Query psy9762
Match_columns 112
No_of_seqs 48 out of 50
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 18:55:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9762.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9762hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4057|consensus 100.0 6.6E-44 1.4E-48 271.1 12.6 103 2-104 9-113 (180)
2 PF10280 Med11: Mediator compl 100.0 6.1E-32 1.3E-36 193.4 6.2 105 2-106 3-116 (117)
3 cd01145 TroA_c Periplasmic bin 70.5 14 0.0003 27.9 5.4 65 15-79 115-180 (203)
4 KOG4117|consensus 66.5 4.7 0.0001 27.4 1.9 18 5-22 48-65 (73)
5 COG0803 LraI ABC-type metal io 65.7 14 0.0003 29.9 4.8 89 16-104 141-239 (303)
6 cd01016 TroA Metal binding pro 60.8 30 0.00066 27.4 5.9 49 15-63 108-157 (276)
7 PF07889 DUF1664: Protein of u 60.3 49 0.0011 24.4 6.5 53 5-57 68-120 (126)
8 PF06825 HSBP1: Heat shock fac 52.8 5.2 0.00011 25.7 0.3 19 5-23 35-53 (54)
9 PRK09545 znuA high-affinity zi 52.2 32 0.00069 27.9 4.8 52 14-65 151-203 (311)
10 cd01017 AdcA Metal binding pro 51.2 39 0.00084 26.6 5.0 50 15-64 120-170 (282)
11 cd01018 ZntC Metal binding pro 48.8 43 0.00093 26.2 4.9 52 14-65 118-170 (266)
12 PF01297 TroA: Periplasmic sol 48.8 44 0.00095 25.6 4.9 63 15-77 99-162 (256)
13 cd01019 ZnuA Zinc binding prot 45.6 53 0.0011 26.1 5.0 51 14-64 127-178 (286)
14 smart00397 t_SNARE Helical reg 45.2 63 0.0014 19.0 6.4 55 2-56 9-63 (66)
15 cd01137 PsaA Metal binding pro 43.7 82 0.0018 25.1 5.9 49 14-62 123-172 (287)
16 TIGR03772 anch_rpt_subst ancho 43.1 77 0.0017 28.0 6.0 49 15-63 318-367 (479)
17 PF11568 Med29: Mediator compl 42.9 1.5E+02 0.0032 22.6 7.6 58 10-67 17-83 (148)
18 PF06013 WXG100: Proteins of 1 42.6 76 0.0017 19.2 8.7 63 5-67 14-78 (86)
19 TIGR03042 PS_II_psbQ_bact phot 42.0 58 0.0013 24.6 4.5 40 66-105 17-62 (142)
20 PF04108 APG17: Autophagy prot 40.8 2.3E+02 0.005 24.1 8.4 90 14-104 285-374 (412)
21 cd09235 V_Alix Middle V-domain 40.3 2.1E+02 0.0046 23.6 9.8 82 22-104 223-313 (339)
22 PF02847 MA3: MA3 domain; Int 39.2 82 0.0018 20.9 4.5 48 19-66 54-102 (113)
23 cd00068 GGL G protein gamma su 34.6 62 0.0013 20.3 3.1 29 83-111 13-42 (57)
24 cd01020 TroA_b Metal binding p 34.4 1.2E+02 0.0027 23.6 5.5 63 15-77 102-165 (264)
25 PF03623 Focal_AT: Focal adhes 31.5 2.3E+02 0.005 21.4 7.1 69 24-103 21-89 (139)
26 PF05008 V-SNARE: Vesicle tran 31.1 1.4E+02 0.0031 18.9 8.2 56 2-57 22-78 (79)
27 smart00544 MA3 Domain in DAP-5 29.6 84 0.0018 21.0 3.4 48 19-66 54-102 (113)
28 PRK07857 hypothetical protein; 29.3 52 0.0011 23.7 2.3 29 5-33 35-63 (106)
29 PF14678 FANCI_S4: FANCI solen 29.1 3.1E+02 0.0067 22.1 7.1 90 6-103 85-177 (256)
30 PF01519 DUF16: Protein of unk 27.3 2.4E+02 0.0053 20.3 7.0 22 78-99 78-101 (102)
31 PF08331 DUF1730: Domain of un 26.5 84 0.0018 20.5 2.8 28 75-106 40-67 (78)
32 TIGR01808 CM_M_hiGC-arch monof 26.4 1E+02 0.0022 20.2 3.3 29 5-33 7-35 (74)
33 PF13404 HTH_AsnC-type: AsnC-t 26.1 65 0.0014 19.0 2.0 24 7-30 1-25 (42)
34 PF09246 PHAT: PHAT; InterPro 26.0 1.5E+02 0.0032 21.7 4.2 54 3-56 1-61 (108)
35 PF11328 DUF3130: Protein of u 25.4 28 0.0006 24.7 0.4 35 74-108 24-63 (90)
36 PRK01203 prefoldin subunit alp 25.0 49 0.0011 24.6 1.7 28 74-104 76-105 (130)
37 PF12731 Mating_N: Mating-type 24.8 2E+02 0.0044 19.6 4.6 49 11-59 11-60 (95)
38 KOG0809|consensus 23.4 4.7E+02 0.01 22.3 8.2 62 6-67 101-168 (305)
39 PF05659 RPW8: Arabidopsis bro 22.8 3.2E+02 0.007 20.2 6.7 85 21-110 11-118 (147)
40 KOG3557|consensus 22.8 3.2E+02 0.007 25.8 6.7 54 6-61 276-350 (721)
41 PF03997 VPS28: VPS28 protein; 22.3 1.3E+02 0.0029 23.4 3.7 62 33-95 92-164 (188)
42 PF10046 BLOC1_2: Biogenesis o 21.7 1.3E+02 0.0028 20.6 3.1 19 4-22 65-83 (99)
43 PF02185 HR1: Hr1 repeat; Int 21.5 2.3E+02 0.0049 17.9 7.2 53 6-58 2-58 (70)
44 PF14523 Syntaxin_2: Syntaxin- 20.9 2.6E+02 0.0055 18.3 6.1 50 6-55 34-90 (102)
45 TIGR01462 greA transcription e 20.9 3.4E+02 0.0073 19.7 5.9 35 67-105 34-68 (151)
46 PF07464 ApoLp-III: Apolipopho 20.4 3.9E+02 0.0084 20.2 7.3 53 10-62 1-56 (155)
47 TIGR01807 CM_P2 chorismate mut 20.2 1.3E+02 0.0028 19.4 2.8 29 5-33 6-34 (76)
No 1
>KOG4057|consensus
Probab=100.00 E-value=6.6e-44 Score=271.05 Aligned_cols=103 Identities=48% Similarity=0.644 Sum_probs=101.2
Q ss_pred hHhhHHHHHHHHHHHHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCCchhHHH
Q psy9762 2 ERIQVLDQIEKDIITCLQSAGQALLELSKEKSSLKQAESQSHNFLKTLSHVETKLTEQINYLTQVSTGQPHEGSGYASQK 81 (112)
Q Consensus 2 ~RL~~L~~iEK~I~~~lq~Ag~~i~ELskek~s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLsqV~tg~phEgS~Y~a~k 81 (112)
+||++|++|||+|..||||||++|.||+|||++.+.+|+++++|+++|.+||++||+||+||||||||+|||||+||++|
T Consensus 9 dri~Al~~iEkeI~~~mq~Ag~iiqeLgKEK~~~kn~e~qa~~F~ksit~VE~eLSaQi~YLtqV~tGqpHeGS~y~s~k 88 (180)
T KOG4057|consen 9 DRIQALVTIEKEIDEMMQCAGEIIQELGKEKQIGKNMEDQANNFKKSITQVENELSAQIQYLTQVCTGQPHEGSTYGSLK 88 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchHHHH
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHH--HHHHHHHHHHHHHh
Q psy9762 82 VLQMAWHRS--ARQQISDVIQSEAD 104 (112)
Q Consensus 82 d~emA~~rv--~~~~l~~l~~~~~~ 104 (112)
||+|||+|| +|++|.++.||++.
T Consensus 89 ~~qmA~~r~~~ars~l~~i~rt~~~ 113 (180)
T KOG4057|consen 89 NSQMAQSRLSSARSELFQIVRTLDP 113 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 999999999 99999999999654
No 2
>PF10280 Med11: Mediator complex protein ; InterPro: IPR019404 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 Med11 of the Mediator complex []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3R84_S 3RJ1_O.
Probab=99.97 E-value=6.1e-32 Score=193.36 Aligned_cols=105 Identities=41% Similarity=0.612 Sum_probs=81.1
Q ss_pred hHhhHHHHHHHHHHHHHHHHHHHHHhhcCCcc-------cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCCCCC
Q psy9762 2 ERIQVLDQIEKDIITCLQSAGQALLELSKEKS-------SLKQAESQSHNFLKTLSHVETKLTEQINYLTQVSTGQPHEG 74 (112)
Q Consensus 2 ~RL~~L~~iEK~I~~~lq~Ag~~i~ELskek~-------s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLsqV~tg~phEg 74 (112)
+||++|++|||+|+++|++||+||.+|||+++ ++++|+++|++|+++|+.|+..|+.||+||+++++++||+|
T Consensus 3 eRL~~L~~Idk~I~~lL~~A~~ai~~Ls~~~~~~~~~~~~k~~f~~~~~~f~~~L~~V~~~Lr~qI~~L~e~~~~~~~~~ 82 (117)
T PF10280_consen 3 ERLQQLNEIDKKIVSLLQHAGQAIQELSNPKSPDQDPESSKEAFESATSEFFSTLSSVEVELRRQIKYLEEVSIIQPHEG 82 (117)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---TGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCBTT-----
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccc
Confidence 79999999999999999999999999999997 89999999999999999999999999999999999999999
Q ss_pred CchhHHHHHHHHHHHH--HHHHHHHHHHHHHhhh
Q psy9762 75 SGYASQKVLQMAWHRS--ARQQISDVIQSEADYF 106 (112)
Q Consensus 75 S~Y~a~kd~emA~~rv--~~~~l~~l~~~~~~~~ 106 (112)
|+||+.++++|+++++ .++++.++.+++.++.
T Consensus 83 s~~~~l~v~~ln~~~~~~~~~~l~el~~~~~~~l 116 (117)
T PF10280_consen 83 SSYGALDVGWLNSKKTEVGRDKLAELWATLREFL 116 (117)
T ss_dssp ---TBS---------------GGGTTTHHHHHHH
T ss_pred ccccccchHHHHHhHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999 9999999999988753
No 3
>cd01145 TroA_c Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=70.51 E-value=14 Score=27.88 Aligned_cols=65 Identities=14% Similarity=0.076 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHhhcCCcc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCCchhH
Q psy9762 15 ITCLQSAGQALLELSKEKS-SLKQAESQSHNFLKTLSHVETKLTEQINYLTQVSTGQPHEGSGYAS 79 (112)
Q Consensus 15 ~~~lq~Ag~~i~ELskek~-s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLsqV~tg~phEgS~Y~a 79 (112)
..+..-|.++-..|++-.| +...++.++..|.+.|+.+.+++.+.+.-+.+...-..|..=+|=+
T Consensus 115 ~~~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~l~~l~~~~~~~l~~~~~~~~v~~H~af~Y~~ 180 (203)
T cd01145 115 NNAPALAKALADALIELDPSEQEEYKENLRVFLAKLNKLLREWERQFEGLKGIQVVAYHPSYQYLA 180 (203)
T ss_pred HHHHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEEEecccHHHHH
Confidence 4556667778888888776 7889999999999999999999998877544322222355555543
No 4
>KOG4117|consensus
Probab=66.45 E-value=4.7 Score=27.42 Aligned_cols=18 Identities=33% Similarity=0.595 Sum_probs=16.2
Q ss_pred hHHHHHHHHHHHHHHHHH
Q psy9762 5 QVLDQIEKDIITCLQSAG 22 (112)
Q Consensus 5 ~~L~~iEK~I~~~lq~Ag 22 (112)
.++|+.||.|..+|+.||
T Consensus 48 ~riDDLEKnIaDLm~qag 65 (73)
T KOG4117|consen 48 SRIDDLEKNIADLMTQAG 65 (73)
T ss_pred hhhHHHHHHHHHHHHHcc
Confidence 367899999999999998
No 5
>COG0803 LraI ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]
Probab=65.69 E-value=14 Score=29.92 Aligned_cols=89 Identities=13% Similarity=0.197 Sum_probs=68.3
Q ss_pred HHHHHHHHHHHhhcCCcc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh-hhccCCCCCCCchhHHH--HHHHHHHHH-
Q psy9762 16 TCLQSAGQALLELSKEKS-SLKQAESQSHNFLKTLSHVETKLTEQINYLT-QVSTGQPHEGSGYASQK--VLQMAWHRS- 90 (112)
Q Consensus 16 ~~lq~Ag~~i~ELskek~-s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLs-qV~tg~phEgS~Y~a~k--d~emA~~rv- 90 (112)
.++.-|-++-..|++-.| ++...+.++.+|.+.|+.++.+....+..+. |...-..|..-+|=++- --+.+...+
T Consensus 141 na~~~v~~I~~~L~~~dP~~~~~y~~N~~~y~~kL~~l~~~~~~~~~~~~~~r~~vt~h~af~Y~~~~~g~~~~~i~~~~ 220 (303)
T COG0803 141 NAKIYAENIADALVELDPENKETYEKNAEAYLKKLNKLDEEAKAKLSKIPAQRDVVTSHGAFGYLARDYGLKQVAIAGIS 220 (303)
T ss_pred HHHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcCcEEEeecchHHHHHhccCCccccccCcC
Confidence 455556666677776555 8999999999999999999999999999988 77777789999998885 244444433
Q ss_pred -----HHHHHHHHHHHHHh
Q psy9762 91 -----ARQQISDVIQSEAD 104 (112)
Q Consensus 91 -----~~~~l~~l~~~~~~ 104 (112)
--.+|.++.+.+.+
T Consensus 221 ~~~e~s~~~l~~l~~~ik~ 239 (303)
T COG0803 221 PEAEPSPKDLAKLVDLIKK 239 (303)
T ss_pred cccCCCHHHHHHHHHHHHH
Confidence 45677777777765
No 6
>cd01016 TroA Metal binding protein TroA. These proteins have been shown to function as initial receptors in ABC transport of Zn2+ and possibly Fe3+ in many eubacterial species. The TroA proteins belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=60.75 E-value=30 Score=27.37 Aligned_cols=49 Identities=10% Similarity=0.117 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHHhhcCCcc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy9762 15 ITCLQSAGQALLELSKEKS-SLKQAESQSHNFLKTLSHVETKLTEQINYL 63 (112)
Q Consensus 15 ~~~lq~Ag~~i~ELskek~-s~~~~e~~~~~F~~sl~~VE~eLs~qI~yL 63 (112)
..+...|..+-..|++-.| +...++.++..|.+.|+.++.++.+.+.-+
T Consensus 108 ~~~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~l~~~ 157 (276)
T cd01016 108 KLWKYAVKAVAEVLSEKLPEHKDEFQANSEAYVEELDSLDAYAKKKIAEI 157 (276)
T ss_pred HHHHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 4566778888888888776 788999999999999999999988877653
No 7
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=60.29 E-value=49 Score=24.39 Aligned_cols=53 Identities=13% Similarity=0.198 Sum_probs=46.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHH
Q psy9762 5 QVLDQIEKDIITCLQSAGQALLELSKEKSSLKQAESQSHNFLKTLSHVETKLT 57 (112)
Q Consensus 5 ~~L~~iEK~I~~~lq~Ag~~i~ELskek~s~~~~e~~~~~F~~sl~~VE~eLs 57 (112)
++|+.++.++-.+......+-.++..=+.....+..-...+...+..+|..|.
T Consensus 68 qRId~vd~klDe~~ei~~~i~~eV~~v~~dv~~i~~dv~~v~~~V~~Le~ki~ 120 (126)
T PF07889_consen 68 QRIDRVDDKLDEQKEISKQIKDEVTEVREDVSQIGDDVDSVQQMVEGLEGKID 120 (126)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 68899999999999999999999988777888888888888888888888873
No 8
>PF06825 HSBP1: Heat shock factor binding protein 1; InterPro: IPR009643 Heat shock factor binding protein 1 (HSBP1) appears to be a negative regulator of the heat shock response [].; PDB: 3CI9_A.
Probab=52.83 E-value=5.2 Score=25.68 Aligned_cols=19 Identities=32% Similarity=0.508 Sum_probs=8.5
Q ss_pred hHHHHHHHHHHHHHHHHHH
Q psy9762 5 QVLDQIEKDIITCLQSAGQ 23 (112)
Q Consensus 5 ~~L~~iEK~I~~~lq~Ag~ 23 (112)
.+||++||.|..++..||.
T Consensus 35 ~RIDdLE~si~dl~~qag~ 53 (54)
T PF06825_consen 35 SRIDDLEKSIADLMTQAGV 53 (54)
T ss_dssp HHHHCCHHHH---------
T ss_pred hhHHHHHHHHHHHHHhcCC
Confidence 3788999999999998873
No 9
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=52.19 E-value=32 Score=27.94 Aligned_cols=52 Identities=12% Similarity=0.084 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHHhhcCCcc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy9762 14 IITCLQSAGQALLELSKEKS-SLKQAESQSHNFLKTLSHVETKLTEQINYLTQ 65 (112)
Q Consensus 14 I~~~lq~Ag~~i~ELskek~-s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLsq 65 (112)
...+.+-|..+-..|++-.| +...++.++.+|.+.|+.++.++.+.+.-+.+
T Consensus 151 p~~~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~l~~~~~ 203 (311)
T PRK09545 151 PEIARATAVAIHDKLVELMPQSKAKLDANLKDFEAQLAQTDKQIGNQLAPVKG 203 (311)
T ss_pred HHHHHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhccCC
Confidence 45566778888888888776 88899999999999999999999988765443
No 10
>cd01017 AdcA Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).
Probab=51.25 E-value=39 Score=26.60 Aligned_cols=50 Identities=12% Similarity=0.149 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHhhcCCcc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy9762 15 ITCLQSAGQALLELSKEKS-SLKQAESQSHNFLKTLSHVETKLTEQINYLT 64 (112)
Q Consensus 15 ~~~lq~Ag~~i~ELskek~-s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLs 64 (112)
..+..-|..+-..|++-.| +...++.++.+|.+.|+.++..+.+.+.-+.
T Consensus 120 ~~~~~~a~~Ia~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~ 170 (282)
T cd01017 120 VLAIQQVENIKDALIKLDPDNKEYYEKNAAAYAKKLEALDQEYRAKLAKAK 170 (282)
T ss_pred HHHHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 4456667777888888666 8889999999999999999999998876543
No 11
>cd01018 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=48.85 E-value=43 Score=26.18 Aligned_cols=52 Identities=12% Similarity=0.118 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHHhhcCCcc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy9762 14 IITCLQSAGQALLELSKEKS-SLKQAESQSHNFLKTLSHVETKLTEQINYLTQ 65 (112)
Q Consensus 14 I~~~lq~Ag~~i~ELskek~-s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLsq 65 (112)
...+.+-|.++=..|++-.| +...++.++..|.+.|+.+..++.+.+.-+.+
T Consensus 118 p~~~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~~ 170 (266)
T cd01018 118 PANAKIMAENIYEALAELDPQNATYYQANLDALLAELDALDSEIRTILSKLKQ 170 (266)
T ss_pred HHHHHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 44566677777788888666 78899999999999999999999988775444
No 12
>PF01297 TroA: Periplasmic solute binding protein family; InterPro: IPR006127 This is a family of ABC transporter metal-binding lipoproteins. An example is the periplasmic zinc-binding protein TroA P96116 from SWISSPROT that interacts with an ATP-binding cassette transport system in Treponema pallidum and plays a role in the transport of zinc across the cytoplasmic membrane. Related proteins are found in both Gram-positive and Gram-negative bacteria. ; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2PS9_A 2PS0_A 2OSV_A 2OGW_A 2PS3_A 2PRS_B 3MFQ_C 3GI1_B 2OV3_A 1PQ4_A ....
Probab=48.83 E-value=44 Score=25.62 Aligned_cols=63 Identities=17% Similarity=0.202 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHhhcCCcc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCCch
Q psy9762 15 ITCLQSAGQALLELSKEKS-SLKQAESQSHNFLKTLSHVETKLTEQINYLTQVSTGQPHEGSGY 77 (112)
Q Consensus 15 ~~~lq~Ag~~i~ELskek~-s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLsqV~tg~phEgS~Y 77 (112)
..+..-|..+-..|++-.| +...++.+...|.+.|+.+..++.+.+.-+.....-..|..=.|
T Consensus 99 ~~~~~~~~~Ia~~L~~~~P~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~~~~~v~~h~~~~Y 162 (256)
T PF01297_consen 99 ENAKKMAEAIADALSELDPANKDYYEKNAEKYLKELDELDAEIKEKLAKLPGRPVVVYHDAFQY 162 (256)
T ss_dssp HHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSGGEEEEEESTTHH
T ss_pred HHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCeEEEEChHHHH
Confidence 3455556666667776565 78899999999999999999999998887665443334444444
No 13
>cd01019 ZnuA Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a single helix and bind their specific ligands in the cleft between these domains. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=45.62 E-value=53 Score=26.13 Aligned_cols=51 Identities=12% Similarity=0.119 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHHhhcCCcc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy9762 14 IITCLQSAGQALLELSKEKS-SLKQAESQSHNFLKTLSHVETKLTEQINYLT 64 (112)
Q Consensus 14 I~~~lq~Ag~~i~ELskek~-s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLs 64 (112)
...+++-|.++-..|++-.| +...++.++.+|.+.|+.+..++...+.-+.
T Consensus 127 p~n~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~ 178 (286)
T cd01019 127 PENAAEVAQAVAEKLSALDPDNAATYAANLEAFNARLAELDATIKERLAPVK 178 (286)
T ss_pred HHHHHHHHHHHHHHHHHHCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Confidence 45667778888888888777 8899999999999999999999988876543
No 14
>smart00397 t_SNARE Helical region found in SNAREs. All alpha-helical motifs that form twisted and parallel four-helix bundles in target soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptor proteins. This motif found in "Q-SNAREs".
Probab=45.25 E-value=63 Score=18.98 Aligned_cols=55 Identities=25% Similarity=0.213 Sum_probs=37.7
Q ss_pred hHhhHHHHHHHHHHHHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHH
Q psy9762 2 ERIQVLDQIEKDIITCLQSAGQALLELSKEKSSLKQAESQSHNFLKTLSHVETKL 56 (112)
Q Consensus 2 ~RL~~L~~iEK~I~~~lq~Ag~~i~ELskek~s~~~~e~~~~~F~~sl~~VE~eL 56 (112)
+|-+.|+.+++.|..+-..+-..-.++..-.+--..++.++......++.....|
T Consensus 9 ~~~~~l~~l~~~i~~l~~l~~~i~~~v~~Q~~~ld~i~~~~d~~~~~~~~~~~~l 63 (66)
T smart00397 9 ERDEELEQLEKSIGELKQIFLDMGTELEEQGEQLDRIEDNVDDADVNLKKANKRL 63 (66)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 5678889999998888877776666666555556666666666666655555444
No 15
>cd01137 PsaA Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=43.72 E-value=82 Score=25.12 Aligned_cols=49 Identities=6% Similarity=0.047 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHhhcCCcc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy9762 14 IITCLQSAGQALLELSKEKS-SLKQAESQSHNFLKTLSHVETKLTEQINY 62 (112)
Q Consensus 14 I~~~lq~Ag~~i~ELskek~-s~~~~e~~~~~F~~sl~~VE~eLs~qI~y 62 (112)
...+..-|..+=..|++-.| +...++.++..|.+.|+++..++.+.+.-
T Consensus 123 p~~~~~~a~~Ia~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~l~~ 172 (287)
T cd01137 123 PKNAIIYVKNIAKALSEADPANAETYQKNAAAYKAKLKALDEWAKAKFAT 172 (287)
T ss_pred HHHHHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34556667777778888677 88899999999999999999988887654
No 16
>TIGR03772 anch_rpt_subst anchored repeat ABC transporter, substrate-binding protein. Members of this protein family are ABC transporter permease subunits as identified by pfam00950, but additionally contain the Actinobacterial insert domain described by TIGR03769. Some homologs (lacking the insert) have been described as transporters of manganese or of chelated iron. Members of this family typically are found along with an ATP-binding cassette protein, a permease, and an LPXTG-anchored protein with two or three copies of the TIGR03769 insert that occurs just once in this protein family.
Probab=43.13 E-value=77 Score=27.99 Aligned_cols=49 Identities=10% Similarity=0.144 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHhhcCCcc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy9762 15 ITCLQSAGQALLELSKEKS-SLKQAESQSHNFLKTLSHVETKLTEQINYL 63 (112)
Q Consensus 15 ~~~lq~Ag~~i~ELskek~-s~~~~e~~~~~F~~sl~~VE~eLs~qI~yL 63 (112)
..+..-|..+-..|++-.| +...++.++..|.+.|+++..++.+.+.-+
T Consensus 318 ~na~~~a~~Ia~~LselDP~na~~Y~~Na~ay~~eL~~Ld~~~~~~la~i 367 (479)
T TIGR03772 318 KNAIAYVEVIRDKLIEVDPRGAQAYRSNASAYIHRLERLDTYVRRTIATI 367 (479)
T ss_pred HHHHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 4456667777788888666 888999999999999999999999887753
No 17
>PF11568 Med29: Mediator complex subunit 29; InterPro: IPR021018 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. Med29, along with Med11 and Med28, in mammals, is part of the core head-region of the complex. Med29 is the apparent orthologue of the Drosophila melanogaster Intersex protein, which interacts directly with, and functions as a transcriptional coactivator for, the DNA-binding transcription factor Doublesex, so it is likely that mammalian Med29 serves as a target for one or more DNA-binding transcriptional activators []. ; GO: 0016592 mediator complex
Probab=42.90 E-value=1.5e+02 Score=22.58 Aligned_cols=58 Identities=19% Similarity=0.343 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHHHHHHhh-----c-CCc---ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Q psy9762 10 IEKDIITCLQSAGQALLEL-----S-KEK---SSLKQAESQSHNFLKTLSHVETKLTEQINYLTQVS 67 (112)
Q Consensus 10 iEK~I~~~lq~Ag~~i~EL-----s-kek---~s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLsqV~ 67 (112)
+--.++.+|+.|++.+..= + +.+ .....|+++..+|...-.+||--|.-=|.=++|.+
T Consensus 17 LreSl~~~~k~AA~~l~qn~~~D~g~~~~~~d~~~~RFdK~lEeFysiCDQIEl~L~ta~ec~~Q~~ 83 (148)
T PF11568_consen 17 LRESLSNLMKTAAQNLQQNSLVDNGTRGKSSDEPVPRFDKNLEEFYSICDQIELHLKTAIECLSQLS 83 (148)
T ss_pred HHHHHHHHHHHHHHHHHHhcccccccccccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3446788999999998765 2 212 25779999999999999999999998888888743
No 18
>PF06013 WXG100: Proteins of 100 residues with WXG; InterPro: IPR010310 ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. Homologues have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the PF01580 from PFAM domains in the YukA-like proteins []. Members of this protein family include secretion targets for type main variants of type VII secretion systems (T7SS), one found in the Actinobacteria, one found in the Firmicutes. This model was derived through iteration from PF06013 from PFAM. The best characterised member of this family is ESAT-6 from Mycobacterium tuberculosis. Members of this family usually are ~100 amino acids in length but occasionally have long C-terminal extension. ; PDB: 3FAV_A 1WA8_A 3Q4H_B 2KG7_A 2VRZ_B 2VS0_B 3OGI_A 3H6P_B 3GVM_B 3GWK_C ....
Probab=42.62 E-value=76 Score=19.17 Aligned_cols=63 Identities=14% Similarity=0.189 Sum_probs=47.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhcC--CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhc
Q psy9762 5 QVLDQIEKDIITCLQSAGQALLELSK--EKSSLKQAESQSHNFLKTLSHVETKLTEQINYLTQVS 67 (112)
Q Consensus 5 ~~L~~iEK~I~~~lq~Ag~~i~ELsk--ek~s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLsqV~ 67 (112)
..+...-.+|-..++.-...+..|.. ..++...|...-.+|...+..+-..|.+...+|.+..
T Consensus 14 ~~~~~~~~~l~~~~~~l~~~~~~l~~~W~G~a~~af~~~~~~~~~~~~~~~~~L~~~~~~l~~~~ 78 (86)
T PF06013_consen 14 QQLQAQADELQSQLQQLESSIDSLQASWQGEAADAFQDKFEEWNQAFRQLNEALEELSQALRQAA 78 (86)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHGGGBTSSTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666777777777777777777743 4467778888888888888888888888888887754
No 19
>TIGR03042 PS_II_psbQ_bact photosystem II protein PsbQ. This protein through the member sll1638 from Synechocystis sp. PCC 6803, was shown to be part of the cyanobacteria photosystem II. It is homologous to (but quite diverged from) the chloroplast PsbQ protein, called oxygen-evolving enhancer protein 3 (OEE3). We designate this cyanobacteria protein PsbQ by homology.
Probab=41.98 E-value=58 Score=24.56 Aligned_cols=40 Identities=18% Similarity=0.258 Sum_probs=30.6
Q ss_pred hccCCCCCCC--chhHHHHHHH--HHHHH--HHHHHHHHHHHHHhh
Q psy9762 66 VSTGQPHEGS--GYASQKVLQM--AWHRS--ARQQISDVIQSEADY 105 (112)
Q Consensus 66 V~tg~phEgS--~Y~a~kd~em--A~~rv--~~~~l~~l~~~~~~~ 105 (112)
|++|.|-.-- ||++.+=-++ -..++ +++|+.+|...+++.
T Consensus 17 vsc~~p~~~~p~tysp~~l~~i~~~~~~i~~~~~r~~eLk~lI~kk 62 (142)
T TIGR03042 17 VSCSGPAAAVPPTYSPAQLAQIQRQAEGIEAAKDRLPELASLVAKE 62 (142)
T ss_pred HHcCCCcccCCCCCCHHHHHHHHHHHHHHHHHHHhhHHHHHHHhhc
Confidence 5667777744 9999887444 34677 999999999999864
No 20
>PF04108 APG17: Autophagy protein Apg17 ; InterPro: IPR007240 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 []. Autophagy protein 17 (Apg17) is required for activating Apg1 protein kinases. This entry also contains Autophagy protein 11 which is involved in cytoplasm to vacuole transport (Cvt) and pexophagy. ; GO: 0006914 autophagy
Probab=40.78 E-value=2.3e+02 Score=24.13 Aligned_cols=90 Identities=21% Similarity=0.234 Sum_probs=48.1
Q ss_pred HHHHHHHHHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCCchhHHHHHHHHHHHHHHH
Q psy9762 14 IITCLQSAGQALLELSKEKSSLKQAESQSHNFLKTLSHVETKLTEQINYLTQVSTGQPHEGSGYASQKVLQMAWHRSARQ 93 (112)
Q Consensus 14 I~~~lq~Ag~~i~ELskek~s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLsqV~tg~phEgS~Y~a~kd~emA~~rv~~~ 93 (112)
+..+-..-..++.+|.+=+......-...+.|...++..-..+..+|.-+.+.+.---.=.++|++ -=.|++..|-++.
T Consensus 285 ~~~~~~~~~~~~~~l~~~~~~l~~yl~~~~~~~~~~~~~~~~i~~~~~~l~~L~~~Y~~F~~aY~~-LL~Ev~RRr~~~~ 363 (412)
T PF04108_consen 285 IRELYNALSEALEELRKFGERLPSYLAAFHDFEERWEEEKESIQAYIDELEQLCEFYEGFLSAYDS-LLLEVERRRAVRD 363 (412)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Confidence 333333334444444443333333333444454444444445666777777766332222368998 5567777666666
Q ss_pred HHHHHHHHHHh
Q psy9762 94 QISDVIQSEAD 104 (112)
Q Consensus 94 ~l~~l~~~~~~ 104 (112)
++..+-+.|..
T Consensus 364 k~~~i~~~~~e 374 (412)
T PF04108_consen 364 KMKKIIREANE 374 (412)
T ss_pred HHHHHHHHHHH
Confidence 66666666553
No 21
>cd09235 V_Alix Middle V-domain of mammalian Alix and related domains are dimerization and protein interaction modules. This family contains the middle V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X) and related domains. It belongs to the V_Alix_like superfamily which includes the V-domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), is part of the ESCRT (Endosomal Sorting Complexes Required for Transport) system, and participates in membrane remodeling processes, including the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), the abscission reactions of mammalian cell division, and in apoptosis. The Alix V-domain is a dimerization domain, and contains a binding site, partially conserved in the
Probab=40.26 E-value=2.1e+02 Score=23.55 Aligned_cols=82 Identities=10% Similarity=0.114 Sum_probs=55.4
Q ss_pred HHHHHhhcCCccc--HHHHHHHHHH-HHHHHHHHHHHHHHHHHhhhhhccCCC----CCCCchhHHHHHHHHHHHH--HH
Q psy9762 22 GQALLELSKEKSS--LKQAESQSHN-FLKTLSHVETKLTEQINYLTQVSTGQP----HEGSGYASQKVLQMAWHRS--AR 92 (112)
Q Consensus 22 g~~i~ELskek~s--~~~~e~~~~~-F~~sl~~VE~eLs~qI~yLsqV~tg~p----hEgS~Y~a~kd~emA~~rv--~~ 92 (112)
...|.++++++.- ...+..+-.. |-...+.|+..+..|.+-|.++.+..+ .-+++ +.....+.+++++ +-
T Consensus 223 ~~ll~~~~~~~~~~~e~l~~~eL~k~f~~~~~~i~~~~~~Q~~ll~~i~~~n~~f~~~~~~~-~~~~~re~~lq~L~~Ay 301 (339)
T cd09235 223 SKFLSALAQDGAINEEAISVEELDRVYGPLQKQVQESLSRQESLLANIQVAHQEFSKEKQSN-SGANEREEVLKDLAAAY 301 (339)
T ss_pred HHHHHHHHhcCCccHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc-chhhHHHHHHHHHHHHH
Confidence 4556666556542 5567777755 999999999999999999988874322 11122 2244566777887 66
Q ss_pred HHHHHHHHHHHh
Q psy9762 93 QQISDVIQSEAD 104 (112)
Q Consensus 93 ~~l~~l~~~~~~ 104 (112)
....+|...+.+
T Consensus 302 ~~y~el~~nl~e 313 (339)
T cd09235 302 DAFMELTANLKE 313 (339)
T ss_pred HHHHHHHHhHHH
Confidence 777777776664
No 22
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=39.22 E-value=82 Score=20.91 Aligned_cols=48 Identities=23% Similarity=0.322 Sum_probs=38.2
Q ss_pred HHHHHHHHhhcCCc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy9762 19 QSAGQALLELSKEK-SSLKQAESQSHNFLKTLSHVETKLTEQINYLTQV 66 (112)
Q Consensus 19 q~Ag~~i~ELskek-~s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLsqV 66 (112)
+..+..+..|.+.+ -+...+...-..|+.++..++........||+..
T Consensus 54 ~~~~~Ll~~L~~~~~~~~~~~~~gf~~~l~~l~Dl~~D~P~~~~~la~~ 102 (113)
T PF02847_consen 54 EYYSKLLSHLCKRKLISKEQFQEGFEDLLESLEDLELDIPKAPEYLAKF 102 (113)
T ss_dssp HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHHHhHhhhccccchHHHHHHHHH
Confidence 34677888888777 4999999999999999999998877788887654
No 23
>cd00068 GGL G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors
Probab=34.57 E-value=62 Score=20.30 Aligned_cols=29 Identities=7% Similarity=0.068 Sum_probs=23.7
Q ss_pred HHHHHHHH-HHHHHHHHHHHHHhhhccccc
Q psy9762 83 LQMAWHRS-ARQQISDVIQSEADYFGVDLA 111 (112)
Q Consensus 83 ~emA~~rv-~~~~l~~l~~~~~~~~~~~~~ 111 (112)
.++...|+ ++.=..+|..+|++|-.-|-.
T Consensus 13 ~el~~~RikvS~a~~~l~~y~e~~~~~Dpl 42 (57)
T cd00068 13 KELSRERLKVSKAAAELLKYCEQNAENDPL 42 (57)
T ss_pred HHHCCchhhHHHHHHHHHHHHHhcCCCCCC
Confidence 46677889 999999999999998766643
No 24
>cd01020 TroA_b Metal binding protein TroA_b. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=34.36 E-value=1.2e+02 Score=23.61 Aligned_cols=63 Identities=16% Similarity=0.140 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHhhcCCcc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCCch
Q psy9762 15 ITCLQSAGQALLELSKEKS-SLKQAESQSHNFLKTLSHVETKLTEQINYLTQVSTGQPHEGSGY 77 (112)
Q Consensus 15 ~~~lq~Ag~~i~ELskek~-s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLsqV~tg~phEgS~Y 77 (112)
..+..-|..+-..|++-.| +...++.++.+|.+.|+.+..++.+.+.-+.+...-.-|..=+|
T Consensus 102 ~n~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~l~~l~~~~~~~~~~~~~~~~v~~H~af~Y 165 (264)
T cd01020 102 ETMSKVANALADALVKADPDNKKYYQANAKKFVASLKPLAAKIAELSAKYKGAPVAATEPVFDY 165 (264)
T ss_pred hHHHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCeEEEeCchHHH
Confidence 3456667777777887666 88899999999999999999999888765444333334544444
No 25
>PF03623 Focal_AT: Focal adhesion targeting region; InterPro: IPR005189 Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signalling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal "focal adhesion targeting" (FAT) region is necessary and sufficient for localizing FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin []. The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not.; GO: 0004713 protein tyrosine kinase activity, 0004871 signal transducer activity, 0006468 protein phosphorylation, 0007172 signal complex assembly, 0005925 focal adhesion; PDB: 1K05_C 1OW8_C 1OW7_C 3S9O_C 3B71_B 1K04_A 1OW6_C 3GM1_B 3GM3_A 3GM2_A ....
Probab=31.48 E-value=2.3e+02 Score=21.38 Aligned_cols=69 Identities=17% Similarity=0.382 Sum_probs=49.2
Q ss_pred HHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9762 24 ALLELSKEKSSLKQAESQSHNFLKTLSHVETKLTEQINYLTQVSTGQPHEGSGYASQKVLQMAWHRSARQQISDVIQSEA 103 (112)
Q Consensus 24 ~i~ELskek~s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLsqV~tg~phEgS~Y~a~kd~emA~~rv~~~~l~~l~~~~~ 103 (112)
++..|+++=... ...+|...++.|=..|.+=+....++..--| ++. +..++|| ||++..-+.+|-+.+.
T Consensus 21 aV~~Ls~~v~~~-----~~~~y~~~VK~VG~~Lr~Ll~sVd~~~~~l~---~s~--~~EVema-~klL~~DM~eLi~~mk 89 (139)
T PF03623_consen 21 AVMQLSNSVQTA-----KPEEYVDLVKNVGLALRDLLTSVDQILPSLP---SSV--RREVEMA-HKLLSKDMAELISAMK 89 (139)
T ss_dssp HHHHHHHHTTTS-----SHHHHHHHHHHHHHHHHHHHHHHHHHGGGSH---TTS--HHHHHHH-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHhhhccC-----ChHHHHHHHHHHHHHHHHHHHHHHHhhccCC---HHH--HHHHHHH-HHHHHHHHHHHHHHHH
Confidence 455566544322 2567999999999999999999888775554 333 8899999 6886666666666554
No 26
>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.
Probab=31.15 E-value=1.4e+02 Score=18.90 Aligned_cols=56 Identities=21% Similarity=0.277 Sum_probs=39.8
Q ss_pred hHhhHHHHHHHHHHHHHHHHHHHHHhhcCCc-ccHHHHHHHHHHHHHHHHHHHHHHH
Q psy9762 2 ERIQVLDQIEKDIITCLQSAGQALLELSKEK-SSLKQAESQSHNFLKTLSHVETKLT 57 (112)
Q Consensus 2 ~RL~~L~~iEK~I~~~lq~Ag~~i~ELskek-~s~~~~e~~~~~F~~sl~~VE~eLs 57 (112)
+|-+.|..||+.|-.+-.+-.+-=.|+-.-. +....+......|...++.+..+|.
T Consensus 22 ~r~~~i~~~e~~l~ea~~~l~qMe~E~~~~p~s~r~~~~~kl~~yr~~l~~lk~~l~ 78 (79)
T PF05008_consen 22 QRKSLIREIERDLDEAEELLKQMELEVRSLPPSERNQYKSKLRSYRSELKKLKKELK 78 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4666778888888777777777666666543 2556677778888888888887765
No 27
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=29.63 E-value=84 Score=20.96 Aligned_cols=48 Identities=19% Similarity=0.208 Sum_probs=37.8
Q ss_pred HHHHHHHHhhcCCcc-cHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q psy9762 19 QSAGQALLELSKEKS-SLKQAESQSHNFLKTLSHVETKLTEQINYLTQV 66 (112)
Q Consensus 19 q~Ag~~i~ELskek~-s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLsqV 66 (112)
+..+..+..|.+.+. +..++...-..+++.+..++......+.|++..
T Consensus 54 ~~~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~l~dl~~D~P~a~~~la~~ 102 (113)
T smart00544 54 EMYSVLLSRLCQANVISTKQFEKGFWRLLEDIEDLELDIPNAWRNLAEF 102 (113)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhChhhhcccccHHHHHHHH
Confidence 345667788887664 888999999999999998888877788887664
No 28
>PRK07857 hypothetical protein; Provisional
Probab=29.25 E-value=52 Score=23.68 Aligned_cols=29 Identities=10% Similarity=0.343 Sum_probs=24.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhcCCcc
Q psy9762 5 QVLDQIEKDIITCLQSAGQALLELSKEKS 33 (112)
Q Consensus 5 ~~L~~iEK~I~~~lq~Ag~~i~ELskek~ 33 (112)
+.+|+|.++|+.++.-=-.+..+.++-|.
T Consensus 35 ~eID~ID~eIl~LL~eR~~la~eIg~~K~ 63 (106)
T PRK07857 35 EEIDRLDAEILALVKRRTEVSQAIGKARM 63 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46899999999999887777778877664
No 29
>PF14678 FANCI_S4: FANCI solenoid 4; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=29.11 E-value=3.1e+02 Score=22.12 Aligned_cols=90 Identities=22% Similarity=0.219 Sum_probs=58.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCCchhHHHHHH
Q psy9762 6 VLDQIEKDIITCLQSAGQALLELSKEK-SSLKQAESQSHNFLKTLSHVETKLTEQINYLTQVSTGQPHEGSGYASQKVLQ 84 (112)
Q Consensus 6 ~L~~iEK~I~~~lq~Ag~~i~ELskek-~s~~~~e~~~~~F~~sl~~VE~eLs~qI~yLsqV~tg~phEgS~Y~a~kd~e 84 (112)
.++.+|+.|..=|..-.+++.||..-. |.. .++..|++.+...=+-|+.=.+|..++++.++- .-+.+..+
T Consensus 85 ~~~~~E~~lc~qL~~l~~~l~~L~~~~lp~G----~~~d~lLK~l~klY~~Lt~l~K~~~~~~~~~~~----~~~~~Fek 156 (256)
T PF14678_consen 85 NLKSLEESLCSQLGHLVTVLSELVQTALPPG----SCSDKLLKLLTKLYTLLTNLVKYYIQVCSSKQG----APSPKFEK 156 (256)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHS---TT----THHHHHHHHHHHHHHHHHHHHHHHHHHTSTT---------HHHHH
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHhhCCCc----chHHHHHHHHHHHHHHHHHHHHHHHHHhccccC----CccHHHHH
Confidence 467899999999999999999999866 332 356678888888888999999998888754332 33444444
Q ss_pred HHH-HHH-HHHHHHHHHHHHH
Q psy9762 85 MAW-HRS-ARQQISDVIQSEA 103 (112)
Q Consensus 85 mA~-~rv-~~~~l~~l~~~~~ 103 (112)
+.. -.- +...+..+-.++.
T Consensus 157 Lvklsg~~Lt~~~Y~fItyvq 177 (256)
T PF14678_consen 157 LVKLSGKHLTPNVYSFITYVQ 177 (256)
T ss_dssp HHTTHHHHTHHHHHHHHHHHH
T ss_pred HHHHhcccccHHHHHHHHHHH
Confidence 432 111 4444444444443
No 30
>PF01519 DUF16: Protein of unknown function DUF16; InterPro: IPR002862 Proteins that contain this domain are of unknown function. It appears to be confined to proteins from Mycoplasma pneumoniae [].; PDB: 2BA2_C.
Probab=27.31 E-value=2.4e+02 Score=20.34 Aligned_cols=22 Identities=18% Similarity=0.249 Sum_probs=13.7
Q ss_pred hHHHHHHHHHHHH--HHHHHHHHH
Q psy9762 78 ASQKVLQMAWHRS--ARQQISDVI 99 (112)
Q Consensus 78 ~a~kd~emA~~rv--~~~~l~~l~ 99 (112)
+..+-+++-++++ ...||+.|+
T Consensus 78 ~qgktL~~I~~~L~~inkRLD~~E 101 (102)
T PF01519_consen 78 AQGKTLQLILKTLQSINKRLDKME 101 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4444466666666 777777664
No 31
>PF08331 DUF1730: Domain of unknown function (DUF1730); InterPro: IPR013542 This domain of unknown function occurs in iron-sulphur cluster-binding proteins together with the 4Fe-4S binding domain (IPR001450 from INTERPRO).
Probab=26.45 E-value=84 Score=20.50 Aligned_cols=28 Identities=11% Similarity=0.186 Sum_probs=21.0
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q psy9762 75 SGYASQKVLQMAWHRSARQQISDVIQSEADYF 106 (112)
Q Consensus 75 S~Y~a~kd~emA~~rv~~~~l~~l~~~~~~~~ 106 (112)
|.|+-..|. |++++.+|++|.+.+.+..
T Consensus 40 arYA~G~DY----H~vlk~~L~~l~~~i~~~~ 67 (78)
T PF08331_consen 40 ARYAWGRDY----HKVLKKKLEQLAEWIRELG 67 (78)
T ss_pred eehhccCCh----HHHHHHHHHHHHHHHHHHC
Confidence 345544443 8889999999999998765
No 32
>TIGR01808 CM_M_hiGC-arch monofunctional chorismate mutase, high GC gram positive type. This model represents the monofunctional chorismate mutase from high GC gram-positive bacteria and archaea. Trusted annotations from Corynebacterium and Pyrococcus are aparrently the sole chorismate mutase enzymes in their respective genomes. This is coupled with the presence in those genomes of the enzymes of the chorismate pathways both up- and downstream of chorismate mutase.
Probab=26.42 E-value=1e+02 Score=20.16 Aligned_cols=29 Identities=10% Similarity=0.351 Sum_probs=23.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhcCCcc
Q psy9762 5 QVLDQIEKDIITCLQSAGQALLELSKEKS 33 (112)
Q Consensus 5 ~~L~~iEK~I~~~lq~Ag~~i~ELskek~ 33 (112)
+.+|+|..+|+.++.-=..+..+.++-|+
T Consensus 7 ~~ID~ID~~ii~LL~~R~~~~~~i~~~K~ 35 (74)
T TIGR01808 7 EEIDRLDAEILALVKRRAEISQAIGKARM 35 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999887777777777664
No 33
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=26.11 E-value=65 Score=18.99 Aligned_cols=24 Identities=29% Similarity=0.571 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHH-HHHHHhhcC
Q psy9762 7 LDQIEKDIITCLQSA-GQALLELSK 30 (112)
Q Consensus 7 L~~iEK~I~~~lq~A-g~~i~ELsk 30 (112)
||++.++|+.+||.- ..-..+||.
T Consensus 1 lD~~D~~Il~~Lq~d~r~s~~~la~ 25 (42)
T PF13404_consen 1 LDELDRKILRLLQEDGRRSYAELAE 25 (42)
T ss_dssp --HHHHHHHHHHHH-TTS-HHHHHH
T ss_pred CCHHHHHHHHHHHHcCCccHHHHHH
Confidence 688999999999874 334455544
No 34
>PF09246 PHAT: PHAT; InterPro: IPR015327 The PHAT (pseudo-HEAT analogous topology) domain assumes a structure consisting of a layer of three parallel helices packed against a layer of two antiparallel helices, into a cylindrical shaped five-helix bundle. It is found in the RNA-binding protein Smaug, where it is essential for high-affinity RNA binding []. ; PDB: 1OXJ_A.
Probab=25.97 E-value=1.5e+02 Score=21.72 Aligned_cols=54 Identities=30% Similarity=0.335 Sum_probs=33.2
Q ss_pred HhhHHHHHHHHHHHHH-HHHHHHHHhhcC-----Ccc-cHHHHHHHHHHHHHHHHHHHHHH
Q psy9762 3 RIQVLDQIEKDIITCL-QSAGQALLELSK-----EKS-SLKQAESQSHNFLKTLSHVETKL 56 (112)
Q Consensus 3 RL~~L~~iEK~I~~~l-q~Ag~~i~ELsk-----ek~-s~~~~e~~~~~F~~sl~~VE~eL 56 (112)
|-.-|-.+||++..-= -.=+++++||-+ =|| ....=+.-..+|+|.|.-|=+.|
T Consensus 1 Ry~tL~~lEkdLl~G~~~~L~~v~EELtnIv~TPMKP~~~~~pedI~~qF~KVL~~v~s~l 61 (108)
T PF09246_consen 1 RYNTLLRLEKDLLSGQKMQLSNVLEELTNIVLTPMKPSEEDQPEDIPGQFTKVLDLVCSIL 61 (108)
T ss_dssp HHHHHHHHHHHHHTT--S-HHHHHHHHHTTTTS----TT--S-G-HHHHHHHHHHHHHHHH
T ss_pred CchHHHHHHHHHHcCcHHHHHHHHHHHHHHhcCCCCccCCCCcchHHHHHHHHHHHHHHHH
Confidence 3445778999998322 124679999866 455 23333888999999999887544
No 35
>PF11328 DUF3130: Protein of unknown function (DUF3130; InterPro: IPR021477 This bacterial family of proteins has no known function.
Probab=25.40 E-value=28 Score=24.71 Aligned_cols=35 Identities=26% Similarity=0.410 Sum_probs=28.2
Q ss_pred CCchhHHHHHHHHHHHH-----HHHHHHHHHHHHHhhhcc
Q psy9762 74 GSGYASQKVLQMAWHRS-----ARQQISDVIQSEADYFGV 108 (112)
Q Consensus 74 gS~Y~a~kd~emA~~rv-----~~~~l~~l~~~~~~~~~~ 108 (112)
|-.|..-|+.-||.+|- .|+-|-+|-+..++++.|
T Consensus 24 ~~~y~plK~gnMaysraNsin~~r~Al~dLv~~Ve~fq~v 63 (90)
T PF11328_consen 24 GVEYLPLKNGNMAYSRANSINQLRTALIDLVDVVENFQQV 63 (90)
T ss_pred CcccccccCCCeehhhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 44599999999999998 788888888887776654
No 36
>PRK01203 prefoldin subunit alpha; Provisional
Probab=25.03 E-value=49 Score=24.56 Aligned_cols=28 Identities=18% Similarity=0.234 Sum_probs=21.7
Q ss_pred CCchhHHHHHHHHHHHH--HHHHHHHHHHHHHh
Q psy9762 74 GSGYASQKVLQMAWHRS--ARQQISDVIQSEAD 104 (112)
Q Consensus 74 gS~Y~a~kd~emA~~rv--~~~~l~~l~~~~~~ 104 (112)
|++|..+|+.+ +++ +..++.+|+..+.+
T Consensus 76 GTGy~VEK~~e---~kie~L~~~ie~Le~~i~~ 105 (130)
T PRK01203 76 GSGVYIAEERE---RTIERLKENLEDLKDSIQK 105 (130)
T ss_pred CCCeEEEecHH---HHHHHHHHHHHHHHHHHHH
Confidence 89999999988 466 77777777777664
No 37
>PF12731 Mating_N: Mating-type protein beta 1; InterPro: IPR024333 This entry represents a group of homeodomain-containing transcription factor proteins involved in mating [].
Probab=24.79 E-value=2e+02 Score=19.62 Aligned_cols=49 Identities=24% Similarity=0.303 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHHHh-hcCCcccHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9762 11 EKDIITCLQSAGQALLE-LSKEKSSLKQAESQSHNFLKTLSHVETKLTEQ 59 (112)
Q Consensus 11 EK~I~~~lq~Ag~~i~E-Lskek~s~~~~e~~~~~F~~sl~~VE~eLs~q 59 (112)
+..|..-|+++-..+.. |..+..+-..|-+++..|...+...+..|++.
T Consensus 11 D~~I~~~L~~~e~~fl~sL~~g~~~L~~F~~~w~~f~~~~~s~~~~L~~~ 60 (95)
T PF12731_consen 11 DADIRQALQALEADFLSSLRGGSDALESFLSSWSSFDATLQSCHDHLSDE 60 (95)
T ss_pred HHHHHHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHHHHHhccccCHH
Confidence 45666666666554443 44444456889999999988888777666554
No 38
>KOG0809|consensus
Probab=23.36 E-value=4.7e+02 Score=22.30 Aligned_cols=62 Identities=16% Similarity=0.247 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCc----ccHHHHH-HHHHHHHHHHHHHHHHHH-HHHHhhhhhc
Q psy9762 6 VLDQIEKDIITCLQSAGQALLELSKEK----SSLKQAE-SQSHNFLKTLSHVETKLT-EQINYLTQVS 67 (112)
Q Consensus 6 ~L~~iEK~I~~~lq~Ag~~i~ELskek----~s~~~~e-~~~~~F~~sl~~VE~eLs-~qI~yLsqV~ 67 (112)
.++.+=++|..+++++-..|..+++.. |+...+. +...-|...|+..=.++. .|=+||.+.-
T Consensus 101 ~IE~ltq~Itqll~~cqk~iq~~~a~~n~~~~~e~~~~~n~~~~la~~LQ~~s~~fR~~Qs~YLK~l~ 168 (305)
T KOG0809|consen 101 EIEELTQEITQLLQKCQKLIQRLSASLNQLSPSERLLRKNAQGYLALQLQTLSREFRGLQSKYLKRLR 168 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 467778999999999999999998743 4666666 344466677777777775 5888998875
No 39
>PF05659 RPW8: Arabidopsis broad-spectrum mildew resistance protein RPW8; InterPro: IPR008808 This entry represents the RPW8 domain found in several broad-spectrum mildew resistance proteins from Arabidopsis thaliana and other dicots. Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The R protein-mediated defences typically involve a rapid, localized necrosis, or hypersensitive response (HR), at the site of infection, and the localised formation of antimicrobial chemicals and proteins that restrict growth of the pathogen. The A. thaliana locus Resistance to Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes: RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localised, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance [, ]. RPW8.1 and RPW8.2 share similarity with an ~150 amino acid module forming the N terminus of a group of disease resistance proteins, which have a nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) [, ]. The RPW8 domain sequences contain a predicted N-terminal transmembrane (TM) region or possibly a signal peptide, and a coiled-coil (CC) motif [].
Probab=22.81 E-value=3.2e+02 Score=20.20 Aligned_cols=85 Identities=22% Similarity=0.322 Sum_probs=49.5
Q ss_pred HHHHHHhhcCCcccHHHHHHHHHHHHHHHHHHHHHHH------HHHHhhhhhccCCCCCCCchhHHH-------H-----
Q psy9762 21 AGQALLELSKEKSSLKQAESQSHNFLKTLSHVETKLT------EQINYLTQVSTGQPHEGSGYASQK-------V----- 82 (112)
Q Consensus 21 Ag~~i~ELskek~s~~~~e~~~~~F~~sl~~VE~eLs------~qI~yLsqV~tg~phEgS~Y~a~k-------d----- 82 (112)
.|.++.||-|. -..+-+.+..|..+++.+++.|. .+|.|++..- .+|. ..-..--+ +
T Consensus 11 lG~~~~eLlk~---v~~~~~k~~~fk~~l~~L~sTl~~i~P~i~eI~~~~~el-d~~~-~ee~e~L~~~L~~g~~LV~k~ 85 (147)
T PF05659_consen 11 LGAVFGELLKA---VIDASKKSLSFKSILKRLESTLESIIPIIKEIDKLNVEL-DRPR-QEEIERLKELLEKGKELVEKC 85 (147)
T ss_pred HHHHHHHHHHH---HHHHHHHHHhhhhHHHHHHHHHHHhhhHHHHHHHHhhhc-CCch-hHHHHHHHHHHHHHHHHHHHh
Confidence 46777888753 22444566778888888887765 5899988755 3331 11110000 0
Q ss_pred HHH----HHHHH-HHHHHHHHHHHHHhhhcccc
Q psy9762 83 LQM----AWHRS-ARQQISDVIQSEADYFGVDL 110 (112)
Q Consensus 83 ~em----A~~rv-~~~~l~~l~~~~~~~~~~~~ 110 (112)
..+ .+.+. ...+|.+++..+..++.+|+
T Consensus 86 sk~~r~n~~kk~~y~~Ki~~le~~l~~f~~v~~ 118 (147)
T PF05659_consen 86 SKVRRWNLYKKPRYARKIEELEESLRRFIQVDL 118 (147)
T ss_pred ccccHHHHHhhHhHHHHHHHHHHHHHHHhcchh
Confidence 000 11223 66788888888888877764
No 40
>KOG3557|consensus
Probab=22.80 E-value=3.2e+02 Score=25.83 Aligned_cols=54 Identities=26% Similarity=0.282 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcC--------------------Cc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy9762 6 VLDQIEKDIITCLQSAGQALLELSK--------------------EK-SSLKQAESQSHNFLKTLSHVETKLTEQIN 61 (112)
Q Consensus 6 ~L~~iEK~I~~~lq~Ag~~i~ELsk--------------------ek-~s~~~~e~~~~~F~~sl~~VE~eLs~qI~ 61 (112)
.||+||+=|. =||.|+.|-.||.. .+ |+...|-..-..|+-+.+-+ ..|..||+
T Consensus 276 ~fDDIE~Fva-RLQkAAeA~reLe~Rkr~~K~~k~~pgeG~LTlRarpP~e~EfvD~fqK~KlsFNLL-AKLk~hI~ 350 (721)
T KOG3557|consen 276 VFDDIESFVA-RLQKAAEAARELEQRKRGRKSKKRAPGEGLLTLRARPPSEAEFVDCFQKIKLSFNLL-AKLKGHIH 350 (721)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHHhhcccccCCCCCCceeEeecCCCchHHHHHHHHHHHHHHHHH-HHHHhhcc
Confidence 5789998665 57999999999975 22 35566777777777666654 67888875
No 41
>PF03997 VPS28: VPS28 protein; InterPro: IPR007143 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ].; PDB: 2J9W_B 2J9U_C 2G3K_A 2F66_E 2F6M_D 2J9V_A 2CAZ_E 2P22_B.
Probab=22.32 E-value=1.3e+02 Score=23.42 Aligned_cols=62 Identities=16% Similarity=0.260 Sum_probs=39.4
Q ss_pred ccHHHHHHHHHHHHH----------HHHHHHHHHHHHHHhhhhhccCCCCCCCchhHHHHHHHHHHHH-HHHHH
Q psy9762 33 SSLKQAESQSHNFLK----------TLSHVETKLTEQINYLTQVSTGQPHEGSGYASQKVLQMAWHRS-ARQQI 95 (112)
Q Consensus 33 ~s~~~~e~~~~~F~~----------sl~~VE~eLs~qI~yLsqV~tg~phEgS~Y~a~kd~emA~~rv-~~~~l 95 (112)
++.+.+-..+..|.+ ++.+++-.|++=+..|..|+. .|-+-.+=+.-+.|..-+++. +.++|
T Consensus 92 ~~ak~Vae~t~~FIT~mDaLKLn~~a~DqLhPlL~dL~~slnr~~~-~~~dfe~r~kl~~Wl~~Ln~m~asdeL 164 (188)
T PF03997_consen 92 NSAKLVAEATQNFITLMDALKLNYRAKDQLHPLLSDLMQSLNRVTD-LPPDFEGRSKLVEWLIKLNGMKASDEL 164 (188)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHTT--BHHHHHHHHHHHHHHHHHCTT-S-TT-CCHHHHHHHHHHHHTS-TT-B-
T ss_pred hHHHHHHHHhChhhhhhHHHhccchhHhhHhhHHHHHHHHHhccCC-CCCCCccHHHHHHHHHHHhCCCccccc
Confidence 568888889999985 556788899999999999974 332233333444455555544 44444
No 42
>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system [].
Probab=21.66 E-value=1.3e+02 Score=20.63 Aligned_cols=19 Identities=32% Similarity=0.393 Sum_probs=14.9
Q ss_pred hhHHHHHHHHHHHHHHHHH
Q psy9762 4 IQVLDQIEKDIITCLQSAG 22 (112)
Q Consensus 4 L~~L~~iEK~I~~~lq~Ag 22 (112)
++.|+.||++|..+-+.|.
T Consensus 65 l~~Id~Ie~~V~~LE~~v~ 83 (99)
T PF10046_consen 65 LQQIDQIEEQVTELEQTVY 83 (99)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 6788999999887766654
No 43
>PF02185 HR1: Hr1 repeat; InterPro: IPR000861 The HR1 repeat was first described as a three times repeated homology region of the N-terminal non-catalytic part of protein kinase PRK1(PKN) []. The first two of these repeats were later shown to bind the small G protein rho [, ] known to activate PKN in its GTP-bound form. Similar rho-binding domains also occur in a number of other protein kinases and in the rho-binding proteins rhophilin and rhotekin. Recently, the structure of the N-terminal HR1 repeat complexed with RhoA has been determined by X-ray crystallography []. It forms an antiparallel coiled-coil fold termed an ACC finger. This entry includes domains found within rho-associated protein kinases.; GO: 0007165 signal transduction, 0005622 intracellular; PDB: 1CXZ_B 3O0Z_C 2RMK_B 1URF_A.
Probab=21.54 E-value=2.3e+02 Score=17.93 Aligned_cols=53 Identities=23% Similarity=0.295 Sum_probs=31.1
Q ss_pred HHHHHHHHHHH---HHHHHHHHHHhhcCCccc-HHHHHHHHHHHHHHHHHHHHHHHH
Q psy9762 6 VLDQIEKDIIT---CLQSAGQALLELSKEKSS-LKQAESQSHNFLKTLSHVETKLTE 58 (112)
Q Consensus 6 ~L~~iEK~I~~---~lq~Ag~~i~ELskek~s-~~~~e~~~~~F~~sl~~VE~eLs~ 58 (112)
+++++.++|-- +.+-|-..+.-++++++. ...++..-.+=..-|..++.+|..
T Consensus 2 ~i~~L~~~i~~E~ki~~Gae~m~~~~~t~~~~~~~~~~~~l~~s~~kI~~L~~~L~~ 58 (70)
T PF02185_consen 2 RIEELQKKIDKELKIKEGAENMLQAYSTDKKKVLSEAESQLRESNQKIELLREQLEK 58 (70)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCH-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555555542 333344444444888876 666776666666666666666654
No 44
>PF14523 Syntaxin_2: Syntaxin-like protein; PDB: 2DNX_A.
Probab=20.91 E-value=2.6e+02 Score=18.32 Aligned_cols=50 Identities=16% Similarity=0.216 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCC-------cccHHHHHHHHHHHHHHHHHHHHH
Q psy9762 6 VLDQIEKDIITCLQSAGQALLELSKE-------KSSLKQAESQSHNFLKTLSHVETK 55 (112)
Q Consensus 6 ~L~~iEK~I~~~lq~Ag~~i~ELske-------k~s~~~~e~~~~~F~~sl~~VE~e 55 (112)
.+..+-.++-.+++..+..|..|..- ++..-+.+.=+.+|..++++.+..
T Consensus 34 ~i~~~~~~~~~l~k~~~~~l~~l~~~~~~~~~~~~~k~~~~KL~~df~~~l~~fq~~ 90 (102)
T PF14523_consen 34 KIHQLIQKTNQLIKEISELLKKLNSLSSDRSNDRQQKLQREKLSRDFKEALQEFQKA 90 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHSH----HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666777777788888888887665 234456777788888888887754
No 45
>TIGR01462 greA transcription elongation factor GreA. In the Chlamydias and some spirochetes, the region described by this model is found as the C-terminal region of a much larger protein.
Probab=20.86 E-value=3.4e+02 Score=19.72 Aligned_cols=35 Identities=20% Similarity=0.146 Sum_probs=23.5
Q ss_pred ccCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy9762 67 STGQPHEGSGYASQKVLQMAWHRSARQQISDVIQSEADY 105 (112)
Q Consensus 67 ~tg~phEgS~Y~a~kd~emA~~rv~~~~l~~l~~~~~~~ 105 (112)
.-|-=-|++.|.+.++-+... ..|+.+|++.++..
T Consensus 34 ~~gDl~Ena~y~aak~~~~~~----e~ri~~L~~~L~~a 68 (151)
T TIGR01462 34 EHGDLSENAEYHAAKEEQGFN----EGRIAELEDLLANA 68 (151)
T ss_pred HCCChhhccchHHHHHHHHHH----HHHHHHHHHHHHhC
Confidence 346777899999988876655 34555666655543
No 46
>PF07464 ApoLp-III: Apolipophorin-III precursor (apoLp-III); InterPro: IPR010009 This family consists of several insect apolipoprotein-III sequences. Exchangeable apolipoproteins constitute a functionally important family of proteins that play critical roles in lipid transport and lipoprotein metabolism. Apolipophorin III (apoLp-III) is a prototypical exchangeable apolipoprotein found in many insect species that functions in transport of diacylglycerol (DAG) from the fat body lipid storage depot to flight muscles in the adult life stage [].; GO: 0008289 lipid binding, 0006869 lipid transport, 0005576 extracellular region; PDB: 1EQ1_A.
Probab=20.38 E-value=3.9e+02 Score=20.20 Aligned_cols=53 Identities=19% Similarity=0.245 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCcc---cHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy9762 10 IEKDIITCLQSAGQALLELSKEKS---SLKQAESQSHNFLKTLSHVETKLTEQINY 62 (112)
Q Consensus 10 iEK~I~~~lq~Ag~~i~ELskek~---s~~~~e~~~~~F~~sl~~VE~eLs~qI~y 62 (112)
||+.|-.+...=+.-+..+-+-+. =.+.+..++..|...|+.+-..|.++|.=
T Consensus 1 ~~~~~~e~~~~~~~~~~~~~~~~~~~Ev~~aik~~sd~~~~~l~~~~~~l~eeik~ 56 (155)
T PF07464_consen 1 IQQHAQEFQKEFQEQVNKLLGSQNQQEVVKAIKEQSDSVAQQLQNVSSSLQEEIKD 56 (155)
T ss_dssp HHHHHHHHHHHHHHHHHHHTSS--SS-SSHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred CchHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHh
Confidence 677788888888888888875542 45788899999999999999999999875
No 47
>TIGR01807 CM_P2 chorismate mutase domain of proteobacterial P-protein, clade 2. This model represents one of two separate clades of the chorismate mutase domain of the gamma and beta and epsilon proteobacterial "P-protein" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain. It is also found in Aquifex aolicus.
Probab=20.24 E-value=1.3e+02 Score=19.41 Aligned_cols=29 Identities=17% Similarity=0.255 Sum_probs=24.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhcCCcc
Q psy9762 5 QVLDQIEKDIITCLQSAGQALLELSKEKS 33 (112)
Q Consensus 5 ~~L~~iEK~I~~~lq~Ag~~i~ELskek~ 33 (112)
+.+|+|..+|+.++.-=..+..+.+.-|.
T Consensus 6 ~~ID~iD~~iv~Ll~~R~~~~~~i~~~K~ 34 (76)
T TIGR01807 6 NKIDAIDDRILDLLSERATYAQAVGELKG 34 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999987778888877664
Done!