Query 048001
Match_columns 48
No_of_seqs 14 out of 16
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 05:19:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048001.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048001hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0095 GTPase Rab30, small G 79.7 1.3 2.8E-05 31.3 1.8 39 4-43 63-105 (213)
2 KOG0083 GTPase Rab26/Rab37, sm 70.7 2.8 6.1E-05 29.3 1.5 36 2-37 52-91 (192)
3 COG0302 FolE GTP cyclohydrolas 62.9 13 0.00027 26.0 3.5 35 11-45 160-194 (195)
4 KOG4147 Uncharacterized conser 62.7 5.6 0.00012 26.5 1.7 14 17-30 4-17 (127)
5 PF02195 ParBc: ParB-like nucl 51.6 8.5 0.00018 20.9 1.0 27 3-29 51-77 (90)
6 PF02197 RIIa: Regulatory subu 51.6 8.9 0.00019 19.7 1.0 16 30-45 18-35 (38)
7 smart00470 ParB ParB-like nucl 39.1 15 0.00033 20.2 0.7 27 2-28 49-75 (89)
8 COG2210 Peroxiredoxin family p 37.7 14 0.00031 24.3 0.6 24 5-32 77-100 (137)
9 PF07503 zf-HYPF: HypF finger; 31.5 21 0.00046 18.4 0.5 9 33-41 3-11 (35)
10 cd00642 GTP_cyclohydro1 GTP cy 29.8 1E+02 0.0022 20.7 3.7 35 10-44 150-184 (185)
11 PF15389 DUF4612: Domain of un 24.2 47 0.001 21.4 1.2 11 33-43 88-98 (115)
12 PRK09347 folE GTP cyclohydrola 22.3 1.7E+02 0.0038 19.6 3.7 34 10-43 153-186 (188)
13 KOG0094 GTPase Rab6/YPT6/Ryh1, 22.0 45 0.00097 23.9 0.9 13 4-16 78-90 (221)
14 KOG0080 GTPase Rab18, small G 20.6 36 0.00078 24.2 0.2 13 4-16 67-79 (209)
15 KOG0084 GTPase Rab1/YPT1, smal 20.5 32 0.0007 24.2 -0.1 11 4-14 65-75 (205)
16 COG5463 Predicted integral mem 20.2 52 0.0011 23.3 0.9 11 28-38 48-58 (198)
17 PRK12606 GTP cyclohydrolase I; 20.1 1.9E+02 0.004 19.8 3.5 35 10-44 165-199 (201)
No 1
>KOG0095 consensus GTPase Rab30, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=79.74 E-value=1.3 Score=31.33 Aligned_cols=39 Identities=21% Similarity=0.348 Sum_probs=31.7
Q ss_pred ehhhhhhheeeee----CeeeEEEEeeeeeeehHhHHHHHHHHh
Q 048001 4 AITLKRYRAVKEV----GKIKMSVGVIAYYQLVQVCQAEYFRQL 43 (48)
Q Consensus 4 a~~qtrfRalK~~----g~~~i~VrvIAcyQ~~q~CQaeyFr~l 43 (48)
.++|.|||++-.. ...-|.|==|.| ||.-+|--|+.|.+
T Consensus 63 tagqerfrsitqsyyrsahalilvydisc-qpsfdclpewlrei 105 (213)
T KOG0095|consen 63 TAGQERFRSITQSYYRSAHALILVYDISC-QPSFDCLPEWLREI 105 (213)
T ss_pred ccchHHHHHHHHHHhhhcceEEEEEeccc-CcchhhhHHHHHHH
Confidence 4789999998765 455677777877 99999999999875
No 2
>KOG0083 consensus GTPase Rab26/Rab37, small G protein superfamily [General function prediction only]
Probab=70.73 E-value=2.8 Score=29.29 Aligned_cols=36 Identities=22% Similarity=0.260 Sum_probs=30.2
Q ss_pred eeehhhhhhheeeee----CeeeEEEEeeeeeeehHhHHH
Q 048001 2 YIAITLKRYRAVKEV----GKIKMSVGVIAYYQLVQVCQA 37 (48)
Q Consensus 2 ~~a~~qtrfRalK~~----g~~~i~VrvIAcyQ~~q~CQa 37 (48)
+-.++|.|||++-|. ...-..+==||+=-+-++||+
T Consensus 52 wdtagqerfrsvt~ayyrda~allllydiankasfdn~~~ 91 (192)
T KOG0083|consen 52 WDTAGQERFRSVTHAYYRDADALLLLYDIANKASFDNCQA 91 (192)
T ss_pred eeccchHHHhhhhHhhhcccceeeeeeecccchhHHHHHH
Confidence 446899999999987 556677888999999999997
No 3
>COG0302 FolE GTP cyclohydrolase I [Coenzyme metabolism]
Probab=62.93 E-value=13 Score=26.03 Aligned_cols=35 Identities=17% Similarity=0.325 Sum_probs=32.0
Q ss_pred heeeeeCeeeEEEEeeeeeeehHhHHHHHHHHhcc
Q 048001 11 RAVKEVGKIKMSVGVIAYYQLVQVCQAEYFRQLLK 45 (48)
Q Consensus 11 RalK~~g~~~i~VrvIAcyQ~~q~CQaeyFr~llk 45 (48)
|.+|..|+.|++.-+-.-|...+.+++|+++.+-+
T Consensus 160 RGv~k~~s~t~Ts~~~G~F~~~~~~R~efl~li~~ 194 (195)
T COG0302 160 RGVRKPGSSTVTSALRGLFKEDAKTRAEFLRLIKG 194 (195)
T ss_pred cCccCCCceEEEEeeeeeeccCHHHHHHHHHHHhc
Confidence 78899999999999999999999999999987653
No 4
>KOG4147 consensus Uncharacterized conserved protein [Function unknown]
Probab=62.68 E-value=5.6 Score=26.45 Aligned_cols=14 Identities=29% Similarity=0.693 Sum_probs=12.2
Q ss_pred CeeeEEEEeeeeee
Q 048001 17 GKIKMSVGVIAYYQ 30 (48)
Q Consensus 17 g~~~i~VrvIAcyQ 30 (48)
|+.+|+||||-.|-
T Consensus 4 ~~~tiTvRvIrsFe 17 (127)
T KOG4147|consen 4 GEVTITVRVIRSFE 17 (127)
T ss_pred CccEEEEEEEeccc
Confidence 67899999999874
No 5
>PF02195 ParBc: ParB-like nuclease domain; InterPro: IPR003115 Proteins containing this domain, appear to be related to the Escherichia coli plasmid protein ParB, which preferentially cleaves single-stranded DNA. ParB also nicks supercoiled plasmid DNA preferably at sites with potential single-stranded character, like AT-rich regions and sequences that can form cruciform structures. ParB also exhibits 5--3 exonuclease activity.; GO: 0003677 DNA binding; PDB: 1VK1_A 3CYI_A 1YZS_A 2RII_X 2B6F_A 3HY2_Y 1XW4_X 1XW3_A 1VZ0_G 1R71_C ....
Probab=51.64 E-value=8.5 Score=20.89 Aligned_cols=27 Identities=30% Similarity=0.286 Sum_probs=21.4
Q ss_pred eehhhhhhheeeeeCeeeEEEEeeeee
Q 048001 3 IAITLKRYRAVKEVGKIKMSVGVIAYY 29 (48)
Q Consensus 3 ~a~~qtrfRalK~~g~~~i~VrvIAcy 29 (48)
+..+..|++|.++.|..+|-|.++..-
T Consensus 51 IidG~~R~~A~~~lg~~~i~v~v~~~~ 77 (90)
T PF02195_consen 51 IIDGHHRLRAARELGLETIPVIVVDVD 77 (90)
T ss_dssp EEE-HHHHHHHHHHT-SEEEEEEEECT
T ss_pred CCCCHHHHHHHHHcCCCeEeEEEEECC
Confidence 567899999999999989999887654
No 6
>PF02197 RIIa: Regulatory subunit of type II PKA R-subunit; InterPro: IPR003117 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. In the absence of cAMP, Protein Kinase A (PKA) exists as an equimolar tetramer of regulatory (R) and catalytic (C) subunits []. In addition to its role as an inhibitor of the C subunit, the R subunit anchors the holoenzyme to specific intracellular locations and prevents the C subunit from entering the nucleus. All R subunits have a conserved domain structure consisting of the N-terminal dimerization domain, inhibitory region, cAMP-binding domain A and cAMP-binding domain B. R subunits interact with C subunits primarily through the inhibitory site. The cAMP-binding domains show extensive sequence similarity and bind cAMP cooperatively. Two types of regulatory (R) subunits exist - types I and I - which differ in molecular weight, sequence, autophosphorylation cabaility, cellular location and tissue distribution. Types I and II were further sub-divided into alpha and beta subtypes, based mainly on sequence similarity. This entry represents types I-alpha, I-beta, II-alpha and II-beta regulatory subunits of PKA proteins. These subunits contain the dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).; GO: 0008603 cAMP-dependent protein kinase regulator activity, 0007165 signal transduction; PDB: 2IZY_E 1R2A_A 1L6E_A 2IZX_B 2KYG_A 2EZW_B 3IM4_B 3IM3_A 4F9K_C 2HWN_B ....
Probab=51.55 E-value=8.9 Score=19.72 Aligned_cols=16 Identities=44% Similarity=0.602 Sum_probs=9.5
Q ss_pred eehHhHH--HHHHHHhcc
Q 048001 30 QLVQVCQ--AEYFRQLLK 45 (48)
Q Consensus 30 Q~~q~CQ--aeyFr~llk 45 (48)
||.+..| ++||..|++
T Consensus 18 qP~Di~~F~a~yF~~L~~ 35 (38)
T PF02197_consen 18 QPDDILQFAADYFEKLEK 35 (38)
T ss_dssp --S-HHHHHHHHHHHHHH
T ss_pred CCCcHHHHHHHHHHHHHH
Confidence 5666655 689988865
No 7
>smart00470 ParB ParB-like nuclease domain. Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB also nicks supercoiled plasmid DNA preferably at sites with potential single-stranded character, like AT-rich regions and sequences that can form cruciform structures. ParB also exhibits 5--3 exonuclease activity.
Probab=39.10 E-value=15 Score=20.21 Aligned_cols=27 Identities=30% Similarity=0.185 Sum_probs=22.5
Q ss_pred eeehhhhhhheeeeeCeeeEEEEeeee
Q 048001 2 YIAITLKRYRAVKEVGKIKMSVGVIAY 28 (48)
Q Consensus 2 ~~a~~qtrfRalK~~g~~~i~VrvIAc 28 (48)
.+..+..|++|.+..|..+|-+.++..
T Consensus 49 ~vidG~~R~~A~~~lg~~~ip~~v~~~ 75 (89)
T smart00470 49 EIIDGERRLRAAKLLGLKEVPVIVRDL 75 (89)
T ss_pred EEEeCHHHHHHHHHcCCCceeEEEEcC
Confidence 456788999999999988888888763
No 8
>COG2210 Peroxiredoxin family protein [General function prediction only]
Probab=37.68 E-value=14 Score=24.29 Aligned_cols=24 Identities=29% Similarity=0.207 Sum_probs=17.6
Q ss_pred hhhhhhheeeeeCeeeEEEEeeeeeeeh
Q 048001 5 ITLKRYRAVKEVGKIKMSVGVIAYYQLV 32 (48)
Q Consensus 5 ~~qtrfRalK~~g~~~i~VrvIAcyQ~~ 32 (48)
.+...+|..|++|. |+||||==.|
T Consensus 77 ~~le~l~~ak~~~~----vkv~AC~mtm 100 (137)
T COG2210 77 AWLELLREAKKDGG----VKVYACSMTM 100 (137)
T ss_pred cHHHHHHHHhhhcC----cEEEEehhHH
Confidence 45667888898877 8889984433
No 9
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=31.45 E-value=21 Score=18.40 Aligned_cols=9 Identities=44% Similarity=0.947 Sum_probs=7.3
Q ss_pred HhHHHHHHH
Q 048001 33 QVCQAEYFR 41 (48)
Q Consensus 33 q~CQaeyFr 41 (48)
++|+.||+.
T Consensus 3 ~~C~~Ey~~ 11 (35)
T PF07503_consen 3 DDCLKEYFD 11 (35)
T ss_dssp HHHHHHHCS
T ss_pred HHHHHHHcC
Confidence 589999973
No 10
>cd00642 GTP_cyclohydro1 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In vertebrates and insects it is the biosynthtic precursor of tetrahydrobiopterin (BH4) which is involved in the formation of catacholamines, nitric oxide, and the stimulation of T lymphocytes. The biosynthetic reaction of BH4 is controlled by a regulatory protein GFRP which mediates feedback inhibition of GTP-CH-I by BH4. This inhibition is reversed by phenylalanine. The decameric GTP-CH-I forms a complex with two pentameric GFRP in the presence of phenylalanine or a combination of GTP and BH4, respectively.
Probab=29.76 E-value=1e+02 Score=20.68 Aligned_cols=35 Identities=14% Similarity=0.344 Sum_probs=30.2
Q ss_pred hheeeeeCeeeEEEEeeeeeeehHhHHHHHHHHhc
Q 048001 10 YRAVKEVGKIKMSVGVIAYYQLVQVCQAEYFRQLL 44 (48)
Q Consensus 10 fRalK~~g~~~i~VrvIAcyQ~~q~CQaeyFr~ll 44 (48)
-|.+|..|..|.+.-.--+|+.-..-..|+|+.+-
T Consensus 150 ~RGv~~~~s~t~T~a~~G~F~~~~~~r~ef~~~~~ 184 (185)
T cd00642 150 MRGVRKPGSKTVTSAMLGVFKEDPKTREEFLRLIR 184 (185)
T ss_pred hcCcccCCCeEEEEEeEEEECCCHHHHHHHHHHhc
Confidence 37788889999999999999998888999998764
No 11
>PF15389 DUF4612: Domain of unknown function (DUF4612)
Probab=24.25 E-value=47 Score=21.43 Aligned_cols=11 Identities=36% Similarity=0.709 Sum_probs=9.0
Q ss_pred HhHHHHHHHHh
Q 048001 33 QVCQAEYFRQL 43 (48)
Q Consensus 33 q~CQaeyFr~l 43 (48)
-.=|++|||-|
T Consensus 88 S~SQqdFFRML 98 (115)
T PF15389_consen 88 SESQQDFFRML 98 (115)
T ss_pred hHHHHHHHHHH
Confidence 46799999976
No 12
>PRK09347 folE GTP cyclohydrolase I; Provisional
Probab=22.30 E-value=1.7e+02 Score=19.63 Aligned_cols=34 Identities=15% Similarity=0.345 Sum_probs=29.9
Q ss_pred hheeeeeCeeeEEEEeeeeeeehHhHHHHHHHHh
Q 048001 10 YRAVKEVGKIKMSVGVIAYYQLVQVCQAEYFRQL 43 (48)
Q Consensus 10 fRalK~~g~~~i~VrvIAcyQ~~q~CQaeyFr~l 43 (48)
-|.+|..|..|++.-.--+|+.-..-..|+|+.+
T Consensus 153 ~RGv~~~~s~t~T~~~~G~F~~~~~~r~ef~~~i 186 (188)
T PRK09347 153 MRGVRKPGSKTVTSALRGLFKTDPATRAEFLSLI 186 (188)
T ss_pred hhCceeCCceEEEEEEEeEeCCCHHHHHHHHHHh
Confidence 4778888999999899999999899999999876
No 13
>KOG0094 consensus GTPase Rab6/YPT6/Ryh1, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.02 E-value=45 Score=23.89 Aligned_cols=13 Identities=15% Similarity=0.312 Sum_probs=11.0
Q ss_pred ehhhhhhheeeee
Q 048001 4 AITLKRYRAVKEV 16 (48)
Q Consensus 4 a~~qtrfRalK~~ 16 (48)
-|+|.|||.|-.-
T Consensus 78 TAGQERFrslips 90 (221)
T KOG0094|consen 78 TAGQERFRSLIPS 90 (221)
T ss_pred cccHHHHhhhhhh
Confidence 5899999999765
No 14
>KOG0080 consensus GTPase Rab18, small G protein superfamily [General function prediction only]
Probab=20.59 E-value=36 Score=24.25 Aligned_cols=13 Identities=15% Similarity=0.355 Sum_probs=10.9
Q ss_pred ehhhhhhheeeee
Q 048001 4 AITLKRYRAVKEV 16 (48)
Q Consensus 4 a~~qtrfRalK~~ 16 (48)
-|+|.|||+|-..
T Consensus 67 TAGqErFRtLTpS 79 (209)
T KOG0080|consen 67 TAGQERFRTLTPS 79 (209)
T ss_pred ccchHhhhccCHh
Confidence 4789999999765
No 15
>KOG0084 consensus GTPase Rab1/YPT1, small G protein superfamily, and related GTP-binding proteins [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.53 E-value=32 Score=24.17 Aligned_cols=11 Identities=18% Similarity=0.504 Sum_probs=8.6
Q ss_pred ehhhhhhheee
Q 048001 4 AITLKRYRAVK 14 (48)
Q Consensus 4 a~~qtrfRalK 14 (48)
-|+|.|||++=
T Consensus 65 TAGQERFrtit 75 (205)
T KOG0084|consen 65 TAGQERFRTIT 75 (205)
T ss_pred ccccHHHhhhh
Confidence 47899999764
No 16
>COG5463 Predicted integral membrane protein [Function unknown]
Probab=20.20 E-value=52 Score=23.26 Aligned_cols=11 Identities=45% Similarity=0.661 Sum_probs=9.1
Q ss_pred eeeehHhHHHH
Q 048001 28 YYQLVQVCQAE 38 (48)
Q Consensus 28 cyQ~~q~CQae 38 (48)
-||.+++|++.
T Consensus 48 lY~svddC~aa 58 (198)
T COG5463 48 LYQSVDDCIAA 58 (198)
T ss_pred eeccHHHHHHc
Confidence 59999999873
No 17
>PRK12606 GTP cyclohydrolase I; Reviewed
Probab=20.14 E-value=1.9e+02 Score=19.84 Aligned_cols=35 Identities=11% Similarity=0.218 Sum_probs=30.2
Q ss_pred hheeeeeCeeeEEEEeeeeeeehHhHHHHHHHHhc
Q 048001 10 YRAVKEVGKIKMSVGVIAYYQLVQVCQAEYFRQLL 44 (48)
Q Consensus 10 fRalK~~g~~~i~VrvIAcyQ~~q~CQaeyFr~ll 44 (48)
-|.+|..|..|.+.-+--.|+....-..|+|+.+-
T Consensus 165 ~RGv~~~~s~t~T~a~~G~F~~d~~~r~efl~~~~ 199 (201)
T PRK12606 165 MRGVRKQNSRMITSVMLGAFRDSAQTRNEFLRLIG 199 (201)
T ss_pred hcCccCCCCeEEEEEeeeEeCCCHHHHHHHHHHhc
Confidence 37788889999999999999999899999998763
Done!