Query psy4340
Match_columns 218
No_of_seqs 146 out of 994
Neff 7.1
Searched_HMMs 29240
Date Fri Aug 16 23:06:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4340.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/4340hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1bm9_A RTP, TER, replication t 19.5 1.1E+02 0.0037 22.5 3.7 31 158-192 13-43 (122)
2 4h62_K Mediator of RNA polymer 19.3 74 0.0025 18.2 2.1 26 189-214 15-40 (40)
3 1xc0_A Pardaxin P-4, PA4; BEND 18.9 66 0.0023 17.6 1.8 17 197-213 16-32 (33)
4 4aw6_A CAAX prenyl protease 1 14.2 1.5E+02 0.0053 26.8 4.1 51 155-205 23-74 (482)
5 1z2z_A Probable tRNA pseudouri 12.3 1.1E+02 0.0037 27.3 2.5 30 146-175 258-288 (446)
6 3cx5_I Cytochrome B-C1 complex 10.2 2.2E+02 0.0074 18.5 2.8 24 1-25 2-26 (65)
7 2ksd_A Aerobic respiration con 9.4 1E+02 0.0035 22.5 1.0 51 20-73 25-76 (115)
8 1szw_A TRNA pseudouridine synt 9.3 2.5E+02 0.0086 24.5 3.7 30 146-175 205-235 (379)
9 1fs1_B SKP1, cyclin A/CDK2-ass 8.8 3.5E+02 0.012 19.6 3.9 37 91-127 101-139 (141)
10 2kii_A Putative uncharacterize 8.4 3E+02 0.01 21.0 3.5 69 63-131 3-77 (181)
No 1
>1bm9_A RTP, TER, replication terminator protein; DNA-binding protein, contrahelicase; 2.00A {Bacillus subtilis} SCOP: a.4.5.7 PDB: 1f4k_A 1j0r_A 2dpd_A 2dpu_A 2efw_A* 2dqr_A
Probab=19.52 E-value=1.1e+02 Score=22.55 Aligned_cols=31 Identities=10% Similarity=0.166 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHhhhhccCcccCcccchhhhhhhh
Q psy4340 158 VNLVSFVYDILLSYIKYNDDVFGLRGEEIVHHVEK 192 (218)
Q Consensus 158 ~n~v~~~W~~yLS~~~~~~~~~~~~~~~~~~~~~~ 192 (218)
+..-+|+|...|..+..++.. |-|+++++++
T Consensus 13 ~~~~~fl~l~IL~ll~~~p~Y----GYeI~~~L~e 43 (122)
T 1bm9_A 13 VKQRAFLKLYMITMTEQERLY----GLKLLEVLRS 43 (122)
T ss_dssp CCHHHHHHHHHHHHHHTTCCB----STTHHHHHHH
T ss_pred HHHHHHHHHHHHHHHccCCch----HHHHHHHHHH
Confidence 456789999999999886654 7777777763
No 2
>4h62_K Mediator of RNA polymerase II transcription subun; mediator complex, nucleus; HET: MES; 3.00A {Saccharomyces cerevisiae}
Probab=19.28 E-value=74 Score=18.16 Aligned_cols=26 Identities=27% Similarity=0.280 Sum_probs=17.6
Q ss_pred hhhhhhHHHHHHHHHhhhhhcCCCCC
Q psy4340 189 HVEKDKIEESLANAVDKRLESNGNGH 214 (218)
Q Consensus 189 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 214 (218)
..|+-|-..-+--|+..-++|+|.|+
T Consensus 15 dtekmeeqldllsaildpskskgags 40 (40)
T 4h62_K 15 DTEKMEEQLDLLSAILDPSKSKGAGS 40 (40)
T ss_pred cHHHHHHHHHHHHHHcCcccccCCCC
Confidence 44554434456678888889999875
No 3
>1xc0_A Pardaxin P-4, PA4; BEND-helix-BEND-helix motif, signaling protein; NMR {Synthetic} SCOP: j.6.1.1 PDB: 2kns_A
Probab=18.88 E-value=66 Score=17.62 Aligned_cols=17 Identities=35% Similarity=0.493 Sum_probs=13.1
Q ss_pred HHHHHHHhhhhhcCCCC
Q psy4340 197 ESLANAVDKRLESNGNG 213 (218)
Q Consensus 197 ~~~~~~~~~~~~~~~~~ 213 (218)
..+-.||+.-|||+|+.
T Consensus 16 ktllsavgsalsssggq 32 (33)
T 1xc0_A 16 KTLLSAVGSALSSSGGQ 32 (33)
T ss_dssp HHHHHHHHHHTTTTTTC
T ss_pred HHHHHHHHHHhhcccCC
Confidence 35667899999998863
No 4
>4aw6_A CAAX prenyl protease 1 homolog; hydrolase, M48 peptidase, integral membrane protein, prelami processing, ageing, progeria; HET: PC1; 3.40A {Homo sapiens} PDB: 2ypt_A
Probab=14.22 E-value=1.5e+02 Score=26.77 Aligned_cols=51 Identities=14% Similarity=0.172 Sum_probs=33.2
Q ss_pred hHHHHHHHHHHHHHHhhhhccCccc-CcccchhhhhhhhhhHHHHHHHHHhh
Q psy4340 155 VIYVNLVSFVYDILLSYIKYNDDVF-GLRGEEIVHHVEKDKIEESLANAVDK 205 (218)
Q Consensus 155 vl~~n~v~~~W~~yLS~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 205 (218)
++...++...|..||++.+.+.-.. ...++|+.+.+.+++-+.+.+-+.+|
T Consensus 23 il~~~~~~~~~e~yL~~RQ~~~~~~~~~vP~~l~~~~~~e~f~ka~~Y~~~k 74 (482)
T 4aw6_A 23 VLLFSWTVYLWETFLAQRQRRIYKTTTHVPPELGQIMDSETFEKSRLYQLDK 74 (482)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHCCSCCSGGGTTCCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHccCCHHHHHHHHHHHHHH
Confidence 6778888999999999998763211 22466666666655555555554443
No 5
>1z2z_A Probable tRNA pseudouridine synthase D; alpha-beta protein., structural genomics, PSI, protein structure initiative; 2.60A {Methanosarcina mazei}
Probab=12.29 E-value=1.1e+02 Score=27.31 Aligned_cols=30 Identities=20% Similarity=0.382 Sum_probs=25.6
Q ss_pred hhcccccchhHHHHHH-HHHHHHHHhhhhcc
Q psy4340 146 FTYISAQYRVIYVNLV-SFVYDILLSYIKYN 175 (218)
Q Consensus 146 F~~VP~~~Rvl~~n~v-~~~W~~yLS~~~~~ 175 (218)
+.-+|...|.+|++.. |.+||-++|..-..
T Consensus 258 ~~~ipr~lr~myv~AyQS~lfN~~lS~Ri~~ 288 (446)
T 1z2z_A 258 FRVLPQNLYRMFVHGYQSYIYNIILCRRIEA 288 (446)
T ss_dssp GTTSCHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHhCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4579999999998866 99999999987764
No 6
>3cx5_I Cytochrome B-C1 complex subunit 9; complex III, electron transfer complex, cytochrome BC1 complex, mitochondrialtransmembrane complex; HET: M3L SUC 6PH UMQ HEM SMA 8PE 9PE CN5 7PH CN3; 1.90A {Saccharomyces cerevisiae} SCOP: f.23.14.1 PDB: 3cxh_I* 2ibz_I* 1kyo_I* 1ezv_I* 1kb9_I* 1p84_I*
Probab=10.21 E-value=2.2e+02 Score=18.52 Aligned_cols=24 Identities=17% Similarity=0.497 Sum_probs=14.8
Q ss_pred ChHHHHHHhhhhch-hHHHHHHHHHH
Q psy4340 1 MTQILRTIFSQKYL-FYTNTLGGGVL 25 (218)
Q Consensus 1 m~~~Y~~~l~~~~P-l~tk~~ts~~l 25 (218)
+..+|+..++ |.. +++-.+.+++.
T Consensus 2 ~~~iY~~~fk-RnSty~~~I~~gaf~ 26 (65)
T 3cx5_I 2 FSSLYKTFFK-RNAVFVGTIFAGAFV 26 (65)
T ss_dssp CHHHHHHHHT-TSCCCHHHHHHHHHH
T ss_pred hHHHHHHHHh-hhhHHHHHHHHHHHH
Confidence 4578999998 555 44444444443
No 7
>2ksd_A Aerobic respiration control sensor protein ARCB; methods development, histidine kinase receptor, membrane domain, two-helical hairpin; NMR {Escherichia coli}
Probab=9.38 E-value=1e+02 Score=22.54 Aligned_cols=51 Identities=14% Similarity=0.156 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHhhhhhc-ccCCCCccHHHHHHHHHHHhhccchHHHHHHHh
Q psy4340 20 LGGGVLMCLGDTIQQTIELYT-KADKTGYDLKRVAHMGITGLFMGPPQHFFYKYL 73 (218)
Q Consensus 20 ~ts~~l~~~gD~iaQ~~~~~~-~~~~~~~D~~Rt~rf~~~G~~~gP~~h~wy~~L 73 (218)
+.++++..+-+++.|.+.... .++-...|.-|+ .+||.+.+|+.-|++..+
T Consensus 25 lL~~~~l~v~A~~~q~~~~~~~~G~v~~~Di~rs---I~Fgli~aP~viYFls~v 76 (115)
T 2ksd_A 25 MLLALALVVLAIVVQMAVTMVLHGQVESIDVIRS---IFFGLLITPWAVYFLSVV 76 (115)
T ss_dssp CSHHHHHHHHHHHHHHHHHHHSCCCSSSSSCCST---TTHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhHhhhhcccchHHHHHHH---HHHHHHHHHHHHHHHHHH
Confidence 344555666667777755431 113444555444 566777888888888765
No 8
>1szw_A TRNA pseudouridine synthase D; novel fold, RNA modification, TRUD, structural proteomics in europe, spine, structural genomics; 2.00A {Escherichia coli} SCOP: d.265.1.4 PDB: 1si7_A 1sb7_A
Probab=9.26 E-value=2.5e+02 Score=24.52 Aligned_cols=30 Identities=7% Similarity=0.087 Sum_probs=22.1
Q ss_pred hhcccccchhHHHHHH-HHHHHHHHhhhhcc
Q psy4340 146 FTYISAQYRVIYVNLV-SFVYDILLSYIKYN 175 (218)
Q Consensus 146 F~~VP~~~Rvl~~n~v-~~~W~~yLS~~~~~ 175 (218)
+.-+|...|.+|++.. |.+||-++|..-..
T Consensus 205 ~~~ipr~lr~~yv~AyQS~lfN~~lS~Ri~~ 235 (379)
T 1szw_A 205 TPVRDRNKRSFWLSAARSALFNQIVAERLKK 235 (379)
T ss_dssp -----CHHHHHHHHHHHHHHHHHHHHHHTTS
T ss_pred hhcCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5679999999999876 99999999988764
No 9
>1fs1_B SKP1, cyclin A/CDK2-associated P45; F-BOX, LRR, leucine-rich repeat, SCF, ubiquitin, ubiquitin protein ligase; 1.80A {Homo sapiens} SCOP: a.157.1.1 d.42.1.1 PDB: 1fs2_B 1ldk_D
Probab=8.80 E-value=3.5e+02 Score=19.65 Aligned_cols=37 Identities=14% Similarity=0.241 Sum_probs=19.3
Q ss_pred HHhhhhhhHHHHHHHHHHHHhcCCChHHHHHH--HHhhh
Q psy4340 91 LDQAIISPVCIIIFLYGIGILEAKPKDEIKEE--VRDKF 127 (218)
Q Consensus 91 ~Dq~v~~P~~~~~f~~~~~~leg~s~~~i~~~--lk~~~ 127 (218)
+|.+=.-++.-.+--.....++|+|++++.+. ++++|
T Consensus 101 AnyL~I~~Lldl~c~~vA~~ikgkt~eeiR~~f~I~~d~ 139 (141)
T 1fs1_B 101 ANYLDIKGLLDVTCKTVANMIKGKTPEEIRKTFNIKNDF 139 (141)
T ss_dssp HHHHTCHHHHHHHHHHHHHHHTTCCHHHHHHHTC-----
T ss_pred HHHHhhhHHHHHHHHHHHHHHcCCCHHHHHHHcCCCCCC
Confidence 34443445553333344567899999888764 35554
No 10
>2kii_A Putative uncharacterized protein; H-NOX, unknown function; HET: HEM; NMR {Shewanella oneidensis} PDB: 2kil_A*
Probab=8.40 E-value=3e+02 Score=20.99 Aligned_cols=69 Identities=4% Similarity=-0.046 Sum_probs=47.1
Q ss_pred cchHHHHHHHhhhhcCCCchhHHHHHHHHHhhhhhhHH------HHHHHHHHHHhcCCChHHHHHHHHhhhHHHH
Q psy4340 63 GPPQHFFYKYLDKYLPKRSGKSIALKLCLDQAIISPVC------IIIFLYGIGILEAKPKDEIKEEVRDKFLVIY 131 (218)
Q Consensus 63 gP~~h~wy~~Ld~~~p~~~~~~~~~Kvl~Dq~v~~P~~------~~~f~~~~~~leg~s~~~i~~~lk~~~~~~l 131 (218)
|-+...|-.++...++...|..++.+.-++.-+|.|.. +.-.+...+-.-|.|.+++.+.+-+.+...+
T Consensus 3 G~I~~~~~~~v~~~~G~e~w~~i~~~a~~~~~~f~~~~~Y~D~~~~~lv~a~s~~~g~~~~~ll~~fG~~~~~~~ 77 (181)
T 2kii_A 3 GIIFNVLEDMVVAQCGMSVWNELLEKHAPKDRVYVSAKSYAESELFSIVQDVAQRLNMPIQDVVKAFGQFLFNGL 77 (181)
T ss_dssp CHHHHHHHHHHHHHTCHHHHHHHHHHHCCSSCCCCSSCCTTTTHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHH
T ss_pred ehHHHHHHHHHHHHcCHHHHHHHHHHhCCCCCceeeccccCHHHHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 55677788888888877778878888777666666542 3344445555668888888877766655433
Done!