Query 029249
Match_columns 196
No_of_seqs 108 out of 151
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 09:54:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029249.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029249hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14009 DUF4228: Domain of un 100.0 1.7E-31 3.7E-36 208.3 6.2 89 1-106 1-95 (181)
2 cd00307 RuBisCO_small_like Rib 52.0 5.8 0.00013 30.1 0.4 21 29-49 43-70 (84)
3 COG1504 Uncharacterized conser 33.1 20 0.00042 29.4 0.8 18 13-30 23-40 (121)
4 cd03527 RuBisCO_small Ribulose 32.9 35 0.00075 26.7 2.1 21 29-49 58-85 (99)
5 PF11211 DUF2997: Protein of u 32.2 35 0.00077 23.3 1.8 12 13-24 3-14 (48)
6 COG4443 Uncharacterized protei 31.9 14 0.00031 27.7 -0.1 29 139-167 38-66 (72)
7 PF04571 Lipin_N: lipin, N-ter 29.1 68 0.0015 25.8 3.2 11 82-92 80-90 (110)
8 PF06483 ChiC: Chitinase C; I 28.2 78 0.0017 27.5 3.6 68 16-88 68-142 (180)
9 cd02980 TRX_Fd_family Thioredo 25.2 88 0.0019 21.3 2.9 27 1-33 44-70 (77)
10 PF01160 Opiods_neuropep: Vert 24.7 18 0.00038 25.0 -0.7 19 154-172 30-48 (48)
11 cd03063 TRX_Fd_FDH_beta TRX-li 24.7 66 0.0014 24.6 2.4 30 1-34 42-71 (92)
12 PF06251 Caps_synth_GfcC: Caps 22.7 58 0.0013 27.7 1.9 34 7-43 164-200 (229)
13 PF06970 RepA_N: Replication i 20.0 1.3E+02 0.0027 22.2 3.0 20 83-102 47-66 (76)
No 1
>PF14009 DUF4228: Domain of unknown function (DUF4228)
Probab=99.97 E-value=1.7e-31 Score=208.35 Aligned_cols=89 Identities=39% Similarity=0.589 Sum_probs=75.8
Q ss_pred CCccccc------cccEEEEEcCCCeEEeeecCccHhHHhhcCCCcEEEeeecCCCCCCCCCCCCCCCCccccceeeeec
Q 029249 1 MGNCQAI------DAAALVIQHPNGRIERLYWPVTASEVMRMNPGHYVSLIIPLPSSSVSDEDKQPDHQKTVRFTRVKLL 74 (196)
Q Consensus 1 MGNCqA~------daa~VVIqHP~GrVEr~y~PVSAaEVM~~nPGHyVal~i~~p~s~~~~~~~~~~~~g~vr~tRIklL 74 (196)
||||.++ +..+|+|+|+||+|++|++||+|+|||.+||||||| .++.. ...+++++|
T Consensus 1 MGn~~~~~~~~~~~~~~vkvv~~~G~v~~~~~pv~a~evm~~~P~h~v~----~~~~~-------------~~~~~~~~l 63 (181)
T PF14009_consen 1 MGNCVSCCLASSSSAATVKVVHPDGKVEEFKRPVTAAEVMLENPGHFVC----DSDSF-------------RFGRRIKPL 63 (181)
T ss_pred CCCcccccccccCCCceEEEEcCCCcEEEeCCCcCHHHHHHHCCCCEEe----ccccc-------------cCCCcccCC
Confidence 9999998 778899999999999999999999999999999998 22111 114799999
Q ss_pred CCCCccCCCCEEEEEehhHHHHHHHHhhHHHH
Q 029249 75 RPSDTLSLGHAYRLVTSQEVMKVLRAKKSAKT 106 (196)
Q Consensus 75 ~PDdtL~lGqvYrLIP~qeV~k~l~akk~~k~ 106 (196)
+|||+|++|++|||+|.+.+.+.+.+...++.
T Consensus 64 ~~d~~L~~G~~Y~llP~~~~~~~~~~~~~~~~ 95 (181)
T PF14009_consen 64 PPDEELQPGQIYFLLPMSRLQSVLSASDMASL 95 (181)
T ss_pred CccCeecCCCEEEEEEccccCcccccchhccc
Confidence 99999999999999999998887766554444
No 2
>cd00307 RuBisCO_small_like Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. This superfamily also contains specific proteins from cyanobacteria. CcmM plays a role in a CO2 concentrating mechanism, which cyanobacteria need to to overcome t
Probab=51.98 E-value=5.8 Score=30.14 Aligned_cols=21 Identities=38% Similarity=0.623 Sum_probs=15.2
Q ss_pred cHhHHh-------hcCCCcEEEeeecCC
Q 029249 29 TASEVM-------RMNPGHYVSLIIPLP 49 (196)
Q Consensus 29 SAaEVM-------~~nPGHyVal~i~~p 49 (196)
.++||| ++||+|||=++--.|
T Consensus 43 ~~~~Vl~el~~c~~~~p~~YVRlig~D~ 70 (84)
T cd00307 43 SEAQVLAALEACLAEHPGEYVRLIGIDP 70 (84)
T ss_pred CHHHHHHHHHHHHHHCCCCeEEEEEEeC
Confidence 466666 899999998655344
No 3
>COG1504 Uncharacterized conserved protein [Function unknown]
Probab=33.07 E-value=20 Score=29.37 Aligned_cols=18 Identities=22% Similarity=0.545 Sum_probs=15.1
Q ss_pred EEEcCCCeEEeeecCccH
Q 029249 13 VIQHPNGRIERLYWPVTA 30 (196)
Q Consensus 13 VIqHP~GrVEr~y~PVSA 30 (196)
++++|||+|++...++|-
T Consensus 23 Ivi~~dG~v~rr~K~lsk 40 (121)
T COG1504 23 IVIRPDGKVERREKELSK 40 (121)
T ss_pred EEEecCCceehhhhhhhh
Confidence 345999999999998883
No 4
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=32.94 E-value=35 Score=26.72 Aligned_cols=21 Identities=24% Similarity=0.419 Sum_probs=16.3
Q ss_pred cHhHHh-------hcCCCcEEEeeecCC
Q 029249 29 TASEVM-------RMNPGHYVSLIIPLP 49 (196)
Q Consensus 29 SAaEVM-------~~nPGHyVal~i~~p 49 (196)
.+++|| ++||||||-++--.+
T Consensus 58 d~~~Vl~ei~~C~~~~p~~YVRliG~D~ 85 (99)
T cd03527 58 DPAQVLREIEACRKAYPDHYVRVVGFDN 85 (99)
T ss_pred CHHHHHHHHHHHHHHCCCCeEEEEEEeC
Confidence 578888 789999998765444
No 5
>PF11211 DUF2997: Protein of unknown function (DUF2997); InterPro: IPR021375 This family of proteins has no known function.
Probab=32.20 E-value=35 Score=23.30 Aligned_cols=12 Identities=33% Similarity=0.578 Sum_probs=9.2
Q ss_pred EEEcCCCeEEee
Q 029249 13 VIQHPNGRIERL 24 (196)
Q Consensus 13 VIqHP~GrVEr~ 24 (196)
++++|||+|+.=
T Consensus 3 ~~I~~dG~V~~~ 14 (48)
T PF11211_consen 3 FTIYPDGRVEEE 14 (48)
T ss_pred EEECCCcEEEEE
Confidence 356999999864
No 6
>COG4443 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.90 E-value=14 Score=27.65 Aligned_cols=29 Identities=24% Similarity=0.469 Sum_probs=25.0
Q ss_pred ccceeeehhhHhhhhccceeccccccccc
Q 029249 139 TNQVSIYLSTFKRIAKGILLTQSEFETCT 167 (196)
Q Consensus 139 ~~~~~~w~~~~~~i~~~~~~~~~~~~~~~ 167 (196)
.-..|+|-|--...-|||-||..||.+-.
T Consensus 38 KyDiR~Wspdh~KMGKGiTLt~eE~~~l~ 66 (72)
T COG4443 38 KYDIRAWSPDHSKMGKGITLTNEEFKALK 66 (72)
T ss_pred cCcccccCcchhhhcCceeecHHHHHHHH
Confidence 34579999999999999999999998643
No 7
>PF04571 Lipin_N: lipin, N-terminal conserved region; InterPro: IPR007651 Mutations in the lipin gene lead to fatty liver dystrophy in mice. The protein has been shown to be phosphorylated by the TOR Ser/Thr protein kinases in response to insulin stimulation. This entry represents a conserved domain found at the N terminus of the member proteins [, ].
Probab=29.09 E-value=68 Score=25.79 Aligned_cols=11 Identities=18% Similarity=0.344 Sum_probs=8.5
Q ss_pred CCCEEEEEehh
Q 029249 82 LGHAYRLVTSQ 92 (196)
Q Consensus 82 lGqvYrLIP~q 92 (196)
-|.+||+.+.+
T Consensus 80 ~GeAfFv~e~~ 90 (110)
T PF04571_consen 80 NGEAFFVEETE 90 (110)
T ss_pred CcEEEEEEecC
Confidence 47899998874
No 8
>PF06483 ChiC: Chitinase C; InterPro: IPR009470 This ~170 aa region is found at the C-terminal to the catalytic domain (IPR001223 from INTERPRO) found in members of glycoside hydrolase family 18.
Probab=28.18 E-value=78 Score=27.49 Aligned_cols=68 Identities=16% Similarity=0.224 Sum_probs=47.8
Q ss_pred cCCCeEEeeecCccHhHHhhcCCCcEEEeeecCCCCCCCCCCCCCCC-------CccccceeeeecCCCCccCCCCEEEE
Q 029249 16 HPNGRIERLYWPVTASEVMRMNPGHYVSLIIPLPSSSVSDEDKQPDH-------QKTVRFTRVKLLRPSDTLSLGHAYRL 88 (196)
Q Consensus 16 HP~GrVEr~y~PVSAaEVM~~nPGHyVal~i~~p~s~~~~~~~~~~~-------~g~vr~tRIklL~PDdtL~lGqvYrL 88 (196)
-|+|-.-+|+-|+||...|+.-.|-=+.++..-- +.+..+-+ +-.+....++-|.|+++..+.-+|+|
T Consensus 68 iPGGt~~~FD~ptSa~~~~kdqSG~g~~vi~sgh-----t~~g~NiGGL~gdfHrvs~tlp~wqslapG~s~~~~~~YyL 142 (180)
T PF06483_consen 68 IPGGTEFEFDYPTSAPDNAKDQSGFGLKVISSGH-----TAAGNNIGGLKGDFHRVSFTLPAWQSLAPGASVELDMVYYL 142 (180)
T ss_pred cCCccEEEEccccCCccccccccCCcEEEEecCC-----cccCCcccccCCceEEEEEECCCccccCCCCEEEEeEEEEe
Confidence 4789999999999999999999988887544211 10111100 11133567788999999999999997
No 9
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=25.15 E-value=88 Score=21.32 Aligned_cols=27 Identities=33% Similarity=0.637 Sum_probs=16.0
Q ss_pred CCccccccccEEEEEcCCCeEEeeecCccHhHH
Q 029249 1 MGNCQAIDAAALVIQHPNGRIERLYWPVTASEV 33 (196)
Q Consensus 1 MGNCqA~daa~VVIqHP~GrVEr~y~PVSAaEV 33 (196)
||+|... -+|++.|+| .+|..+++..+
T Consensus 44 lg~C~~~---P~v~i~~~~---~~y~~v~~~~~ 70 (77)
T cd02980 44 LGACGLA---PVVVVYPDG---VWYGRVTPEDV 70 (77)
T ss_pred cCcccCC---CEEEEeCCC---eEEccCCHHHH
Confidence 6777443 333345766 47788876655
No 10
>PF01160 Opiods_neuropep: Vertebrate endogenous opioids neuropeptide; InterPro: IPR006024 Vertebrate endogenous opioid neuropeptides are released by post-translational proteolytic cleavage of precursor proteins. The precursors consist of the following components: a signal sequence that precedes a conserved region of about 50 residues; a variable-length region; and the sequence of the neuropeptide itself. Three types of precursor are known: preproenkephalin A (gene PENK), which is processed to produce 6 copies of Met-enkephalin, plus Leu-enkephalin; preproenkephalin B (gene PDYN), which is processed to produce neoendorphin, dynorphin, leumorphin, rimorphin and Leu-enkephalin; and prepronocipeptin (gene PNOC), whose processing produces nociceptin (orphanin FQ) and two other potential neuropeptides. Sequence analysis reveals that the conserved N-terminal region of the precursors contains 6 cysteines, which are probably involved in disulphide bond formation. It is speculated that this region might be important for neuropeptide processing [].; GO: 0007218 neuropeptide signaling pathway
Probab=24.75 E-value=18 Score=24.98 Aligned_cols=19 Identities=32% Similarity=0.684 Sum_probs=16.3
Q ss_pred ccceeccccccccccccee
Q 029249 154 KGILLTQSEFETCTGFLSF 172 (196)
Q Consensus 154 ~~~~~~~~~~~~~~~~~~~ 172 (196)
||-+.+..++|.|+.||++
T Consensus 30 Eg~l~ss~~We~C~~~l~~ 48 (48)
T PF01160_consen 30 EGKLSSSKEWEPCKKLLQL 48 (48)
T ss_pred CCCCCChhHHHHHHHHhcC
Confidence 6888889999999998864
No 11
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=24.73 E-value=66 Score=24.55 Aligned_cols=30 Identities=30% Similarity=0.427 Sum_probs=19.5
Q ss_pred CCccccccccEEEEEcCCCeEEeeecCccHhHHh
Q 029249 1 MGNCQAIDAAALVIQHPNGRIERLYWPVTASEVM 34 (196)
Q Consensus 1 MGNCqA~daa~VVIqHP~GrVEr~y~PVSAaEVM 34 (196)
||-|..--- |.|+.|+|+ -+|..|+..+|=
T Consensus 42 ~G~C~~ePl--V~V~~p~g~--v~Y~~V~~edv~ 71 (92)
T cd03063 42 RGMYWLEPL--VEVETPGGR--VAYGPVTPADVA 71 (92)
T ss_pred ceecCCCCE--EEEEeCCCc--EEEEeCCHHHHH
Confidence 455544333 334479988 699999988653
No 12
>PF06251 Caps_synth_GfcC: Capsule biosynthesis GfcC; InterPro: IPR010425 This entry represents uncharacterised bacterial proteins that contain a central beta-grasp like domain related to the SLBB domain [].; PDB: 3P42_B.
Probab=22.71 E-value=58 Score=27.70 Aligned_cols=34 Identities=24% Similarity=0.670 Sum_probs=17.9
Q ss_pred ccccEEEEEcCCCeEEee---ecCccHhHHhhcCCCcEEE
Q 029249 7 IDAAALVIQHPNGRIERL---YWPVTASEVMRMNPGHYVS 43 (196)
Q Consensus 7 ~daa~VVIqHP~GrVEr~---y~PVSAaEVM~~nPGHyVa 43 (196)
+|.-.|.|++|||.|+.. ||--.-.++| ||=.|-
T Consensus 164 Ad~s~v~VI~pdG~v~~~~~a~Wn~~~~~l~---PG~~I~ 200 (229)
T PF06251_consen 164 ADKSRVYVIQPDGSVQKVPVAYWNNQHQELA---PGATIY 200 (229)
T ss_dssp B-SSEEEEE-TTS-EEEEE-STTT--EEE-----TT-EEE
T ss_pred CCcccEEEEeCCCcEEEcceehhccCCCCCC---CCCEEE
Confidence 355688889999999876 5533333333 776654
No 13
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=20.02 E-value=1.3e+02 Score=22.16 Aligned_cols=20 Identities=30% Similarity=0.640 Sum_probs=17.4
Q ss_pred CCEEEEEehhHHHHHHHHhh
Q 029249 83 GHAYRLVTSQEVMKVLRAKK 102 (196)
Q Consensus 83 GqvYrLIP~qeV~k~l~akk 102 (196)
|++|+..|-+|+++.|.-.+
T Consensus 47 G~vYi~~s~eel~~~L~~s~ 66 (76)
T PF06970_consen 47 GNVYIIFSIEELMELLNCSK 66 (76)
T ss_pred CCEEEEeeHHHHHHHHCCCH
Confidence 99999999999999886544
Done!