Query 002224
Match_columns 951
No_of_seqs 26 out of 28
Neff 1.8
Searched_HMMs 29240
Date Mon Mar 25 17:40:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002224.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/002224hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2lcq_A Putative toxin VAPC6; P 57.0 4 0.00014 37.3 1.7 28 902-949 133-160 (165)
2 2kdx_A HYPA, hydrogenase/ureas 41.6 9 0.00031 33.9 1.4 32 899-950 71-103 (119)
3 1qyp_A RNA polymerase II; tran 40.2 8.5 0.00029 30.4 0.9 50 890-948 5-54 (57)
4 2g31_A Reticulon-4; NOGO, heli 26.3 27 0.00093 28.9 1.7 23 485-507 33-55 (60)
5 2gmg_A Hypothetical protein PF 22.0 43 0.0015 30.8 2.3 33 898-949 64-96 (105)
6 2f9i_B Acetyl-coenzyme A carbo 19.5 29 0.001 35.3 0.8 32 897-945 26-57 (285)
7 3h0g_L DNA-directed RNA polyme 19.2 42 0.0014 28.4 1.5 30 898-946 18-47 (63)
8 2ko2_A Reticulon-4; NOGO, memb 18.4 41 0.0014 29.5 1.3 23 486-508 47-69 (79)
9 2jr7_A DPH3 homolog; DESR1, CS 17.7 33 0.0011 30.6 0.6 12 935-947 21-32 (89)
10 4ayb_P DNA-directed RNA polyme 17.0 30 0.001 28.4 0.1 11 902-912 4-14 (48)
No 1
>2lcq_A Putative toxin VAPC6; PIN domain, Zn ribbon domain, ribosome biogenesis, metal BIN protein; NMR {Pyrococcus horikoshii}
Probab=57.01 E-value=4 Score=37.33 Aligned_cols=28 Identities=32% Similarity=0.657 Sum_probs=20.7
Q ss_pred ehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCceEE
Q 002224 902 YKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWVR 949 (951)
Q Consensus 902 yKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGtWvr 949 (951)
|+|..|++....+. + ..-||.||+.=.|
T Consensus 133 y~C~~Cg~~~~~~~-----------~---------~~~Cp~CG~~~~~ 160 (165)
T 2lcq_A 133 YVCIGCGRKFSTLP-----------P---------GGVCPDCGSKVKL 160 (165)
T ss_dssp EEESSSCCEESSCC-----------G---------GGBCTTTCCBEEE
T ss_pred EECCCCCCcccCCC-----------C---------CCcCCCCCCccee
Confidence 99999999887650 0 1259999998444
No 2
>2kdx_A HYPA, hydrogenase/urease nickel incorporation protein HYPA; metallochaperone, metal-binding, metal- binding protein; NMR {Helicobacter pylori}
Probab=41.59 E-value=9 Score=33.92 Aligned_cols=32 Identities=19% Similarity=0.374 Sum_probs=22.7
Q ss_pred ceeehhhhcccccccccCCCCCCCCCCCccchheehhccc-CCCCCCCceEEe
Q 002224 899 GVWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAF-GCPMCGGTWVRV 950 (951)
Q Consensus 899 GvWyKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~-~CPMCGGtWvrv 950 (951)
-+.|||..|+..-.. . ...+ -||-||+.=+++
T Consensus 71 p~~~~C~~CG~~~e~----~----------------~~~~~~CP~Cgs~~~~i 103 (119)
T 2kdx_A 71 KVELECKDCSHVFKP----N----------------ALDYGVCEKCHSKNVII 103 (119)
T ss_dssp CCEEECSSSSCEECS----C----------------CSTTCCCSSSSSCCCEE
T ss_pred cceEEcCCCCCEEeC----C----------------CCCCCcCccccCCCcEE
Confidence 357899999976432 0 1256 799999987665
No 3
>1qyp_A RNA polymerase II; transcription, RPB9, Zn ribbon, hyperthermophilic, extremophIle; NMR {Thermococcus celer} SCOP: g.41.3.1
Probab=40.20 E-value=8.5 Score=30.41 Aligned_cols=50 Identities=24% Similarity=0.381 Sum_probs=31.0
Q ss_pred EeeecCCCcceeehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCceE
Q 002224 890 TAVWKTGLEGVWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWV 948 (951)
Q Consensus 890 Ta~WKtgleGvWyKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGtWv 948 (951)
...|++.-.- -.+|.+|+.+...|..-- +-.. .|-+. =-|-|+-||-+|-
T Consensus 5 e~~~~~~~~~-~~~Cp~Cg~~~~~~~q~Q-~rsa--dep~T-----~fy~C~~Cg~~w~ 54 (57)
T 1qyp_A 5 EQDLKTLPTT-KITCPKCGNDTAYWWEMQ-TRAG--DEPST-----IFYKCTKCGHTWR 54 (57)
T ss_dssp CCCCSSSCEE-ECCCTTTCCSEEEEEEEC-CSSS--SCSSE-----EEEEESSSCCEEE
T ss_pred hhhhhcCCce-EeECCCCCCCEEEEEEee-cccC--CCCCc-----EEEEcCCCCCEec
Confidence 3467776554 679999999877776421 1111 11111 2377999999994
No 4
>2g31_A Reticulon-4; NOGO, helix, signaling protein; NMR {Homo sapiens} PDB: 2jv5_A
Probab=26.31 E-value=27 Score=28.87 Aligned_cols=23 Identities=30% Similarity=0.452 Sum_probs=20.8
Q ss_pred hHHHHHHHHHHHHHHHHHHhhhh
Q 002224 485 SIQAYVDAVLDLASHFITRLRRY 507 (951)
Q Consensus 485 ~iQaYVDavlDLashfitRLRrY 507 (951)
.++.|+|.+++...+++++|||-
T Consensus 33 ~~~~~~~~~v~~in~~l~~lrrL 55 (60)
T 2g31_A 33 LVQKYSNSALGHVNCTIKELRRL 55 (60)
T ss_dssp HHHHHHHHGGGTCHHHHHHHHTS
T ss_pred HHHHHHHHHHHHHHHHHHHHhHh
Confidence 36899999999999999999984
No 5
>2gmg_A Hypothetical protein PF0610; winged-helix like protein with metal binding site, structura genomics, PSI, protein structure initiative; NMR {Pyrococcus furiosus} SCOP: a.4.5.82
Probab=22.01 E-value=43 Score=30.81 Aligned_cols=33 Identities=27% Similarity=0.582 Sum_probs=22.0
Q ss_pred cceeehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCceEE
Q 002224 898 EGVWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGTWVR 949 (951)
Q Consensus 898 eGvWyKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGtWvr 949 (951)
.-.=|||..|+-+ | . ...+.| --||.|+.+|+.
T Consensus 64 ~v~p~~C~~CG~~---F-~-~~~~kP--------------srCP~CkSe~Ie 96 (105)
T 2gmg_A 64 LIKPAQCRKCGFV---F-K-AEINIP--------------SRCPKCKSEWIE 96 (105)
T ss_dssp EECCCBBTTTCCB---C-C-CCSSCC--------------SSCSSSCCCCBC
T ss_pred EEECcChhhCcCe---e-c-ccCCCC--------------CCCcCCCCCccC
Confidence 3445899999987 4 1 111222 359999999974
No 6
>2f9i_B Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta; zinc ribbon, crotonase superfamily, spiral domain; 1.98A {Staphylococcus aureus}
Probab=19.50 E-value=29 Score=35.28 Aligned_cols=32 Identities=19% Similarity=0.356 Sum_probs=21.9
Q ss_pred CcceeehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCC
Q 002224 897 LEGVWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGG 945 (951)
Q Consensus 897 leGvWyKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGG 945 (951)
.||.|.||..|....- .++. .+|.+-||.|+-
T Consensus 26 ~~~l~~kc~~~~~~~y------------~~~l-----~~~~~v~p~~~~ 57 (285)
T 2f9i_B 26 PAGIMTKCPKCKKIMY------------TKEL-----AENLNVCFNCDH 57 (285)
T ss_dssp CCSSEEECTTTCCEEE------------HHHH-----HHTTTBCTTTCC
T ss_pred ChHHHHhhHhhCCccc------------hhhh-----HHhcCcCCCCCC
Confidence 5799999999986321 1122 456678999975
No 7
>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=19.23 E-value=42 Score=28.37 Aligned_cols=30 Identities=20% Similarity=0.540 Sum_probs=20.5
Q ss_pred cceeehhhhcccccccccCCCCCCCCCCCccchheehhcccCCCCCCCc
Q 002224 898 EGVWYKCIRCLRQTAAFASPGATNPPNQNDREAWWISRWAFGCPMCGGT 946 (951)
Q Consensus 898 eGvWyKciRC~RQTsAf~sp~a~~~p~qn~rE~wWisRW~~~CPMCGGt 946 (951)
+.+-|+|.+|+.-..- . .+=..-||.||.+
T Consensus 18 ~~v~Y~C~~Cg~~~~l----------~---------~~~~iRC~~CG~R 47 (63)
T 3h0g_L 18 ATMIYLCADCGARNTI----------Q---------AKEVIRCRECGHR 47 (63)
T ss_dssp -CCCCBCSSSCCBCCC----------C---------SSSCCCCSSSCCC
T ss_pred CCeEEECCCCCCeeec----------C---------CCCceECCCCCcE
Confidence 3789999999775541 0 1234579999986
No 8
>2ko2_A Reticulon-4; NOGO, membrane protein, peripheral, DPC micelle, myelin INHI endoplasmic reticulum, membrane, phosphoprotein, transmembr; NMR {Mus musculus}
Probab=18.40 E-value=41 Score=29.49 Aligned_cols=23 Identities=30% Similarity=0.465 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhh
Q 002224 486 IQAYVDAVLDLASHFITRLRRYA 508 (951)
Q Consensus 486 iQaYVDavlDLashfitRLRrYA 508 (951)
++.|+|.+++....++++|||-.
T Consensus 47 ~~~~~~~~v~~in~~l~~LRrLf 69 (79)
T 2ko2_A 47 VQKYSNSALGHVNSTIKELRRLF 69 (79)
T ss_dssp HHHHHHCTTTHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhHHh
Confidence 68999999999999999999964
No 9
>2jr7_A DPH3 homolog; DESR1, CSL zinc finger, metal binding protein; NMR {Homo sapiens}
Probab=17.75 E-value=33 Score=30.59 Aligned_cols=12 Identities=33% Similarity=1.290 Sum_probs=10.1
Q ss_pred hcccCCCCCCCce
Q 002224 935 RWAFGCPMCGGTW 947 (951)
Q Consensus 935 RW~~~CPMCGGtW 947 (951)
.|.|.|| ||+..
T Consensus 21 ~y~ypCr-CGd~F 32 (89)
T 2jr7_A 21 TYFYPCP-CGDNF 32 (89)
T ss_dssp EEEEECT-TSSEE
T ss_pred EEEEcCC-CCCEE
Confidence 5889999 99874
No 10
>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P 2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X
Probab=16.99 E-value=30 Score=28.45 Aligned_cols=11 Identities=27% Similarity=0.972 Sum_probs=8.4
Q ss_pred ehhhhcccccc
Q 002224 902 YKCIRCLRQTA 912 (951)
Q Consensus 902 yKciRC~RQTs 912 (951)
|+|.||++-.+
T Consensus 4 Y~C~rCg~~fs 14 (48)
T 4ayb_P 4 YRCGKCWKTFT 14 (48)
T ss_dssp -CCCCTTTTCC
T ss_pred EEeeccCCCcc
Confidence 99999998654
Done!