYLYPFLNTTSKTRPFEYLRLTSLGVIGALVK 125 (262)
T ss_dssp HHHHHHHHHHHHHHH--TTTHHHHHHT---------TGGGGGHHHHH----SHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHc-ChHHHHHHHHc---------CchhhehhhhhccccccccchhhHhHHHHHHHHHc
Confidence 468999999999988 67788889863 3556776 5677889999999974 67888887
No 31
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=26.86 E-value=2.2e+02 Score=20.14 Aligned_cols=7 Identities=14% Similarity=0.657 Sum_probs=4.9
Q ss_pred hhhhhhh
Q 034224 56 TFDSYLY 62 (101)
Q Consensus 56 TfdSYly 62 (101)
+|.+||+
T Consensus 72 ~~~~wl~ 78 (189)
T PRK06811 72 SFKKWIA 78 (189)
T ss_pred cHHHHHH
Confidence 6777775
No 32
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=26.33 E-value=53 Score=21.83 Aligned_cols=24 Identities=33% Similarity=0.569 Sum_probs=21.1
Q ss_pred HHHHHHHHhcCchhHHHHHhhhCC
Q 034224 26 LDLLQRVFYGSNVGREALVELCGD 49 (101)
Q Consensus 26 L~iLQ~v~Y~sd~~RE~FVemC~D 49 (101)
+..|-+-.|+-|..|+.|=.||.|
T Consensus 20 i~tl~~SL~Gad~lr~klG~IC~~ 43 (60)
T PF10892_consen 20 IRTLSRSLIGADDLRVKLGGICGD 43 (60)
T ss_pred HHHHHHHhhChHHHHHHHcchhhc
Confidence 556778889999999999999986
No 33
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=24.41 E-value=1.6e+02 Score=20.14 Aligned_cols=39 Identities=33% Similarity=0.463 Sum_probs=21.2
Q ss_pred HHHHHHHhcCchhHHHHHhhhCCcchhhhhhhhhhhhhhcCCChhHHHH
Q 034224 27 DLLQRVFYGSNVGREALVELCGDEYVQRMTFDSYLYKKLAEGSRFQDVK 75 (101)
Q Consensus 27 ~iLQ~v~Y~sd~~RE~FVemC~D~dVQrlTfdSYlyK~lv~~~p~~~~k 75 (101)
|++|.+|-+-=...+.| + .+ .|.+||++ +++..-..++|
T Consensus 30 DlvQe~fl~~~~~~~~~-----~--~~--~~~~wL~~-i~~n~~~d~~R 68 (165)
T PRK09644 30 DLLQETFYRAYIYLEDY-----D--NQ--KVKPWLFK-VAYHTFIDFVR 68 (165)
T ss_pred HHHHHHHHHHHHhHHhc-----c--cc--chHHHHHH-HHHHHHHHHHH
Confidence 56776666554444444 1 12 47778776 55544444443
No 34
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=24.12 E-value=1.4e+02 Score=20.38 Aligned_cols=56 Identities=9% Similarity=0.191 Sum_probs=29.6
Q ss_pred CHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCchhHHHHHhhhCCcc--hhhhhhhhhhh
Q 034224 3 SESDLKREYLRKWDDEYLMTYRFLDLLQRVFYGSNVGREALVELCGDEY--VQRMTFDSYLY 62 (101)
Q Consensus 3 te~~l~~~Ylkrf~k~yg~tf~vL~iLQ~v~Y~sd~~RE~FVemC~D~d--VQrlTfdSYly 62 (101)
.++.+...|.+-+...|+-.++.++ ..--.-|...|.|+.+....+ ... .|.+||+
T Consensus 3 ~~~a~~~l~~~~~~~l~~~~~~~~~---~~~~AeDv~Qe~f~~~~~~~~~~~~~-~~~~wl~ 60 (161)
T PRK12541 3 RKQSLEEIYSEHMQDLFRYLLSLTG---DSHFAEDLMQETFYRMLVHIDYYKGE-EIRPWLF 60 (161)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhc---CHHHHHHHHHHHHHHHHHhHHHccCC-ChHHHHH
Confidence 4556666677777767766666553 222334445555666543221 122 4666664
No 35
>PF02397 Bac_transf: Bacterial sugar transferase; InterPro: IPR003362 This entry represents a conserved region from a number of different bacterial sugar transferases, involved in diverse biosynthesis pathways. Examples include galactosyl-P-P-undecaprenol synthetase (2.7.8.6 from EC), which transfers galatose-1-phosphate to the lipid precursor undecaprenol phosphate in the first steps of O-polysaccharide biosynthesis; UDP-galactose-lipid carrier transferase, which is involved in the biosynthesis of amylovoran; and galactosyl transferase CpsD, which is essential for assembly of the group B Streptococci (GBS) type III capsular polysaccharide.
Probab=24.09 E-value=1.2e+02 Score=23.09 Aligned_cols=33 Identities=24% Similarity=0.506 Sum_probs=26.3
Q ss_pred hhhhhhhhhhhhhcCCChhHHHHHHHHHHHHhhhcc
Q 034224 53 QRMTFDSYLYKKLAEGSRFQDVKMVMKTIGSFMRCN 88 (101)
Q Consensus 53 QrlTfdSYlyK~lv~~~p~~~~ki~~k~i~~L~r~~ 88 (101)
|++-+|.|--+ ..+.+-|++|.++|+..+++-+
T Consensus 153 ~k~~~D~~Yi~---~~s~~~Dl~Ii~~Ti~~vl~~g 185 (187)
T PF02397_consen 153 EKLELDLYYIE---NWSLWLDLKIILKTIRAVLKKG 185 (187)
T ss_pred HHHHHHHHHHh---hCCHHHHHHHHHHHHHHHhhCC
Confidence 47888877644 4568999999999999998733
No 36
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=23.10 E-value=1.5e+02 Score=20.81 Aligned_cols=55 Identities=9% Similarity=0.148 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCchhHHHHHhhhCCcchhh---hhhhhhhh
Q 034224 5 SDLKREYLRKWDDEYLMTYRFLDLLQRVFYGSNVGREALVELCGDEYVQR---MTFDSYLY 62 (101)
Q Consensus 5 ~~l~~~Ylkrf~k~yg~tf~vL~iLQ~v~Y~sd~~RE~FVemC~D~dVQr---lTfdSYly 62 (101)
..+..-|.+-+...|+-+++.+ +..--..|-.-|.|+.+....+-.+ -.|.+||+
T Consensus 23 ~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDivQe~fl~l~~~~~~~~~~~~~~~~wL~ 80 (182)
T PRK12537 23 RALQALYQQESARLLGVARRIV---RDRALAEDIVHDAFIKIWTGAASFDPARGSARGWIY 80 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHhccccCCcccccHHHHHH
Confidence 3344455555555666555544 3344556666777887765533221 25667765
No 37
>smart00025 Pumilio Pumilio-like repeats. Pumilio-like repeats that bind RNA.
Probab=22.99 E-value=45 Score=16.90 Aligned_cols=24 Identities=33% Similarity=0.534 Sum_probs=14.6
Q ss_pred HHHHHhhhCCcchhhhhhhhhhhhhhcCCC
Q 034224 40 REALVELCGDEYVQRMTFDSYLYKKLAEGS 69 (101)
Q Consensus 40 RE~FVemC~D~dVQrlTfdSYlyK~lv~~~ 69 (101)
.+.+++||.|++ -||.-.++....
T Consensus 3 ~~~~~~l~~~~~------g~~viqk~l~~~ 26 (36)
T smart00025 3 KGHLLELSKDQY------GNRVVQKLLEHA 26 (36)
T ss_pred hHHHHHHHhcch------hhHHHHHHHHHC
Confidence 367889998874 455444444333
No 38
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=22.94 E-value=1.7e+02 Score=21.18 Aligned_cols=58 Identities=9% Similarity=0.168 Sum_probs=30.7
Q ss_pred CHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCchhHHHHHhhhCCcc-h-hhhhhhhhhhh
Q 034224 3 SESDLKREYLRKWDDEYLMTYRFLDLLQRVFYGSNVGREALVELCGDEY-V-QRMTFDSYLYK 63 (101)
Q Consensus 3 te~~l~~~Ylkrf~k~yg~tf~vL~iLQ~v~Y~sd~~RE~FVemC~D~d-V-QrlTfdSYlyK 63 (101)
++.|....+...+...|+-.+..|+ .---..|-..|.|+.+....+ . ..-+|.+||+.
T Consensus 5 ~~~~~~~~l~~~~~~l~~~a~~~l~---~~~~AEDivQevfl~l~~~~~~~~~~~~~~awL~~ 64 (188)
T PRK12546 5 KHRDPRDELVEHLPALRAFAISLTR---NVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFT 64 (188)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHcC---ChhhHHHHHHHHHHHHHHHHhccCCCcchHHHHHH
Confidence 4566666777777777777776653 222233444455555443211 1 12367777753
No 39
>cd03572 ENTH_epsin_related ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the t
Probab=22.81 E-value=86 Score=22.64 Aligned_cols=29 Identities=31% Similarity=0.388 Sum_probs=21.7
Q ss_pred hhhhhhhhcCCChhHHHHHHHHHHHHhhhc
Q 034224 58 DSYLYKKLAEGSRFQDVKMVMKTIGSFMRC 87 (101)
Q Consensus 58 dSYlyK~lv~~~p~~~~ki~~k~i~~L~r~ 87 (101)
-.||-|||-..+|-+-+| .++-|-||++.
T Consensus 40 ~d~L~kRL~~~~~hVK~K-~Lrilk~l~~~ 68 (122)
T cd03572 40 LEYLLKRLKRSSPHVKLK-VLKIIKHLCEK 68 (122)
T ss_pred HHHHHHHhcCCCCcchHH-HHHHHHHHHhh
Confidence 359999999988766555 45777777764
No 40
>cd05611 STKc_Rim15_like Catalytic domain of fungal Rim15-like Protein Serine/Threonine Kinases. Serine/Threonine Kinases (STKs), Microtubule-associated serine/threonine (MAST) kinase subfamily, fungal Rim15-like kinases, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MAST kinase subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. Members of this group include Saccharomyces cerevisiae Rim15, Schizosaccharomyces pombe cek1, and similar fungal proteins. They contain a central catalytic domain, which contains an insert relative to MAST kinases. In addition, Rim15 contains a C-terminal signal receiver (REC) domain while cek1 contains an N-terminal PAS domain. Rim15 (or Rim15p) functions as a regulator of meiosis. It acts as a do
Probab=21.91 E-value=47 Score=23.39 Aligned_cols=35 Identities=17% Similarity=0.361 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhcCchhHH---HHHhhhCCcchhhhhhh
Q 034224 24 RFLDLLQRVFYGSNVGRE---ALVELCGDEYVQRMTFD 58 (101)
Q Consensus 24 ~vL~iLQ~v~Y~sd~~RE---~FVemC~D~dVQrlTfd 58 (101)
.+.+++++.+-.+...|- .+-++..++...+++||
T Consensus 223 ~~~~~i~~~l~~~p~~R~~~~~~~~~l~~~~~~~~~~~ 260 (260)
T cd05611 223 EAVDLINRLLCMDPAKRLGANGYQEIKSHPFFKSINWD 260 (260)
T ss_pred HHHHHHHHHccCCHHHccCCCcHHHHHcChHhhcCCCC
Confidence 467788888877777776 55678888877777775
No 41
>PF11951 Fungal_trans_2: Fungal specific transcription factor domain; InterPro: IPR021858 This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 454 to 826 amino acids in length. This protein is found associated with PF00172 from PFAM.
Probab=21.20 E-value=98 Score=22.30 Aligned_cols=30 Identities=23% Similarity=0.325 Sum_probs=23.2
Q ss_pred HHHHHHH-HhhhhHHHHHHHHHHHHhcCchh
Q 034224 10 EYLRKWD-DEYLMTYRFLDLLQRVFYGSNVG 39 (101)
Q Consensus 10 ~Ylkrf~-k~yg~tf~vL~iLQ~v~Y~sd~~ 39 (101)
..+++.- ..+|++-.+.++|+.+|=+.|..
T Consensus 333 ~~l~~~~~~~~~~~~~~~~~l~~vW~~~~~~ 363 (383)
T PF11951_consen 333 ARLRRLQSSGFGNVRRARELLEEVWRRRDDG 363 (383)
T ss_pred HHHHHHHHHhcccHHHHHHHHHHHHHhhcCC
Confidence 4445555 66789999999999999888854
No 42
>PF12909 DUF3832: Protein of unknown function (DUF3832); InterPro: IPR024308 This domain found in bacteria and Acanthamoeba polyphaga mimivirus (APMV) L591 protein has no known function. In Q0AZ30 from SWISSPROT and other uncharacterised proteins this domain is found C-terminal, while the N terminus shows remote homology to the bacterial toxin/antitoxin 'addiction module' (PF12910 from PFAM).; PDB: 3K6Q_C.
Probab=20.78 E-value=1.2e+02 Score=20.91 Aligned_cols=29 Identities=24% Similarity=0.655 Sum_probs=19.7
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHHHhcCchhHHHH-----HhhhCC
Q 034224 10 EYLRKWDDEYLMTYRFLDLLQRVFYGSNVGREAL-----VELCGD 49 (101)
Q Consensus 10 ~Ylkrf~k~yg~tf~vL~iLQ~v~Y~sd~~RE~F-----VemC~D 49 (101)
.|-..|+... .+||.+-.+|+.| |.+|.|
T Consensus 48 dYAedy~~~~-----------~~~~~apnR~~H~pYv~rI~l~~d 81 (89)
T PF12909_consen 48 DYAEDYMNRF-----------PLFYNAPNRRHHYPYVRRILLCDD 81 (89)
T ss_dssp HHHHHHHHTH-----------HHHHTSTTTGGGHHHHHHHHHSSS
T ss_pred HHHHHHHHHH-----------HHHhcCCCcccchHHHHHHHHhCC
Confidence 5666655543 3688888888877 677754
No 43
>PF01221 Dynein_light: Dynein light chain type 1 ; InterPro: IPR001372 Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Dynein is composed of a number of ATP-binding large subunits (see IPR004273 from INTERPRO), intermediate size subunits and small subunits. Among the small subunits, there is a family of highly conserved proteins which make up this family [, ]. Both type 1 (DLC1) and 2 (DLC2) dynein light chains have a similar two-layer alpha-beta core structure consisting of beta-alpha(2)-beta-X-beta(2) [, ].; GO: 0007017 microtubule-based process, 0005875 microtubule associated complex; PDB: 1F95_A 1F96_A 1F3C_A 3P8M_B 2XQQ_C 1RE6_A 1CMI_A 1PWK_A 1PWJ_A 4DS1_C ....
Probab=20.69 E-value=1.1e+02 Score=19.98 Aligned_cols=21 Identities=24% Similarity=0.574 Sum_probs=14.0
Q ss_pred CCHHHHHHHHHH-HHHHhhhhHH
Q 034224 2 ISESDLKREYLR-KWDDEYLMTY 23 (101)
Q Consensus 2 ~te~~l~~~Ylk-rf~k~yg~tf 23 (101)
+++.++- .++| .+|++||++.
T Consensus 33 ~~~~eiA-~~iK~~lD~~yG~~W 54 (89)
T PF01221_consen 33 QDEKEIA-EFIKQELDKKYGPTW 54 (89)
T ss_dssp SSHHHHH-HHHHHHHHHHHSS-E
T ss_pred CcHHHHH-HHHHHHHhcccCCce
Confidence 4677776 6665 5688899864
No 44
>PF08707 PriCT_2: Primase C terminal 2 (PriCT-2) ; InterPro: IPR014819 This alpha helical domain is found at the C-terminal of primases. ; GO: 0016817 hydrolase activity, acting on acid anhydrides
Probab=20.14 E-value=2.5e+02 Score=17.85 Aligned_cols=43 Identities=23% Similarity=0.186 Sum_probs=32.4
Q ss_pred hhhhHHHHHHHHHHHHhcCchhHHHHHhhhC-----Ccchhhhhhhhh
Q 034224 18 EYLMTYRFLDLLQRVFYGSNVGREALVELCG-----DEYVQRMTFDSY 60 (101)
Q Consensus 18 ~yg~tf~vL~iLQ~v~Y~sd~~RE~FVemC~-----D~dVQrlTfdSY 60 (101)
.|..=.+|.-.|...+.+++..++-|.+.|+ |+.--+-.|+|.
T Consensus 16 ~y~~W~~vg~Al~~~~~g~~~g~~l~~~wS~~~~ky~~~e~~~~W~s~ 63 (78)
T PF08707_consen 16 DYDDWIRVGMALKHEFGGGEEGLDLWDEWSRQSPKYDEEECERKWRSF 63 (78)
T ss_pred CHHHHHHHHHHHHHhccCChHHHHHHHHHhcCCCCCCHHHHHHHHHhC
Confidence 3444456777888888889999999999998 444446677777
Done!