Query psy7934
Match_columns 138
No_of_seqs 94 out of 96
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 22:34:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7934.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7934hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0245|consensus 99.6 6.5E-17 1.4E-21 153.4 0.2 96 29-137 651-746 (1221)
2 KOG0241|consensus 93.2 0.35 7.6E-06 48.3 7.6 72 54-137 660-731 (1714)
3 PF10562 CaM_bdg_C0: Calmoduli 87.2 0.59 1.3E-05 27.6 2.1 19 31-49 8-26 (29)
4 PF00249 Myb_DNA-binding: Myb- 57.6 12 0.00025 22.9 2.4 30 31-60 3-32 (48)
5 smart00717 SANT SANT SWI3, AD 44.2 26 0.00057 19.8 2.4 30 31-60 3-32 (49)
6 cd00167 SANT 'SWI3, ADA2, N-Co 40.6 31 0.00068 19.2 2.3 29 31-59 1-29 (45)
7 PF01394 Clathrin_propel: Clat 32.8 34 0.00074 20.4 1.6 22 112-135 16-37 (37)
8 PF08310 LGFP: LGFP repeat; I 30.7 42 0.00091 21.2 1.9 15 119-134 16-30 (54)
9 PRK13870 transcriptional regul 29.2 54 0.0012 26.5 2.7 16 29-44 171-186 (234)
10 cd07130 ALDH_F7_AASADH NAD+-de 27.1 87 0.0019 27.7 3.9 41 37-79 40-87 (474)
11 cd07081 ALDH_F20_ACDH_EutE-lik 24.8 1.5E+02 0.0033 26.4 4.9 46 35-80 3-53 (439)
12 cd07147 ALDH_F21_RNP123 Aldehy 23.7 89 0.0019 27.2 3.3 42 37-80 27-75 (452)
13 cd07097 ALDH_KGSADH-YcbD Bacil 21.1 1.8E+02 0.0039 25.6 4.7 44 36-79 42-90 (473)
No 1
>KOG0245|consensus
Probab=99.61 E-value=6.5e-17 Score=153.35 Aligned_cols=96 Identities=55% Similarity=0.732 Sum_probs=92.1
Q ss_pred CCCCCHHHHHHHHHHHHhchhcCCccHHHHHHhhhhhHHHHHHHHHHhccceeeeEEEeeCCCcCCCCccccCCCccccc
Q psy7934 29 ECTWTEREFALAAWAFRKWKYHQFTSLRDDLWGNAIFLKEANAISVELKKKVQFQFTLLTDTLYSPLPPDLVSSVEEEDE 108 (138)
Q Consensus 29 ~~~~s~rE~~lar~a~~kWk~~~~~smaE~ll~nAv~LKEAN~iS~EL~K~V~fQF~lv~~~~~sp~~~dL~~~g~~d~~ 108 (138)
+.+|+.++.+++-|+++|||+|+|++.+|.+|+|+.+|++||+|+.|++|+|.|+|++++++.+++.+++++
T Consensus 651 ~~~~~~~~~~~~~~~~~k~k~~~~~s~~~~~~~~~~~l~~~~a~~~e~~k~v~~e~al~td~q~~~~~~ell-------- 722 (1221)
T KOG0245|consen 651 EVQWTVKECELALWAKRKAKRHQEQSLRDLLEGNAIFLAAAAALEVELKKKVRFEEALLTDTQKSMKEEELL-------- 722 (1221)
T ss_pred hhhhhhhhhhhhHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHhccchhhhhhhcccccccccccccc--------
Confidence 679999999999999999999999999999999999999999999999999999999999999999888876
Q ss_pred CCCCCCcEEEEEEEecCCCeeEEeecccc
Q psy7934 109 DRPLPRTIVAVEVLDTKNGATHYWALQKL 137 (138)
Q Consensus 109 l~~~~kpcVaV~ViD~kn~a~h~WSL~Kl 137 (138)
| +.|.|+|.|.+++++|+|+.+||
T Consensus 723 --~---t~i~~~v~d~~~~~t~~w~~ekl 746 (1221)
T KOG0245|consen 723 --P---TEILVNVSDKSDGATHLWSKEKL 746 (1221)
T ss_pred --c---hhhhhhccccccchHHHHHHHHH
Confidence 1 89999999999999999999986
No 2
>KOG0241|consensus
Probab=93.18 E-value=0.35 Score=48.26 Aligned_cols=72 Identities=25% Similarity=0.473 Sum_probs=48.4
Q ss_pred cHHHHHHhhhhhHHHHHHHHHHhccceeeeEEEeeCCCcCCCCccccCCCcccccCCCCCCcEEEEEEEecCCCeeEEee
Q psy7934 54 SLRDDLWGNAIFLKEANAISVELKKKVQFQFTLLTDTLYSPLPPDLVSSVEEEDEDRPLPRTIVAVEVLDTKNGATHYWA 133 (138)
Q Consensus 54 smaE~ll~nAv~LKEAN~iS~EL~K~V~fQF~lv~~~~~sp~~~dL~~~g~~d~~l~~~~kpcVaV~ViD~kn~a~h~WS 133 (138)
+|++++..--.+++|||-||.||+|+-.||-||-- | +..|- +-..- -.=..-|.|-|| .++.-..+|+
T Consensus 660 rLr~~iv~AN~LVrEAN~laeEm~KkT~y~VTLQI-----P-aanL~-~nrkr--Ga~vsEPaI~Vr---R~g~gsQiWt 727 (1714)
T KOG0241|consen 660 RLREQIVKANTLVREANFLAEEMSKKTDYQVTLQI-----P-AANLS-ANRKR--GAFVSEPAIQVR---RKGKGSQIWT 727 (1714)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccceeEEEEc-----c-hhcCC-ccccc--CceeccceeEEE---ecCCCceeee
Confidence 46788888889999999999999999999877642 2 12221 11000 011233444444 5777899999
Q ss_pred cccc
Q psy7934 134 LQKL 137 (138)
Q Consensus 134 L~Kl 137 (138)
++||
T Consensus 728 ~ekL 731 (1714)
T KOG0241|consen 728 IEKL 731 (1714)
T ss_pred HHHh
Confidence 9997
No 3
>PF10562 CaM_bdg_C0: Calmodulin-binding domain C0 of NMDA receptor NR1 subunit; InterPro: IPR018882 This is a very short highly conserved domain that is C-terminal to the cytosolic transmembrane region IV of the NMDA-receptor 1. It has been shown to bind Calmodulin-Calcium with high affinity. The ionotropic N-methyl-D-aspartate receptor (NMDAR) is a major source of calcium flux into neurons in the brain and plays a critical role in learning, memory, neural development, and synaptic plasticity. Calmodulin (CaM) regulates NMDARs by binding tightly to the C0 and C1 regions of their NR1 subunit. The conserved tryptophan is considered to be the anchor residue [].
Probab=87.19 E-value=0.59 Score=27.61 Aligned_cols=19 Identities=26% Similarity=0.473 Sum_probs=16.3
Q ss_pred CCCHHHHHHHHHHHHhchh
Q psy7934 31 TWTEREFALAAWAFRKWKY 49 (138)
Q Consensus 31 ~~s~rE~~lar~a~~kWk~ 49 (138)
.+-+++.+||+.|.+|||.
T Consensus 8 ~~kqk~~elAr~a~dkWR~ 26 (29)
T PF10562_consen 8 IRKQKQLELARHAADKWRG 26 (29)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 3557899999999999995
No 4
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=57.58 E-value=12 Score=22.85 Aligned_cols=30 Identities=20% Similarity=0.285 Sum_probs=25.6
Q ss_pred CCCHHHHHHHHHHHHhchhcCCccHHHHHH
Q psy7934 31 TWTEREFALAAWAFRKWKYHQFTSLRDDLW 60 (138)
Q Consensus 31 ~~s~rE~~lar~a~~kWk~~~~~smaE~ll 60 (138)
+||++|-++...++.+-...++..+|+.+-
T Consensus 3 ~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~ 32 (48)
T PF00249_consen 3 PWTEEEDEKLLEAVKKYGKDNWKKIAKRMP 32 (48)
T ss_dssp SS-HHHHHHHHHHHHHSTTTHHHHHHHHHS
T ss_pred CCCHHHHHHHHHHHHHhCCcHHHHHHHHcC
Confidence 699999999999999998888888887765
No 5
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=44.21 E-value=26 Score=19.79 Aligned_cols=30 Identities=23% Similarity=0.368 Sum_probs=23.8
Q ss_pred CCCHHHHHHHHHHHHhchhcCCccHHHHHH
Q psy7934 31 TWTEREFALAAWAFRKWKYHQFTSLRDDLW 60 (138)
Q Consensus 31 ~~s~rE~~lar~a~~kWk~~~~~smaE~ll 60 (138)
.||++|..+...++.+....++..+|+.+-
T Consensus 3 ~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~ 32 (49)
T smart00717 3 EWTEEEDELLIELVKKYGKNNWEKIAKELP 32 (49)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHHHcC
Confidence 699999999999988877666777776653
No 6
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=40.58 E-value=31 Score=19.21 Aligned_cols=29 Identities=28% Similarity=0.477 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHHHHHhchhcCCccHHHHH
Q psy7934 31 TWTEREFALAAWAFRKWKYHQFTSLRDDL 59 (138)
Q Consensus 31 ~~s~rE~~lar~a~~kWk~~~~~smaE~l 59 (138)
.||++|..+...++.+....++..+|+.+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~ 29 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKEL 29 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHc
Confidence 48999999999998877655566666554
No 7
>PF01394 Clathrin_propel: Clathrin propeller repeat; InterPro: IPR022365 This entry represents the propeller repeat found in clathrin heavy chains. The N terminus of the heavy chain is known as the globular domain, and is composed of seven repeats which form a beta propeller []. Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. Clathrin is a trimer composed of three heavy chains and three light chains, each monomer projecting outwards like a leg; this three-legged structure is known as a triskelion [, ]. The heavy chains form the legs, their N-terminal beta-propeller regions extending outwards, while their C-terminal alpha-alpha-superhelical regions form the central hub of the triskelion. Peptide motifs can bind between the beta-propeller blades. The light chains appear to have a regulatory role, and may help orient the assembly and disassembly of clathrin coats as they interact with hsc70 uncoating ATPase []. Clathrin triskelia self-polymerise into a curved lattice by twisting individual legs together. The clathrin lattice forms around a vesicle as it buds from the TGN, plasma membrane or endosomes, acting to stabilise the vesicle and facilitate the budding process []. The multiple blades created when the triskelia polymerise are involved in multiple protein interactions, enabling the recruitment of different cargo adaptors and membrane attachment proteins []. More information about these proteins can be found at Protein of the Month: Clathrin [].; PDB: 1UTC_B 3GD1_I 3GC3_B 1BPO_C 1C9I_B 1C9L_A 2XZG_A 2XZH_A.
Probab=32.77 E-value=34 Score=20.39 Aligned_cols=22 Identities=9% Similarity=0.298 Sum_probs=16.3
Q ss_pred CCCcEEEEEEEecCCCeeEEeecc
Q psy7934 112 LPRTIVAVEVLDTKNGATHYWALQ 135 (138)
Q Consensus 112 ~~kpcVaV~ViD~kn~a~h~WSL~ 135 (138)
..+-|+||. -.+-|.+|+||+|
T Consensus 16 s~~~iigi~--~~~~G~v~l~sve 37 (37)
T PF01394_consen 16 SWKFIIGIS--GRVKGQVQLYSVE 37 (37)
T ss_dssp EEEEEEEEE--TCTEEEEEEEETT
T ss_pred CeEEEEEEE--eeeeeEEEEEECC
Confidence 345667776 4577999999986
No 8
>PF08310 LGFP: LGFP repeat; InterPro: IPR013207 This 54 amino acid repeat is found in many hypothetical proteins. Several hypothetical proteins from Corynebacterium glutamicum (Brevibacterium flavum) and Corynebacterium efficiens along with PS1 protein contain this repeat region. The N-terminal region of PS1 contains an esterase domain which transfers corynomycolic acid. The C-terminal region consists of 4 tandem LGFP repeats. It is hypothesised that the PS1 proteins in Corynebacterium, when associated with the cell wall, may be anchored via the LGFP tandem repeats that may be important for maintaining cell wall integrity. Deletion of Q01377 from SWISSPROT protein results in a 10-fold increase in the cell volume of the organism and infers the corresponding involvement of the protein in the cell shape formation []. The secondary structure of each repeat is predicted to comprise two beta-strands and one alpha-helix.
Probab=30.71 E-value=42 Score=21.18 Aligned_cols=15 Identities=27% Similarity=0.437 Sum_probs=12.3
Q ss_pred EEEEecCCCeeEEeec
Q psy7934 119 VEVLDTKNGATHYWAL 134 (138)
Q Consensus 119 V~ViD~kn~a~h~WSL 134 (138)
-+++++.||+|| ||-
T Consensus 16 G~~q~F~~G~Iy-wsp 30 (54)
T PF08310_consen 16 GRYQDFQNGTIY-WSP 30 (54)
T ss_pred EEEEEcCCeEEE-EeC
Confidence 678899999987 763
No 9
>PRK13870 transcriptional regulator TraR; Provisional
Probab=29.20 E-value=54 Score=26.50 Aligned_cols=16 Identities=13% Similarity=0.204 Sum_probs=13.9
Q ss_pred CCCCCHHHHHHHHHHH
Q psy7934 29 ECTWTEREFALAAWAF 44 (138)
Q Consensus 29 ~~~~s~rE~~lar~a~ 44 (138)
...+|+||.++.+|+-
T Consensus 171 ~~~LT~RE~E~L~W~A 186 (234)
T PRK13870 171 AAWLDPKEATYLRWIA 186 (234)
T ss_pred cCCCCHHHHHHHHHHH
Confidence 4579999999999875
No 10
>cd07130 ALDH_F7_AASADH NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B. Alpha-aminoadipic semialdehyde dehydrogenase (AASADH, EC=1.2.1.31), also known as ALDH7A1, Antiquitin-1, ALDH7B, or delta-1-piperideine-6-carboxylate dehydrogenase (P6CDH), is a NAD+-dependent ALDH. Human ALDH7A1 is involved in the pipecolic acid pathway of lysine catabolism, catalyzing the oxidation of alpha-aminoadipic semialdehyde to alpha-aminoadipate. Arabidopsis thaliana ALDH7B4 appears to be an osmotic-stress-inducible ALDH gene encoding a turgor-responsive or stress-inducible ALDH. The Streptomyces clavuligerus P6CDH appears to be involved in cephamycin biosynthesis, catalyzing the second stage of the two-step conversion of lysine to alpha-aminoadipic acid. The ALDH7A1 enzyme and others in this group have been observed as tetramers, yet the bacterial P6CDH enzyme has been reported as a monomer.
Probab=27.07 E-value=87 Score=27.68 Aligned_cols=41 Identities=24% Similarity=0.338 Sum_probs=29.9
Q ss_pred HHHHHHHHHhchhc-------CCccHHHHHHhhhhhHHHHHHHHHHhccc
Q psy7934 37 FALAAWAFRKWKYH-------QFTSLRDDLWGNAIFLKEANAISVELKKK 79 (138)
Q Consensus 37 ~~lar~a~~kWk~~-------~~~smaE~ll~nAv~LKEAN~iS~EL~K~ 79 (138)
++.|+.|++.|+.. ...++++.|..|+-.| |+.++.|.+|.
T Consensus 40 v~~a~~A~~~w~~~~~~~R~~~L~~~a~~l~~~~~~l--a~~~~~e~Gk~ 87 (474)
T cd07130 40 IKAAQEAFKEWRDVPAPKRGEIVRQIGDALRKKKEAL--GKLVSLEMGKI 87 (474)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHcCCC
Confidence 56789999999654 3446667777777666 77888888875
No 11
>cd07081 ALDH_F20_ACDH_EutE-like Coenzyme A acylating aldehyde dehydrogenase (ACDH), Ethanolamine utilization protein EutE, and related proteins. Coenzyme A acylating aldehyde dehydrogenase (ACDH), an NAD+ and CoA-dependent acetaldehyde dehydrogenase, acetylating (EC=1.2.1.10), functions as a single enzyme (such as the Ethanolamine utilization protein, EutE, in Salmonella typhimurium) or as part of a multifunctional enzyme to convert acetaldehyde into acetyl-CoA. The E. coli aldehyde-alcohol dehydrogenase includes the functional domains, alcohol dehydrogenase (ADH), ACDH, and pyruvate-formate-lyase deactivase; and the Entamoeba histolytica aldehyde-alcohol dehydrogenase 2 (ALDH20A1) includes the functional domains ADH and ACDH, and may be critical enzymes in the fermentative pathway.
Probab=24.77 E-value=1.5e+02 Score=26.36 Aligned_cols=46 Identities=13% Similarity=-0.095 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHhchhcCCccHHHHHHhhhhhHHH-----HHHHHHHhccce
Q psy7934 35 REFALAAWAFRKWKYHQFTSLRDDLWGNAIFLKE-----ANAISVELKKKV 80 (138)
Q Consensus 35 rE~~lar~a~~kWk~~~~~smaE~ll~nAv~LKE-----AN~iS~EL~K~V 80 (138)
+=++-|++|++.|+......=++.|..-|-.|.+ |..++.|.+|-+
T Consensus 3 ~Ai~~A~~A~~~W~~~~~~~R~~iL~~~a~~l~~~~~ela~~~~~E~Gk~~ 53 (439)
T cd07081 3 DAVAAAKVAQQGLSCKSQEMVDLIFRAAAEAAEDARIDLAKLAVSETGMGR 53 (439)
T ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCh
Confidence 4467899999999987766555555555555554 567888888864
No 12
>cd07147 ALDH_F21_RNP123 Aldehyde dehydrogenase family 21A1-like. Aldehyde dehydrogenase ALDH21A1 (gene name RNP123) was first described in the moss Tortula ruralis and is believed to play an important role in the detoxification of aldehydes generated in response to desiccation- and salinity-stress, and ALDH21A1 expression represents a unique stress tolerance mechanism. So far, of plants, only the bryophyte sequence has been observed, but similar protein sequences from bacteria and archaea are also present in this CD.
Probab=23.68 E-value=89 Score=27.16 Aligned_cols=42 Identities=26% Similarity=0.115 Sum_probs=29.1
Q ss_pred HHHHHHHHHhchhcCC-------ccHHHHHHhhhhhHHHHHHHHHHhccce
Q psy7934 37 FALAAWAFRKWKYHQF-------TSLRDDLWGNAIFLKEANAISVELKKKV 80 (138)
Q Consensus 37 ~~lar~a~~kWk~~~~-------~smaE~ll~nAv~LKEAN~iS~EL~K~V 80 (138)
++-|+.|++.|+...+ ..+++.|..|+-.| |+.++.|.+|..
T Consensus 27 v~~A~~A~~~w~~~~~~~R~~~L~~~a~~l~~~~~~l--a~~~~~e~Gk~~ 75 (452)
T cd07147 27 IAAAVKAFRPMRALPAHRRAAILLHCVARLEERFEEL--AETIVLEAGKPI 75 (452)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhHHHH--HHHHHHHcCCCH
Confidence 5778999999986443 44555555555555 678888888764
No 13
>cd07097 ALDH_KGSADH-YcbD Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like. Kinetic studies of the Bacillus subtilis ALDH-like ycbD protein, which is involved in d-glucarate/d-galactarate utilization, reveal that it is a NADP+-dependent, alpha-ketoglutaric semialdehyde dehydrogenase (KGSADH). KGSADHs (EC 1.2.1.26) catalyze the NAD(P)+-dependent conversion of KGSA to alpha-ketoglutarate. Interestingly, the NADP+-dependent, tetrameric, 2,5-dioxopentanoate dehydrogenase (EC=1.2.1.26), an enzyme involved in the catabolic pathway for D-arabinose in Sulfolobus solfataricus, also clusters in this group. This CD shows a distant phylogenetic relationship to the Azospirillum brasilense KGSADH-II (-III) group.
Probab=21.12 E-value=1.8e+02 Score=25.60 Aligned_cols=44 Identities=27% Similarity=0.184 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhchhcCCccHHHHHHhhhhhHHH-----HHHHHHHhccc
Q psy7934 36 EFALAAWAFRKWKYHQFTSLRDDLWGNAIFLKE-----ANAISVELKKK 79 (138)
Q Consensus 36 E~~lar~a~~kWk~~~~~smaE~ll~nAv~LKE-----AN~iS~EL~K~ 79 (138)
=++-|+.|++.|+...+..-++.|..=|-.|.+ |..++.|.+|-
T Consensus 42 av~~A~~A~~~W~~~~~~~R~~~L~~~a~~l~~~~~ela~~~~~e~Gk~ 90 (473)
T cd07097 42 AIAAAAAAFPAWRRTSPEARADILDKAGDELEARKEELARLLTREEGKT 90 (473)
T ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhHHHHHHHHHHHcCCC
Confidence 366788899999887666544544444444444 55566666554
Done!