Query psy11354
Match_columns 120
No_of_seqs 145 out of 244
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 16:14:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11354.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11354hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0272|consensus 99.7 2.3E-16 5.1E-21 136.2 7.8 70 50-119 16-85 (459)
2 smart00500 SFM Splicing Factor 99.6 7.7E-16 1.7E-20 96.5 4.6 37 82-118 1-37 (44)
3 PF08799 PRP4: pre-mRNA proces 99.6 3.5E-15 7.6E-20 87.1 3.5 30 87-116 1-30 (30)
4 KOG2808|consensus 97.4 0.00014 3E-09 62.0 3.6 33 84-116 77-109 (341)
5 PF04900 Fcf1: Fcf1; InterPro 60.9 3.4 7.4E-05 28.4 0.5 25 78-102 67-92 (101)
6 COG1412 Uncharacterized protei 44.7 16 0.00034 27.7 1.8 28 77-104 99-126 (136)
7 PF12535 Nudix_N: Hydrolase of 43.5 13 0.00027 24.2 1.0 35 85-119 5-41 (58)
8 PF08294 TIM21: TIM21; InterP 39.2 2.1 4.4E-05 32.3 -3.7 22 84-108 53-75 (145)
9 PF14842 FliG_N: FliG N-termin 37.2 76 0.0017 22.2 4.3 41 55-95 46-87 (108)
10 smart00540 LEM in nuclear memb 33.4 42 0.0009 20.9 2.1 19 83-101 7-25 (44)
11 PF13104 DUF3956: Protein of u 33.4 30 0.00066 21.8 1.5 14 86-99 31-44 (45)
12 PF02348 CTP_transf_3: Cytidyl 32.6 37 0.0008 25.1 2.2 44 74-117 39-82 (217)
13 PF06628 Catalase-rel: Catalas 27.5 18 0.0004 23.6 -0.2 20 12-31 11-30 (68)
14 COG0514 RecQ Superfamily II DN 27.4 94 0.002 28.8 4.2 34 12-45 255-299 (590)
15 PF10454 DUF2458: Protein of u 26.2 1.1E+02 0.0024 23.3 3.7 32 86-119 109-147 (150)
16 PF08619 Nha1_C: Alkali metal 25.6 46 0.001 29.2 1.8 19 97-115 403-421 (434)
17 cd06321 PBP1_ABC_sugar_binding 25.1 1E+02 0.0022 22.9 3.4 46 59-104 43-91 (271)
18 PF11199 DUF2891: Protein of u 24.4 32 0.0007 29.6 0.7 22 1-22 24-45 (326)
19 cd04374 RhoGAP_Graf RhoGAP_Gra 23.4 1.2E+02 0.0026 23.6 3.6 36 84-119 90-136 (203)
20 cd06285 PBP1_LacI_like_7 Ligan 23.2 1E+02 0.0022 22.9 3.0 45 60-104 42-87 (265)
21 cd06277 PBP1_LacI_like_1 Ligan 23.2 80 0.0017 23.5 2.5 41 64-104 49-89 (268)
22 PF04871 Uso1_p115_C: Uso1 / p 22.6 51 0.0011 24.5 1.4 14 86-99 102-115 (136)
23 cd06310 PBP1_ABC_sugar_binding 22.3 1.5E+02 0.0033 22.0 3.9 45 60-104 44-91 (273)
24 cd01542 PBP1_TreR_like Ligand- 21.3 94 0.002 22.8 2.5 45 60-104 42-87 (259)
25 cd01538 PBP1_ABC_xylose_bindin 21.1 1.2E+02 0.0026 23.2 3.2 46 59-104 41-89 (288)
26 PF10673 DUF2487: Protein of u 20.6 2.1E+02 0.0046 21.7 4.4 47 56-117 31-78 (142)
27 PF08245 Mur_ligase_M: Mur lig 20.3 34 0.00074 24.9 -0.0 30 77-106 110-139 (188)
No 1
>KOG0272|consensus
Probab=99.65 E-value=2.3e-16 Score=136.16 Aligned_cols=70 Identities=47% Similarity=0.688 Sum_probs=63.6
Q ss_pred ccccccHhhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHhhCCCccccCCChHHHHHHHHHHHhhc
Q psy11354 50 VYMEIDDEMAKDKQALLQEFERRKKARHVNVSTDDNQVKLNLRQLGEPICLFGEGPAERRSRLRDLLSSL 119 (120)
Q Consensus 50 e~~~~~~~~~~~~~~~L~e~E~~rr~r~~~vPT~D~eVr~~LR~LgePi~LFGE~~~~RR~RLr~ll~~~ 119 (120)
+++.......+.++++|++|+++++++.+.|||+|.+|+..||.||||||+|||++.+||+||++||+..
T Consensus 16 ~~~e~~~q~~~~~a~~l~e~e~r~ra~~l~vpteD~evr~~Lr~l~ePi~~fgE~~~~RR~RL~~lL~~~ 85 (459)
T KOG0272|consen 16 EQSEGSTQNERRQAALLAEFERRRRARLLKVPTEDSEVRSPLRALKEPITLFGEDALARRQRLRELLSVA 85 (459)
T ss_pred hhhhhhhhhHHHHHHHHHHhhHHhhHHHhcCCccHHHHHHHHHHhCCCCcccCCCHHHHHHHHHHHHHHh
Confidence 4455555567899999999999999999999999999999999999999999999999999999999853
No 2
>smart00500 SFM Splicing Factor Motif, present in Prp18 and Pr04.
Probab=99.61 E-value=7.7e-16 Score=96.51 Aligned_cols=37 Identities=57% Similarity=0.842 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHhhCCCccccCCChHHHHHHHHHHHhh
Q psy11354 82 TDDNQVKLNLRQLGEPICLFGEGPAERRSRLRDLLSS 118 (120)
Q Consensus 82 T~D~eVr~~LR~LgePi~LFGE~~~~RR~RLr~ll~~ 118 (120)
|+|.+|+.+||+||||||||||++.+||+||++|+..
T Consensus 1 ~~d~eV~~~LR~lgePi~lFGE~~~~Rr~RL~~ll~~ 37 (44)
T smart00500 1 LPDSEVIRRLRELGEPITLFGEDDQERRQRLRQLLIV 37 (44)
T ss_pred CCHHHHHHHHHHcCCCeeecCCChHHHHHHHHHHHHc
Confidence 6899999999999999999999999999999999864
No 3
>PF08799 PRP4: pre-mRNA processing factor 4 (PRP4) like; InterPro: IPR014906 This small protein is found on PRP4 ribonuleoproteins. PRP4 is a U4/U6 small nuclear ribonucleoprotein that is involved in pre-mRNA processing. ; PDB: 1MZW_B 2DK4_A.
Probab=99.55 E-value=3.5e-15 Score=87.06 Aligned_cols=30 Identities=67% Similarity=1.056 Sum_probs=24.8
Q ss_pred HHHHHHhhCCCccccCCChHHHHHHHHHHH
Q psy11354 87 VKLNLRQLGEPICLFGEGPAERRSRLRDLL 116 (120)
Q Consensus 87 Vr~~LR~LgePi~LFGE~~~~RR~RLr~ll 116 (120)
|+++||+||||||||||++.+|++||++|+
T Consensus 1 V~~~LR~lgePi~lFGE~~~~R~~RLr~l~ 30 (30)
T PF08799_consen 1 VRRRLRELGEPITLFGETDADRRERLRRLL 30 (30)
T ss_dssp HHHHHHHCT--SCETT--HHHHHHHHHHHH
T ss_pred ChHHHHhcCCChhhhCCChHHHHHHHHHhC
Confidence 789999999999999999999999999985
No 4
>KOG2808|consensus
Probab=97.41 E-value=0.00014 Score=61.97 Aligned_cols=33 Identities=42% Similarity=0.625 Sum_probs=30.8
Q ss_pred HHHHHHHHHhhCCCccccCCChHHHHHHHHHHH
Q psy11354 84 DNQVKLNLRQLGEPICLFGEGPAERRSRLRDLL 116 (120)
Q Consensus 84 D~eVr~~LR~LgePi~LFGE~~~~RR~RLr~ll 116 (120)
-.+|..+||++|+||+||||++.++++||+.+.
T Consensus 77 ~sev~~rLre~~~Pi~lfGEtd~~~k~rl~~~e 109 (341)
T KOG2808|consen 77 RSEVIRRLRERGEPIILFGETDKSAKDRLRQKE 109 (341)
T ss_pred hHHHHHHHHHcCCCccccCCCCHHHHHHHHHhc
Confidence 578999999999999999999999999998764
No 5
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=60.88 E-value=3.4 Score=28.41 Aligned_cols=25 Identities=28% Similarity=0.449 Sum_probs=23.2
Q ss_pred cCCCCCHHHHHHHHH-hhCCCccccC
Q psy11354 78 VNVSTDDNQVKLNLR-QLGEPICLFG 102 (120)
Q Consensus 78 ~~vPT~D~eVr~~LR-~LgePi~LFG 102 (120)
+.|=|.|.++|.+|| .-|-|+..+.
T Consensus 67 ~~VaT~D~~Lr~~lr~~~GvPvi~l~ 92 (101)
T PF04900_consen 67 YIVATQDKELRRRLRKIPGVPVIYLR 92 (101)
T ss_pred EEEEecCHHHHHHHhcCCCCCEEEEE
Confidence 889999999999999 9999998876
No 6
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=44.74 E-value=16 Score=27.65 Aligned_cols=28 Identities=29% Similarity=0.447 Sum_probs=24.0
Q ss_pred hcCCCCCHHHHHHHHHhhCCCccccCCC
Q psy11354 77 HVNVSTDDNQVKLNLRQLGEPICLFGEG 104 (120)
Q Consensus 77 ~~~vPT~D~eVr~~LR~LgePi~LFGE~ 104 (120)
...|=|+|.+++++||.-|-|+..+..+
T Consensus 99 ~~iVaTnD~eLk~rlr~~GIPvi~lr~r 126 (136)
T COG1412 99 RYIVATNDKELKRRLRENGIPVITLRQR 126 (136)
T ss_pred CEEEEeCCHHHHHHHHHcCCCEEEEeCC
Confidence 4668999999999999999999877643
No 7
>PF12535 Nudix_N: Hydrolase of X-linked nucleoside diphosphate N terminal ; PDB: 3Q1P_B 3Q4I_B.
Probab=43.52 E-value=13 Score=24.21 Aligned_cols=35 Identities=17% Similarity=0.323 Sum_probs=25.5
Q ss_pred HHHHHHHHhhCCCccccCCChHH--HHHHHHHHHhhc
Q psy11354 85 NQVKLNLRQLGEPICLFGEGPAE--RRSRLRDLLSSL 119 (120)
Q Consensus 85 ~eVr~~LR~LgePi~LFGE~~~~--RR~RLr~ll~~~ 119 (120)
.++..+|..+.+----|+.+++| |.++|+++..++
T Consensus 5 l~~a~~lqaiAqtGL~Yskd~yD~ERy~~lr~ia~el 41 (58)
T PF12535_consen 5 LEWAKRLQAIAQTGLAYSKDPYDRERYEELREIAAEL 41 (58)
T ss_dssp HHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhhhhCCChhhHHHHHHHHHHHHHH
Confidence 35677888888888899999965 999999987753
No 8
>PF08294 TIM21: TIM21; InterPro: IPR013261 TIM21 interacts with the outer mitochondrial TOM complex and promotes the insertion of proteins into the inner mitochondrial membrane [].; PDB: 2CIU_A.
Probab=39.23 E-value=2.1 Score=32.33 Aligned_cols=22 Identities=45% Similarity=0.693 Sum_probs=13.0
Q ss_pred HHHHHHHHHhhCCCccccCCChH-HH
Q psy11354 84 DNQVKLNLRQLGEPICLFGEGPA-ER 108 (120)
Q Consensus 84 D~eVr~~LR~LgePi~LFGE~~~-~R 108 (120)
|++|...| |+||+-+||... .|
T Consensus 53 d~~v~~~L---G~~ikayGe~~~~~R 75 (145)
T PF08294_consen 53 DPRVQDLL---GEPIKAYGEETGRNR 75 (145)
T ss_dssp -HHHHHHT-------EEEE-EEE-SS
T ss_pred CHHHHHHh---CCCeEEecCCCCCCc
Confidence 77788777 999999999886 66
No 9
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=37.15 E-value=76 Score=22.21 Aligned_cols=41 Identities=22% Similarity=0.248 Sum_probs=24.2
Q ss_pred cHhhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHH-hhC
Q psy11354 55 DDEMAKDKQALLQEFERRKKARHVNVSTDDNQVKLNLR-QLG 95 (120)
Q Consensus 55 ~~~~~~~~~~~L~e~E~~rr~r~~~vPT~D~eVr~~LR-~Lg 95 (120)
..-.++...++|.+|...-......++-...-++..|. .||
T Consensus 46 ~~v~~~~~~~Vl~EF~~~~~~~~~~~~gg~~~~~~lL~~alg 87 (108)
T PF14842_consen 46 GSVSPEEVEEVLEEFYDEIRAQGGIVSGGRDFARRLLEKALG 87 (108)
T ss_dssp ----HHHHHHHHHHHHHHHHHTT---S-HHHHHHH-HHHHS-
T ss_pred CCCCHHHHHHHHHHHHHHHHHccccccChHHHHHHHHHHHCC
Confidence 33446788899999999777667777777888888873 444
No 10
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=33.42 E-value=42 Score=20.87 Aligned_cols=19 Identities=26% Similarity=0.452 Sum_probs=15.7
Q ss_pred CHHHHHHHHHhhCCCcccc
Q psy11354 83 DDNQVKLNLRQLGEPICLF 101 (120)
Q Consensus 83 ~D~eVr~~LR~LgePi~LF 101 (120)
.|.|+++.|.++|.|...-
T Consensus 7 Sd~eL~~~L~~~G~~~gPI 25 (44)
T smart00540 7 SDAELRAELKQYGLPPGPI 25 (44)
T ss_pred CHHHHHHHHHHcCCCCCCc
Confidence 5899999999999976433
No 11
>PF13104 DUF3956: Protein of unknown function (DUF3956)
Probab=33.39 E-value=30 Score=21.79 Aligned_cols=14 Identities=64% Similarity=1.013 Sum_probs=12.2
Q ss_pred HHHHHHHhhCCCcc
Q psy11354 86 QVKLNLRQLGEPIC 99 (120)
Q Consensus 86 eVr~~LR~LgePi~ 99 (120)
.|.-.|+.||-|||
T Consensus 31 qval~l~~lgipic 44 (45)
T PF13104_consen 31 QVALTLIALGIPIC 44 (45)
T ss_pred HHHHHHHHcCCccc
Confidence 57888999999997
No 12
>PF02348 CTP_transf_3: Cytidylyltransferase; InterPro: IPR003329 Synonym(s): CMP-N-acetylneuraminic acid synthetase Acylneuraminate cytidylyltransferase (2.7.7.43 from EC) (CMP-NeuAc synthetase) catalyzes the reaction of CTP and NeuAc to form CMP-NeuAc, which is the nucleotide sugar donor used by sialyltransferases []. The outer membrane lipooligosaccharides of some microorganisms contain terminal sialic acid attached to N-acetyllactosamine and so this modification may be important in pathogenesis.; GO: 0009103 lipopolysaccharide biosynthetic process; PDB: 3K8D_C 1VH1_B 3K8E_C 1QWJ_A 3EWI_A 1VIC_B 3DUV_A 1VH3_C 3TQD_A 2Y6P_C ....
Probab=32.64 E-value=37 Score=25.12 Aligned_cols=44 Identities=16% Similarity=0.242 Sum_probs=33.9
Q ss_pred hhhhcCCCCCHHHHHHHHHhhCCCccccCCChHHHHHHHHHHHh
Q psy11354 74 KARHVNVSTDDNQVKLNLRQLGEPICLFGEGPAERRSRLRDLLS 117 (120)
Q Consensus 74 r~r~~~vPT~D~eVr~~LR~LgePi~LFGE~~~~RR~RLr~ll~ 117 (120)
....+.|.|+|.++...+...|-.+.+|-+...+=..|..+.+.
T Consensus 39 ~~d~IvVaTd~~~i~~~~~~~g~~v~~~~~~~~~~~~r~~~~~~ 82 (217)
T PF02348_consen 39 LIDEIVVATDDEEIDDIAEEYGAKVIFRRGSLADDTDRFIEAIK 82 (217)
T ss_dssp TTSEEEEEESSHHHHHHHHHTTSEEEE--TTSSSHHHHHHHHHH
T ss_pred CCCeEEEeCCCHHHHHHHHHcCCeeEEcChhhcCCcccHHHHHH
Confidence 34457899999999999999999998888877776677766554
No 13
>PF06628 Catalase-rel: Catalase-related immune-responsive; InterPro: IPR010582 Catalases (1.11.1.6 from EC) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects []. Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (IPR000763 from INTERPRO) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (IPR007760 from INTERPRO) that are found in bacteria []. This entry represents a small conserved region within catalase enzymes that carries the immune-responsive amphipathic octa-peptide that is recognised by T cells [].; PDB: 2CAH_A 1NM0_A 1H7K_A 1E93_A 1H6N_A 3HB6_A 2CAG_A 1M85_A 1MQF_A 1A4E_C ....
Probab=27.48 E-value=18 Score=23.56 Aligned_cols=20 Identities=35% Similarity=0.504 Sum_probs=17.7
Q ss_pred hcccccccchHHHHHHHHhh
Q psy11354 12 KQNTVHYGSLEEQERKRLAA 31 (120)
Q Consensus 12 k~~~i~yGsLee~er~rl~~ 31 (120)
.+.+.||-+|.+.||++|..
T Consensus 11 ~Qa~~ly~~l~~~er~~lv~ 30 (68)
T PF06628_consen 11 SQARDLYRVLSDEERERLVE 30 (68)
T ss_dssp HHHHHHHHHSSHHHHHHHHH
T ss_pred hhHHHHHHHCCHHHHHHHHH
Confidence 56889999999999999975
No 14
>COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair]
Probab=27.42 E-value=94 Score=28.77 Aligned_cols=34 Identities=15% Similarity=0.108 Sum_probs=25.6
Q ss_pred hcccccccchHHHHHHHHhh-----------cccccccccccccc
Q psy11354 12 KQNTVHYGSLEEQERKRLAA-----------NKDVDDDQEKYTNV 45 (120)
Q Consensus 12 k~~~i~yGsLee~er~rl~~-----------~~~~~~~gi~~~~i 45 (120)
.....|+|.|+..||++... .+.|..+|||..|+
T Consensus 255 ~~a~~YHaGl~~~eR~~~q~~f~~~~~~iiVAT~AFGMGIdKpdV 299 (590)
T COG0514 255 ISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDV 299 (590)
T ss_pred CceEEecCCCCHHHHHHHHHHHhcCCCcEEEEeccccCccCCCCc
Confidence 35578999999999987654 13445689999976
No 15
>PF10454 DUF2458: Protein of unknown function (DUF2458); InterPro: IPR018858 This entry represents a family of uncharacterised proteins.
Probab=26.15 E-value=1.1e+02 Score=23.26 Aligned_cols=32 Identities=31% Similarity=0.491 Sum_probs=23.5
Q ss_pred HHHHHHHhhCCCccccCCCh-------HHHHHHHHHHHhhc
Q psy11354 86 QVKLNLRQLGEPICLFGEGP-------AERRSRLRDLLSSL 119 (120)
Q Consensus 86 eVr~~LR~LgePi~LFGE~~-------~~RR~RLr~ll~~~ 119 (120)
+....|+.||-|- |+.++ .+.+.|+-+||..+
T Consensus 109 ~~~~~L~~LgVPf--F~~~~~~~~~el~~~q~rmL~lL~Dl 147 (150)
T PF10454_consen 109 EQQAELKELGVPF--FYIKEDISDEELRELQKRMLQLLEDL 147 (150)
T ss_pred HHHHHHHhcCCCe--eeCCCCCCcHHHHHHHHHHHHHHHHH
Confidence 4667899999985 55544 56888888888643
No 16
>PF08619 Nha1_C: Alkali metal cation/H+ antiporter Nha1 C terminus; InterPro: IPR013928 The C terminus of the plasma membrane Nha1 antiporter plays an important role in the immediate cell response to hypo-osmotic shock which prevents an excessive loss of ions and water []. This protein is found C-terminal to IPR006153 from INTERPRO. ; GO: 0015385 sodium:hydrogen antiporter activity, 0006814 sodium ion transport, 0016020 membrane
Probab=25.59 E-value=46 Score=29.18 Aligned_cols=19 Identities=53% Similarity=0.529 Sum_probs=15.6
Q ss_pred CccccCCChHHHHHHHHHH
Q psy11354 97 PICLFGEGPAERRSRLRDL 115 (120)
Q Consensus 97 Pi~LFGE~~~~RR~RLr~l 115 (120)
..---+|++++||.||..|
T Consensus 403 ~~~d~~ET~aERrRRLaAL 421 (434)
T PF08619_consen 403 DSDDEGETPAERRRRLAAL 421 (434)
T ss_pred cccccccchHHHHHHHHHh
Confidence 3455689999999999887
No 17
>cd06321 PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=25.12 E-value=1e+02 Score=22.94 Aligned_cols=46 Identities=9% Similarity=0.045 Sum_probs=29.7
Q ss_pred hHHHHHHHHHHHHHHhhhhcCCCCCHH---HHHHHHHhhCCCccccCCC
Q psy11354 59 AKDKQALLQEFERRKKARHVNVSTDDN---QVKLNLRQLGEPICLFGEG 104 (120)
Q Consensus 59 ~~~~~~~L~e~E~~rr~r~~~vPT~D~---eVr~~LR~LgePi~LFGE~ 104 (120)
...+...++.+..++-...+..|+++. ++.+.|...|-|+++++-+
T Consensus 43 ~~~~~~~i~~~~~~~~dgiIi~~~~~~~~~~~i~~~~~~~ipvv~~~~~ 91 (271)
T cd06321 43 LNKQVSQIDNFIAAKVDLILLNAVDSKGIAPAVKRAQAAGIVVVAVDVA 91 (271)
T ss_pred HHHHHHHHHHHHHhCCCEEEEeCCChhHhHHHHHHHHHCCCeEEEecCC
Confidence 345556677766555444455677643 4556677779999999853
No 18
>PF11199 DUF2891: Protein of unknown function (DUF2891); InterPro: IPR021365 This is a bacterial family of uncharacterised proteins.
Probab=24.38 E-value=32 Score=29.65 Aligned_cols=22 Identities=18% Similarity=0.469 Sum_probs=18.7
Q ss_pred CCCccchhhhhhcccccccchH
Q psy11354 1 MSDDEDVIYVKKQNTVHYGSLE 22 (120)
Q Consensus 1 msdde~~~~~~k~~~i~yGsLe 22 (120)
|++++|+.+++.--.+|||++.
T Consensus 24 l~~~~D~~~P~~LhP~FyGcfD 45 (326)
T PF11199_consen 24 LNGPDDVKTPRELHPAFYGCFD 45 (326)
T ss_pred cCChhhcCChHHhCCccccCCh
Confidence 6778888888889999999973
No 19
>cd04374 RhoGAP_Graf RhoGAP_Graf: GTPase-activator protein (GAP) domain for Rho-like GTPases found in GRAF (GTPase regulator associated with focal adhesion kinase); Graf is a multi-domain protein, containing SH3 and PH domains, that binds focal adhesion kinase and influences cytoskeletal changes mediated by Rho proteins. Graf exhibits GAP activity toward RhoA and Cdc42, but only weakly activates Rac1. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=23.40 E-value=1.2e+02 Score=23.62 Aligned_cols=36 Identities=28% Similarity=0.469 Sum_probs=25.0
Q ss_pred HHHHHHHHHhhCCCcccc-----------CCChHHHHHHHHHHHhhc
Q psy11354 84 DNQVKLNLRQLGEPICLF-----------GEGPAERRSRLRDLLSSL 119 (120)
Q Consensus 84 D~eVr~~LR~LgePi~LF-----------GE~~~~RR~RLr~ll~~~ 119 (120)
-.-++.-||+|-+|+..| .++...|...|+.++..+
T Consensus 90 a~lLK~fLReLPePLi~~~~y~~~i~~~~~~~~~~ri~~l~~li~~L 136 (203)
T cd04374 90 TSALKTYLRNLPEPLMTYELHNDFINAAKSENLESRVNAIHSLVHKL 136 (203)
T ss_pred HHHHHHHHHcCCCCcCCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHC
Confidence 345678889999988765 234566777777777653
No 20
>cd06285 PBP1_LacI_like_7 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=23.18 E-value=1e+02 Score=22.94 Aligned_cols=45 Identities=13% Similarity=0.158 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHhhhhcCCCCC-HHHHHHHHHhhCCCccccCCC
Q psy11354 60 KDKQALLQEFERRKKARHVNVSTD-DNQVKLNLRQLGEPICLFGEG 104 (120)
Q Consensus 60 ~~~~~~L~e~E~~rr~r~~~vPT~-D~eVr~~LR~LgePi~LFGE~ 104 (120)
..+.+.++.+...+-...+..|+. +.++...|...|-|+++|+.+
T Consensus 42 ~~~~~~i~~l~~~~~dgiii~~~~~~~~~~~~~~~~~iPvv~~~~~ 87 (265)
T cd06285 42 DAQRRAIEMLLDRRVDGLILGDARSDDHFLDELTRRGVPFVLVLRH 87 (265)
T ss_pred HHHHHHHHHHHHcCCCEEEEecCCCChHHHHHHHHcCCCEEEEccC
Confidence 344556666655444444555654 445566778889999999864
No 21
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=23.18 E-value=80 Score=23.49 Aligned_cols=41 Identities=17% Similarity=0.167 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhhhhcCCCCCHHHHHHHHHhhCCCccccCCC
Q psy11354 64 ALLQEFERRKKARHVNVSTDDNQVKLNLRQLGEPICLFGEG 104 (120)
Q Consensus 64 ~~L~e~E~~rr~r~~~vPT~D~eVr~~LR~LgePi~LFGE~ 104 (120)
.++..+..++-...+..|+++.++...|+..|-|+.+++-.
T Consensus 49 ~~~~~l~~~~vdgiii~~~~~~~~~~~l~~~~ipvV~~~~~ 89 (268)
T cd06277 49 ELPSFLEDGKVDGIILLGGISTEYIKEIKELGIPFVLVDHY 89 (268)
T ss_pred HHHHHHHHCCCCEEEEeCCCChHHHHHHhhcCCCEEEEccC
Confidence 44444433222223446777777778888999999998743
No 22
>PF04871 Uso1_p115_C: Uso1 / p115 like vesicle tethering protein, C terminal region; InterPro: IPR006955 This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein. This myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region []. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the acidic C-terminal region, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport, 0005737 cytoplasm, 0016020 membrane
Probab=22.59 E-value=51 Score=24.47 Aligned_cols=14 Identities=36% Similarity=0.629 Sum_probs=12.0
Q ss_pred HHHHHHHhhCCCcc
Q psy11354 86 QVKLNLRQLGEPIC 99 (120)
Q Consensus 86 eVr~~LR~LgePi~ 99 (120)
.-+.+|+.||+||.
T Consensus 102 kyk~rLk~LG~eVS 115 (136)
T PF04871_consen 102 KYKERLKELGEEVS 115 (136)
T ss_pred HHHHHHHHcCCCcc
Confidence 46889999999994
No 23
>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=22.26 E-value=1.5e+02 Score=21.96 Aligned_cols=45 Identities=20% Similarity=0.251 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHhhhhcCCCCCHH---HHHHHHHhhCCCccccCCC
Q psy11354 60 KDKQALLQEFERRKKARHVNVSTDDN---QVKLNLRQLGEPICLFGEG 104 (120)
Q Consensus 60 ~~~~~~L~e~E~~rr~r~~~vPT~D~---eVr~~LR~LgePi~LFGE~ 104 (120)
....+.+..+-.++-...|.+|+++. ++.+.|+..|-|+++++..
T Consensus 44 ~~~~~~i~~l~~~~vdgvii~~~~~~~~~~~l~~~~~~~ipvV~~~~~ 91 (273)
T cd06310 44 AGQVNLLENAIARGPDAILLAPTDAKALVPPLKEAKDAGIPVVLIDSG 91 (273)
T ss_pred HHHHHHHHHHHHhCCCEEEEcCCChhhhHHHHHHHHHCCCCEEEecCC
Confidence 44556666665544344455687764 4667788889999999754
No 24
>cd01542 PBP1_TreR_like Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding wh
Probab=21.26 E-value=94 Score=22.83 Aligned_cols=45 Identities=16% Similarity=0.345 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHhhhhcCCCCC-HHHHHHHHHhhCCCccccCCC
Q psy11354 60 KDKQALLQEFERRKKARHVNVSTD-DNQVKLNLRQLGEPICLFGEG 104 (120)
Q Consensus 60 ~~~~~~L~e~E~~rr~r~~~vPT~-D~eVr~~LR~LgePi~LFGE~ 104 (120)
+.+.+.++++-.++=...+.+|++ +..+...|+..|-|+.+++-.
T Consensus 42 ~~~~~~i~~l~~~~~dgii~~~~~~~~~~~~~~~~~~ipvv~~~~~ 87 (259)
T cd01542 42 EKEIEALELLARQKVDGIILLATTITDEHREAIKKLNVPVVVVGQD 87 (259)
T ss_pred HHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHhcCCCCEEEEecc
Confidence 444566666644333333445554 457778888889999999753
No 25
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=21.05 E-value=1.2e+02 Score=23.23 Aligned_cols=46 Identities=9% Similarity=0.093 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHHHHHhhhhcCCCCCH---HHHHHHHHhhCCCccccCCC
Q psy11354 59 AKDKQALLQEFERRKKARHVNVSTDD---NQVKLNLRQLGEPICLFGEG 104 (120)
Q Consensus 59 ~~~~~~~L~e~E~~rr~r~~~vPT~D---~eVr~~LR~LgePi~LFGE~ 104 (120)
++.+...++.+-.++=...+.+|++. .++...|+..|-|+++|+-.
T Consensus 41 ~~~~~~~i~~~~~~~vdgiii~~~~~~~~~~~l~~l~~~~ipvV~~~~~ 89 (288)
T cd01538 41 PAKQISQIENMIAKGVDVLVIAPVDGEALASAVEKAADAGIPVIAYDRL 89 (288)
T ss_pred HHHHHHHHHHHHHcCCCEEEEecCChhhHHHHHHHHHHCCCCEEEECCC
Confidence 44556667776654433345567653 45667788889999999743
No 26
>PF10673 DUF2487: Protein of unknown function (DUF2487); InterPro: IPR019615 This entry represents proteins with unknown function that appears to be restricted to Bacillus sp.
Probab=20.62 E-value=2.1e+02 Score=21.69 Aligned_cols=47 Identities=23% Similarity=0.221 Sum_probs=36.5
Q ss_pred HhhhHHHHHHHHHHHHHHhhhhcCCCCCHHHHHHHHHhhCCCccccCCChHH-HHHHHHHHHh
Q psy11354 56 DEMAKDKQALLQEFERRKKARHVNVSTDDNQVKLNLRQLGEPICLFGEGPAE-RRSRLRDLLS 117 (120)
Q Consensus 56 ~~~~~~~~~~L~e~E~~rr~r~~~vPT~D~eVr~~LR~LgePi~LFGE~~~~-RR~RLr~ll~ 117 (120)
....+....+..++|++=+-|.+..| |.++++++..+ ..+||.....
T Consensus 31 a~~~E~~~~l~~~lErqfKGRv~l~P---------------~~~Y~~~~~~~~~~~~L~~w~~ 78 (142)
T PF10673_consen 31 ASQGEFLRLLADELERQFKGRVLLFP---------------AFTYLKEEDEEELVERLNDWCE 78 (142)
T ss_pred HHHHHHHHHHHHHHHHhcCceEEecC---------------CeeeecccchhHHHHHHHHHHH
Confidence 44577778888999999999999998 78888877765 4457766544
No 27
>PF08245 Mur_ligase_M: Mur ligase middle domain; InterPro: IPR013221 The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages: (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer. Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) [], MurD (6.3.2.9 from EC) [], MurE (6.3.2.13 from EC) [] and MurF (6.3.2.10 from EC) []. These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales []. This entry represents the C-terminal domain from all four stage 2 Mur enzymes: UDP-N-acetylmuramate-L-alanine ligase (MurC), UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD), UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase (MurE), and UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF). This entry also includes folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate and cyanophycin synthetase that catalyses the biosynthesis of the cyanobacterial reserve material multi-L-arginyl-poly-L-aspartate (cyanophycin) [].; GO: 0005524 ATP binding, 0009058 biosynthetic process; PDB: 3LK7_A 2XJA_A 2WTZ_A 2GCA_A 1JBW_A 1JBV_A 2GC5_A 1FGS_A 2GCB_A 2GC6_A ....
Probab=20.26 E-value=34 Score=24.87 Aligned_cols=30 Identities=13% Similarity=0.103 Sum_probs=26.0
Q ss_pred hcCCCCCHHHHHHHHHhhCCCccccCCChH
Q psy11354 77 HVNVSTDDNQVKLNLRQLGEPICLFGEGPA 106 (120)
Q Consensus 77 ~~~vPT~D~eVr~~LR~LgePi~LFGE~~~ 106 (120)
.++++.+|+.+...+...+.++..||.++.
T Consensus 110 ~~v~n~dd~~~~~~~~~~~~~v~~~~~~~~ 139 (188)
T PF08245_consen 110 VAVLNADDPELAEIAANSKCKVITFGLDNS 139 (188)
T ss_dssp EEEEETTSHHHHHHHHHHTTTEEEEESSSS
T ss_pred EEEecCCCHHHHHHHHhcCCcEEEeccCcc
Confidence 566889999999999999999999997653
Done!