Query psy1216
Match_columns 628
No_of_seqs 110 out of 128
Neff 1.8
Searched_HMMs 46136
Date Fri Aug 16 20:14:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1216.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1216hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4037|consensus 100.0 2.7E-89 5.9E-94 646.9 12.2 199 403-627 39-240 (240)
2 PF05351 GMP_PDE_delta: GMP-PD 100.0 2.3E-74 5.1E-79 526.9 13.7 157 441-626 1-157 (157)
3 KOG4038|consensus 99.9 9.6E-25 2.1E-29 197.9 -1.4 94 520-617 48-141 (150)
4 PF14796 AP3B1_C: Clathrin-ada 44.1 28 0.0006 32.9 3.7 53 511-564 65-120 (145)
5 PHA02697 hypothetical protein; 39.5 23 0.00051 36.3 2.6 41 575-617 64-117 (255)
6 PF06218 NPR2: Nitrogen permea 37.6 46 0.001 36.0 4.6 70 508-584 12-99 (428)
7 TIGR03780 Bac_Flav_CT_N Bacter 35.6 25 0.00054 36.5 2.2 14 447-460 197-210 (285)
8 PF13595 DUF4138: Domain of un 34.5 28 0.0006 34.9 2.2 16 447-462 158-173 (246)
9 PHA02994 hypothetical protein; 30.2 31 0.00068 35.0 1.8 41 575-617 51-104 (218)
10 cd01676 RNR_II_monomer Class I 19.0 86 0.0019 35.6 2.7 61 224-284 570-633 (658)
No 1
>KOG4037|consensus
Probab=100.00 E-value=2.7e-89 Score=646.92 Aligned_cols=199 Identities=62% Similarity=1.081 Sum_probs=181.6
Q ss_pred CCCCCCCCCCCHHH-hhcCCCCChhhhhccccCCCccccCCCCceeeeeeeeEEEeeCCCCcEEEEeeCCCCCC--CCCC
Q psy1216 403 SPSSKEASPVTEEE-LLRKPYITPEDVLCLNHITENYLCSPDANIYEIEFLRFKIRDIDSNTVLFEIAKPANTA--STPS 479 (628)
Q Consensus 403 ~~~~~~~~~~TEee-Ll~k~~ITPEdVL~LtkpTe~YLC~PsANIYnIdFtRFKIRDlESG~VLFEIaKPp~se--~~p~ 479 (628)
+++..++.+-++.+ |.++..|||+|||+|++||++|||+|+||+|+|||+||||||||||+|||||+|||.+. .++
T Consensus 39 ~~~~~~ag~~~~a~~la~~~~itP~dVL~L~~IT~dyLCSp~aNvy~IdFtrFkIRDldsg~VLFEIaKPp~eteE~l~- 117 (240)
T KOG4037|consen 39 SESEPDAGPGPRAGPLARKQPITPEDVLGLQRITGDYLCSPEANVYKIDFTRFKIRDLDSGTVLFEIAKPPVETEERLP- 117 (240)
T ss_pred CCCCCCCCCCCCCCcccccCCCChHHhhccccccCCceeCcccceEEeeeEEEEEeeccCCcEEEEecCCCCcchhhcc-
Confidence 44444455555555 45567999999999999999999999999999999999999999999999999998762 221
Q ss_pred CCCCCCCCCCCCcCCCCCCCCCccCCCCCCCCCCCceEEEEeCccccccccceeEEEEeecccccccceeEEEeeeCCcc
Q psy1216 480 STPGNNAESPESQGDRNSTSHDTQANNIPKDPNTGRFVRYQFTPKFLNLKNIGATITFSIGDFEINNFRMIEKHYFNDTV 559 (628)
Q Consensus 480 ~e~~~~a~spe~~~~r~~~s~d~d~~l~~~DpnagRfVRYQFppkFLklKtVgreIeFSVGdEPI~NFRMIERHYFRdqL 559 (628)
.+.++.+|||||+|||||+|.||+||+|||+|+|+||++||+||||||||||||+|
T Consensus 118 ------------------------a~ae~lspnagRyVRYqFtPaFL~LktVGATVEFtVGd~PvnnFRMIERHfFrdrL 173 (240)
T KOG4037|consen 118 ------------------------ANAEDLSPNAGRYVRYQFTPAFLRLKTVGATVEFTVGDKPVNNFRMIERHFFRDRL 173 (240)
T ss_pred ------------------------hhhhccCCcccceEEEeechhHeeeeecccEEEEEeCCeecchhhHHHHHHHHHHH
Confidence 12345679999999999999999999999999999999999999999999999999
Q ss_pred eeeeeeeeeeeeecCCcccceEEEecCCCCHHHHHHHHhCCCcccccceEEeCCeEeeeccccccccC
Q psy1216 560 HLKTFDFNFGYCIPNSINTCEHIYVFPNLSKSLTQEMIDNPFHTKSDSFYFINNKLFMHNKAEYSYNG 627 (628)
Q Consensus 560 ~LKsfDFeFGFCIPnStNTWEhIYE~PqLsedLieEMI~~PyETkSDSFYFVDNKLVMHNKADYaYnG 627 (628)
||+|||+||||||+|+||||||||||+|+++|+.|||.|||||+|||||||+|+|||||||||+|+|
T Consensus 174 -LK~FDFeFGFC~P~SkNtcEHIYeFP~Ls~~L~~eMI~~P~ETrSDSFYFV~nrLVMHNKADYsYdg 240 (240)
T KOG4037|consen 174 -LKSFDFEFGFCIPSSKNTCEHIYEFPPLSEELMAEMINNPNETRSDSFYFVENRLVMHNKADYSYDG 240 (240)
T ss_pred -HhhccceeeEeecCCCCcchhhhcCCCCCHHHHHHHhcCccccCCcceEEEccEEEEecccccccCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999987
No 2
>PF05351 GMP_PDE_delta: GMP-PDE, delta subunit; InterPro: IPR008015 GMP-PDE delta subunit was originally identified as a fourth subunit of rod-specific cGMP phosphodiesterase (PDE) (3.1.4.35 from EC). The precise function of PDE delta subunit in the rod specific GMP-PDE complex is unclear. In addition, PDE delta subunit is not confined to photoreceptor cells but is widely distributed in different tissues. PDE delta subunit is thought to be a specific soluble transport factor for certain prenylated proteins and Arl2-GTP a regulator of PDE-mediated transport [].; PDB: 3RBQ_B 3GQQ_C 3T5I_A 3T5G_B 1KSG_B 1KSJ_B 1KSH_B.
Probab=100.00 E-value=2.3e-74 Score=526.88 Aligned_cols=157 Identities=62% Similarity=1.095 Sum_probs=138.9
Q ss_pred CCCCceeeeeeeeEEEeeCCCCcEEEEeeCCCCCCCCCCCCCCCCCCCCCCcCCCCCCCCCccCCCCCCCCCCCceEEEE
Q psy1216 441 SPDANIYEIEFLRFKIRDIDSNTVLFEIAKPANTASTPSSTPGNNAESPESQGDRNSTSHDTQANNIPKDPNTGRFVRYQ 520 (628)
Q Consensus 441 ~PsANIYnIdFtRFKIRDlESG~VLFEIaKPp~se~~p~~e~~~~a~spe~~~~r~~~s~d~d~~l~~~DpnagRfVRYQ 520 (628)
+|+||+|+|+|++|+|||+|||+||||+++|+++.. ...+.+++++|+|+||
T Consensus 1 ~~~~n~ygi~f~~f~iRD~dtg~vlfe~~~~~~~~~----------------------------~~~~~~~~~~r~v~y~ 52 (157)
T PF05351_consen 1 KPEANIYGIEFTRFKIRDADTGKVLFEINKDPSDVE----------------------------QLEPEDPNAGREVRYR 52 (157)
T ss_dssp -HHHHCCHEEEEEEEEEETTTTEEEEEEESSTTS------------------------------STT-----TTTEEEEE
T ss_pred ChhhceeCcEEEEEEEEECCCCcEEEEecCCCCchh----------------------------hcccccCCCceEEEEE
Confidence 478999999999999999999999999999966511 2345689999999999
Q ss_pred eCccccccccceeEEEEeecccccccceeEEEeeeCCcceeeeeeeeeeeeecCCcccceEEEecCCCCHHHHHHHHhCC
Q psy1216 521 FTPKFLNLKNIGATITFSIGDFEINNFRMIEKHYFNDTVHLKTFDFNFGYCIPNSINTCEHIYVFPNLSKSLTQEMIDNP 600 (628)
Q Consensus 521 FppkFLklKtVgreIeFSVGdEPI~NFRMIERHYFRdqL~LKsfDFeFGFCIPnStNTWEhIYE~PqLsedLieEMI~~P 600 (628)
|||+||+||+|||+|+||||++||+||||||||||||+| ||+|||+||||||||+||||||||+|+|+++++++||++|
T Consensus 53 fp~~~L~~k~V~~~i~Fsvg~~pv~nFRmierhyF~~~l-lk~~dF~FGFcIP~S~NTwE~iye~p~l~~~l~~~mi~gp 131 (157)
T PF05351_consen 53 FPPKFLKLKTVGREIEFSVGDEPVNNFRMIERHYFRDQL-LKSFDFEFGFCIPNSTNTWEHIYEFPPLSQMLPAEMISGP 131 (157)
T ss_dssp EEGGGGG-SEEEEEEEEEE-SS-ECCEEEEEEEEETTEE-EEEEEEEEEEE-TTCEEEEEEEEEB--CSCCHHHHHHCTT
T ss_pred cCHHHhcchhheEEEEEEECceeccccEeeEeeeecCce-eeEEEeeeeeEcCCCccceeEEEEcCCCCchhHHHHHcCC
Confidence 999999999999999999999999999999999999999 9999999999999999999999999999999999999999
Q ss_pred CcccccceEEeCCeEeeecccccccc
Q psy1216 601 FHTKSDSFYFINNKLFMHNKAEYSYN 626 (628)
Q Consensus 601 yETkSDSFYFVDNKLVMHNKADYaYn 626 (628)
|||+|||||||||+|||||||+|+|+
T Consensus 132 ~et~sdSfyfv~~~Limhnka~y~Y~ 157 (157)
T PF05351_consen 132 YETKSDSFYFVDDKLIMHNKARYFYS 157 (157)
T ss_dssp TTEEEEEEEEETTEEEEEEEEEEEES
T ss_pred CcceEEEEEEeCCEEEEEEEEEEecC
Confidence 99999999999999999999999996
No 3
>KOG4038|consensus
Probab=99.88 E-value=9.6e-25 Score=197.95 Aligned_cols=94 Identities=29% Similarity=0.436 Sum_probs=78.2
Q ss_pred EeCccccccccceeEEEEeecccccccceeEEEeeeCCcceeeeeeeeeeeeecCCcccceEEEecCCCCHHHHHHHHhC
Q psy1216 520 QFTPKFLNLKNIGATITFSIGDFEINNFRMIEKHYFNDTVHLKTFDFNFGYCIPNSINTCEHIYVFPNLSKSLTQEMIDN 599 (628)
Q Consensus 520 QFppkFLklKtVgreIeFSVGdEPI~NFRMIERHYFRdqL~LKsfDFeFGFCIPnStNTWEhIYE~PqLsedLieEMI~~ 599 (628)
+.|+++|+|++|+|+|+|| +-+.|++|||.||+||+|++ +++|.|+||||||||+||||++||+++=|+=.- .-+.+
T Consensus 48 rvpkkilkcravsreinfs-s~e~mekfrleqkvyfkg~i-~eewffefgfvipnstntwqs~ieaapesqmmp-asvl~ 124 (150)
T KOG4038|consen 48 RVPKKILKCRAVSREINFS-SIESMEKFRLEQKVYFKGRI-MEEWFFEFGFVIPNSTNTWQSTIEAAPESQMMP-ASVLN 124 (150)
T ss_pred cccHHHHhhHhhhhhcccc-hHHHHHhhhhhheeeeccee-HHHhhhhhceeccCCcchHHHHHhhCchhccCC-hhhcc
Confidence 5899999999999999999 88999999999999999999 999999999999999999999999987654222 22344
Q ss_pred CCcccccceEEeCCeEee
Q psy1216 600 PFHTKSDSFYFINNKLFM 617 (628)
Q Consensus 600 PyETkSDSFYFVDNKLVM 617 (628)
-.-|.--||| -++-||-
T Consensus 125 gnv~iet~fy-d~dllvs 141 (150)
T KOG4038|consen 125 GNVTIETSFY-DNDLLVS 141 (150)
T ss_pred CceEEEEEEe-cCCEEEE
Confidence 4555666888 4444543
No 4
>PF14796 AP3B1_C: Clathrin-adaptor complex-3 beta-1 subunit C-terminal
Probab=44.06 E-value=28 Score=32.94 Aligned_cols=53 Identities=23% Similarity=0.351 Sum_probs=42.8
Q ss_pred CCCCceEEEEeCcc--ccccccceeEEEEee-cccccccceeEEEeeeCCcceeeee
Q psy1216 511 PNTGRFVRYQFTPK--FLNLKNIGATITFSI-GDFEINNFRMIEKHYFNDTVHLKTF 564 (628)
Q Consensus 511 pnagRfVRYQFppk--FLklKtVgreIeFSV-GdEPI~NFRMIERHYFRdqL~LKsf 564 (628)
...|=.|.|+|+.+ ...-+-|+-+|.|++ ++++|++.++.++.+=.|.- |++|
T Consensus 65 ~G~GL~v~Y~F~RqP~~~s~~mvsIql~ftN~s~~~i~~I~i~~k~l~~g~~-i~~F 120 (145)
T PF14796_consen 65 NGKGLSVEYRFSRQPSLYSPSMVSIQLTFTNNSDEPIKNIHIGEKKLPAGMR-IHEF 120 (145)
T ss_pred CCCceeEEEEEccCCcCCCCCcEEEEEEEEecCCCeecceEECCCCCCCCcE-eecc
Confidence 34577899999874 455667899999998 99999999999999877777 5444
No 5
>PHA02697 hypothetical protein; Provisional
Probab=39.49 E-value=23 Score=36.33 Aligned_cols=41 Identities=12% Similarity=0.240 Sum_probs=32.5
Q ss_pred CcccceEE----------EecCCCC---HHHHHHHHhCCCcccccceEEeCCeEee
Q psy1216 575 SINTCEHI----------YVFPNLS---KSLTQEMIDNPFHTKSDSFYFINNKLFM 617 (628)
Q Consensus 575 StNTWEhI----------YE~PqLs---edLieEMI~~PyETkSDSFYFVDNKLVM 617 (628)
+.+||+.| |.+-+++ ++|-..|+. .-+.-+++|||.|-|+.
T Consensus 64 ~sdTWd~ir~~~I~hVVFFqakQv~isVeeLY~~~~e--nl~~~~~LYFVrD~L~f 117 (255)
T PHA02697 64 GEDTWDLARSHDVRHVVLFKASVVDWRVEELFLGFGE--KLGGLDALYFVADGFYV 117 (255)
T ss_pred CccHHHHhhcCCcCEEEEEEeeeeceeHHHHHHHHHh--cCCCceEEEEEecceEe
Confidence 45899987 6677777 888888886 45667899999998875
No 6
>PF06218 NPR2: Nitrogen permease regulator 2; InterPro: IPR009348 This family of regulators are involved in post-translational control of nitrogen permease.
Probab=37.57 E-value=46 Score=36.05 Aligned_cols=70 Identities=23% Similarity=0.346 Sum_probs=42.5
Q ss_pred CCCCCCCceEEEEeCcccc--cccc--------------ceeEEEEeecccccccc--eeEEEeeeCCcceeeeeeeeee
Q psy1216 508 PKDPNTGRFVRYQFTPKFL--NLKN--------------IGATITFSIGDFEINNF--RMIEKHYFNDTVHLKTFDFNFG 569 (628)
Q Consensus 508 ~~DpnagRfVRYQFppkFL--klKt--------------VgreIeFSVGdEPI~NF--RMIERHYFRdqL~LKsfDFeFG 569 (628)
.-+|.+|--|.||+|+..+ .+-. -++.|.+..+.-.|=.| .|...+|=|+. |-|+||
T Consensus 12 ~F~p~~GpkI~~Q~P~~~i~~~~~~Fd~is~yIIPk~~lc~rlitv~~~~~kIlg~PV~I~~~kY~RN~-----f~FN~c 86 (428)
T PF06218_consen 12 EFHPTEGPKIVHQVPEGSIKPSLFNFDSISNYIIPKPELCNRLITVNAGGYKILGYPVCIEDPKYERNE-----FIFNFC 86 (428)
T ss_pred ecCCCCCCEEEEECCcccccccccchhhcccEEecChHHhCceeEEeeCCeEEEEeeeEecCCeeccce-----EEEEEE
Confidence 3467788899999999888 2211 13444554333322222 12334565555 489999
Q ss_pred eeecCCcccceEEEe
Q psy1216 570 YCIPNSINTCEHIYV 584 (628)
Q Consensus 570 FCIPnStNTWEhIYE 584 (628)
||.+...++ .-||
T Consensus 87 fV~~~~~~~--~~Ye 99 (428)
T PF06218_consen 87 FVFDYDSDT--SPYE 99 (428)
T ss_pred EEEcCCCCc--cchH
Confidence 999998664 4555
No 7
>TIGR03780 Bac_Flav_CT_N Bacteroides conjugative transposon TraN protein. Members of this family are the TraN protein encoded by transfer region genes of conjugative transposons of Bacteroides. The family is related to conjugative transfer proteins VirB9 and TrbG of Agrobacterium Ti plasmids.
Probab=35.64 E-value=25 Score=36.45 Aligned_cols=14 Identities=50% Similarity=1.054 Sum_probs=12.9
Q ss_pred eeeeeeeEEEeeCC
Q psy1216 447 YEIEFLRFKIRDID 460 (628)
Q Consensus 447 YnIdFtRFKIRDlE 460 (628)
|+|||.+|+|+|--
T Consensus 197 ydID~irfki~DKK 210 (285)
T TIGR03780 197 FDIDFIRFKIVDKK 210 (285)
T ss_pred cEeEEEEEEEEecc
Confidence 99999999999964
No 8
>PF13595 DUF4138: Domain of unknown function (DUF4138)
Probab=34.54 E-value=28 Score=34.87 Aligned_cols=16 Identities=50% Similarity=0.974 Sum_probs=14.1
Q ss_pred eeeeeeeEEEeeCCCC
Q psy1216 447 YEIEFLRFKIRDIDSN 462 (628)
Q Consensus 447 YnIdFtRFKIRDlESG 462 (628)
|+|||.+|+|+|-...
T Consensus 158 ydID~irf~i~DkK~~ 173 (246)
T PF13595_consen 158 YDIDFIRFKIVDKKKA 173 (246)
T ss_pred eEEeEEEEEEEecchh
Confidence 9999999999997653
No 9
>PHA02994 hypothetical protein; Provisional
Probab=30.16 E-value=31 Score=34.97 Aligned_cols=41 Identities=32% Similarity=0.460 Sum_probs=32.9
Q ss_pred CcccceEE----------EecCCCC---HHHHHHHHhCCCcccccceEEeCCeEee
Q psy1216 575 SINTCEHI----------YVFPNLS---KSLTQEMIDNPFHTKSDSFYFINNKLFM 617 (628)
Q Consensus 575 StNTWEhI----------YE~PqLs---edLieEMI~~PyETkSDSFYFVDNKLVM 617 (628)
+..||+.+ |.+-||+ ++|-+.|+. --...+.+|||.|-|+.
T Consensus 51 ~~~tW~~i~~~~I~~vVFyq~kQlsisv~~Ly~~l~~--~~~~~~~iyFV~D~l~f 104 (218)
T PHA02994 51 SSKTWEDIQNNKIDALVFYQVKQLSISVEKLYNSMMR--NRIKPIKIYFVRDNLAF 104 (218)
T ss_pred CccHHHHhhcCCCCEEEEEEEEEeeeeHHHHHHHHHh--cCCCceEEEEEeeceee
Confidence 46899987 7788888 888899984 55667899999998864
No 10
>cd01676 RNR_II_monomer Class II ribonucleotide reductase, monomeric form. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). Class II RNRs are found in bacteria that can live under both aerobic and anaerobic conditions. Man
Probab=18.99 E-value=86 Score=35.64 Aligned_cols=61 Identities=15% Similarity=0.207 Sum_probs=38.3
Q ss_pred CCCCCCCCC-ChhhHHHHHhhccc--ccccccccccccchhhhhhhcccchhhHHHHhcccccc
Q psy1216 224 SEGTNVDPD-DVEDVEEIVMENRN--VDANFDRRTSRYSSQEFVETRRVDEKTYEERKMNLKTM 284 (628)
Q Consensus 224 ~~~~~~~~~-~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 284 (628)
|---|++|+ .++||.+++..++. .-+.|=+|.++--+..-+---.+|+++||++..++|..
T Consensus 570 SkTIn~p~~~~~~dV~~~l~~~~~~~KG~t~l~~~d~~~~~~q~P~E~I~ke~ye~~~~~~~~~ 633 (658)
T cd01676 570 SNTISFDPSPEGPALIQALQQFQYQYKSVSLLPRFDTTKNAAQMPFEPITKERYEQRIAKLKDV 633 (658)
T ss_pred cceEeeCCCCCHHHHHHHHHHhhcCCeEEEEeecCCcccCcccCCccccCHHHHHHHHhhcCcc
Confidence 334578888 89999999999866 11223233222111011222349999999999999855
Done!