Query T0627 NP_791563.1, Pseudomonas syringae pv. tomato str. DC3000, 261 residues
Match_columns 261
No_of_seqs 117 out of 602
Neff 8.6
Searched_HMMs 11830
Date Thu Jul 22 15:05:49 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0627.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0627.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03070 TENA_THI-4: TENA/THI- 100.0 1E-40 8.4E-45 275.3 23.1 209 25-246 1-210 (210)
2 PF11251 DUF3050: Protein of u 99.6 3.2E-14 2.7E-18 106.2 17.0 199 35-243 2-232 (232)
3 PF01126 Heme_oxygenase: Heme 98.7 4.8E-07 4.1E-11 60.4 15.1 202 19-241 2-204 (205)
4 PF11583 AurF: P-aminobenzoate 95.8 0.044 3.7E-06 28.8 10.3 138 90-238 114-252 (304)
5 PF05974 DUF892: Domain of unk 59.6 3.5 0.00029 16.7 11.0 84 51-144 3-86 (159)
6 PF02840 Prp18: Prp18 domain; 56.9 3.7 0.00031 16.5 3.1 42 39-80 45-91 (144)
7 PF04305 DUF455: Protein of un 36.8 7.9 0.00067 14.4 11.7 113 90-218 100-214 (253)
8 PF09441 Abp2: ARS binding pro 34.3 8.6 0.00073 14.1 4.4 59 77-135 42-100 (175)
9 PF05138 PaaA_PaaC: Phenylacet 34.2 8.6 0.00073 14.1 10.4 68 52-125 16-86 (263)
10 PF00268 Ribonuc_red_sm: Ribon 27.8 11 0.00094 13.4 20.2 213 15-244 14-238 (281)
11 PF03970 Herpes_UL37_1: Herpes 26.5 12 0.00099 13.3 2.2 57 15-85 23-79 (270)
No 1
>PF03070 TENA_THI-4: TENA/THI-4/PQQC family; InterPro: IPR004305 Proteins containing this domain are found in all the three major phyla of life: archaebacteria, eubacteria, and eukaryotes. In Bacillus subtilis, TENA is one of a number of proteins that enhance the expression of extracellular enzymes, such as alkaline protease, neutral protease and levansucrase . The THI-4 protein, which is involved in thiamine biosynthesis, also contains this domain. The C-terminal part of these proteins consistently show significant sequence similarity to TENA proteins. This similarity was first noted with the Neurospora crassa THI-4 . The exact molecular function of this domain is uncertain.; PDB: 2gm7_B 2gm8_A 1udd_D 2qzc_A 2rd3_D 1to9_A 2qcx_B 1tyh_E 1yaf_A 1yak_C ....
Probab=100.00 E-value=1e-40 Score=275.26 Aligned_cols=209 Identities=18% Similarity=0.206 Sum_probs=180.1
Q ss_pred HHHHHHHHHHHHHCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999998718478998568999899999999989999999999999987278876689999999999866432679
Q T0627 25 INDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFGRHPGEDMARRWLMRNIRVELNH 104 (261)
Q Consensus 25 ~~~~~~~w~~~~~HPF~~~l~~G~L~~e~f~~yl~Qdy~yl~~f~r~la~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~h 104 (261)
++++.|+|+++++|||+++|++|+||++.|++|++|||+||++|+|+++.++++||+.+.+..+..... . ....+
T Consensus 1 ~~~~~~~w~~~~~HPF~~~l~~G~L~~e~f~~yl~Qdy~yl~~~~r~~a~~~a~~~~~~~~~~~~~~~~--~---~~~~e 75 (210)
T PF03070_consen 1 HEKVDPIWQAITNHPFVQELADGTLPKEAFRYYLIQDYHYLKHFARALAAAAARAPDPEDRRELLENLI--E---EIGGE 75 (210)
T ss_dssp -HHTHHHHHHHHTSHHHHHHHTT-EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSHHHHHHHHHHHH--H---HHHHH
T ss_pred CHHHHHHHHHHHCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH--H---HHHHH
T ss_conf 963699999997899999965799999999999995299999999999999871979999999999999--9---98889
Q ss_pred HHHHHHHHHHCCCCHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 99999999871899888720457778999999999974278899999999999850158999999876654203577665
Q T0627 105 ADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAIEGATGEWSAVVCSTGVYAEAFAEETR 184 (261)
Q Consensus 105 ~~l~~~~~~~~Gi~~e~l~~~~p~p~t~ay~~~l~~~a~~~~~~~~laA~~~~~E~~~~~~~~~~~~~~~~~~~~~~~~~ 184 (261)
.++|+++++.+|++.+++.+.+|+|+|++|+++|++++..+++.++++|+.|| +|+|+.++..+..... ...+
T Consensus 76 ~~~~~~~~~~~Gi~~~~~~~~~~~p~~~~y~~~l~~~~~~~~~~~~l~Al~p~-~~~y~~i~~~~~~~~~------~~~~ 148 (210)
T PF03070_consen 76 LELHERFLEELGISREDLENIEPSPATRAYIDYLLSLARTGSYAEGLAALLPC-EWIYAEIAKRLAEELR------APED 148 (210)
T ss_dssp HHHHHHHHHHTT-HHHHHHHST--HHHHHHHHHHHHHHHHT-HHHHHHHHHHH-HHHHHHHHHHCHHHSS------CTSS
T ss_pred HHHHHHHHHHCCCCHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHH-HHHHHHHHHHHHHHHC------CCCC
T ss_conf 99999999983999888743246668999999999976359899999999999-9999999999874113------4676
Q ss_pred HHHHHHHHHHCCCCHHHHHHHH-HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 6889999962485356899999-9999997537999899999999999999999999999988
Q T0627 185 KKSMKWLKMHAQYDDAHPWEAL-EIICTLVGNKPSLQLQAELRQAVTKSYDYMYLFLERCIQL 246 (261)
Q Consensus 185 ~~~~~w~~~h~~~D~~h~~e~~-~~i~~~~~~~~~~~~~~~~~~~~~~s~~~e~~f~D~~y~~ 246 (261)
+++.+|++.|+++++.+..+.. .+++.++ ...++.++++++++|.+++++|++|||+||++
T Consensus 149 ~~y~~wi~~y~~~~f~~~~~~~~~~~d~~~-~~~~~~~~~~~~~~f~~~~~~E~~Fwd~a~~~ 210 (210)
T PF03070_consen 149 NPYKEWIDMYASEEFEAAVEELEELLDELA-ADASDEERERLREIFLRSCELEYDFWDMAYRY 210 (210)
T ss_dssp HHHHHHHHHHHSHHHHHHHHHHHHHHHHHH-HTHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred CHHHHHHHHHCCHHHHHHHHHHHHHHHHHH-HHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 017999998577999999999999999998-76899999999999999999999999987559
No 2
>PF11251 DUF3050: Protein of unknown function (DUF3050)
Probab=99.61 E-value=3.2e-14 Score=106.22 Aligned_cols=199 Identities=14% Similarity=0.131 Sum_probs=159.2
Q ss_pred HHHCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHH---------HHHHHHHHHHHHHH-----
Q ss_conf 8718478998568999899999999989999999999999987278876689---------99999999986643-----
Q T0627 35 VVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFGRHPG---------EDMARRWLMRNIRV----- 100 (261)
Q Consensus 35 ~~~HPF~~~l~~G~L~~e~f~~yl~Qdy~yl~~f~r~la~~~~~~~~~~~~~---------~~~~~~~~~~~~~~----- 100 (261)
+.+||.++.+. +.+.++.|+...-+-|.+|+..+..+..++++...+. .+.+-+.+.+...+
T Consensus 2 L~~HplY~~i~----t~~dl~~FMe~HVfAVWDFMSLlK~LQ~~LTc~~~PW~P~~~p~~~rlINEIVl~EEsD~~~~g~ 77 (232)
T PF11251_consen 2 LINHPLYKKIN----TLEDLRIFMEHHVFAVWDFMSLLKALQQHLTCTSVPWVPPGDPEARRLINEIVLGEESDEDPDGG 77 (232)
T ss_pred CCCCCHHHHHC----CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf 76684466518----89999999984477650398899999970747899988999845888887777433034688998
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHH-----------------CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 26799999999987189988872-----------------0457778999999999974278899999999999850158
Q T0627 101 ELNHADYWVNWCAAHDVTLEDLH-----------------DQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAIEGATG 163 (261)
Q Consensus 101 e~~h~~l~~~~~~~~Gi~~e~l~-----------------~~~p~p~t~ay~~~l~~~a~~~~~~~~laA~~~~~E~~~~ 163 (261)
-.+|.++|.+-++..|.+...+. .....++++.++++.+.++.++.++.+.||..++-|.++|
T Consensus 78 ~~SHFElYl~AM~e~GAdt~~I~~fi~~~~~g~~v~~al~~~~~p~~~~~Fv~~Tf~~i~~~~~H~iAAaF~fGREdlIP 157 (232)
T PF11251_consen 78 YISHFELYLDAMREVGADTSPIDAFISLLRSGTSVFAALQQAGLPEPAKEFVRFTFELIESGPPHEIAAAFTFGREDLIP 157 (232)
T ss_pred CCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHCHHHHHH
T ss_conf 15399999999999189849999999998769989999870599879999999999998659718999999726165538
Q ss_pred HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999987665420357766568899999624853-56899999999999753799989999999999999999999999
Q T0627 164 EWSAVVCSTGVYAEAFAEETRKKSMKWLKMHAQYD-DAHPWEALEIICTLVGNKPSLQLQAELRQAVTKSYDYMYLFLER 242 (261)
Q Consensus 164 ~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~h~~~D-~~h~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~s~~~e~~f~D~ 242 (261)
.....+.+.... .....+.+..|++.|.+.| +.|+.-.++++.++|+++ ++..+++.++...+++.+..+||.
T Consensus 158 ~MF~~il~~~~~----~~~~~~~f~yYL~RHIElDgdeHgPla~~m~~~Lcg~D--~~kw~e~~~~a~~Al~~Ri~LWd~ 231 (232)
T PF11251_consen 158 DMFRSILDRLNI----PEQQLPTFRYYLERHIELDGDEHGPLALQMLEELCGDD--PQKWQEAEQAAIEALEARIALWDG 231 (232)
T ss_pred HHHHHHHHHHCC----CCCCCHHHHHHHHHHHEECCCCCHHHHHHHHHHHHCCC--HHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 999999998616----85522488887765510067644499999999997879--999999999999999999987526
Q ss_pred H
Q ss_conf 9
Q T0627 243 C 243 (261)
Q Consensus 243 ~ 243 (261)
+
T Consensus 232 I 232 (232)
T PF11251_consen 232 I 232 (232)
T ss_pred C
T ss_conf 9
No 3
>PF01126 Heme_oxygenase: Heme oxygenase; InterPro: IPR016053 Haem oxygenase (1.14.99.3 from EC) (HO) is the microsomal enzyme that, in animals, carries out the oxidation of haem, it cleaves the haem ring at the alpha-methene bridge to form biliverdin and carbon monoxide . Biliverdin is subsequently converted to bilirubin by biliverdin reductase. In mammals there are three isozymes of haem oxygenase: HO-1 to HO-3. The first two isozymes differ in their tissue expression and their inducibility: HO-1 is highly inducible by its substrate haem and by various non-haem substances, while HO-2 is non-inducible. It has been suggested that HO-2 could be implicated in the production of carbon monoxide in the brain where it is said to act as a neurotransmitter. In the genome of the chloroplast of red algae as well as in cyanobacteria, there is a haem oxygenase (gene pbsA) that is the key enzyme in the synthesis of the chromophoric part of the photosynthetic antennae . A haem oxygenase is also present in the bacteria Corynebacterium diphtheriae (gene hmuO), where it is involved in the acquisition of iron from the host haem . There is, in the central section of these enzymes, a well-conserved region centred on a histidine residue.; GO: 0004392 heme oxygenase (decyclizing) activity, 0006788 heme oxidation; PDB: 1we1_A 1wox_B 1wow_A 1wov_A 2qpp_A 2q32_B 2rgz_A 1j2c_A 1ivj_A 1irm_A ....
Probab=98.72 E-value=4.8e-07 Score=60.39 Aligned_cols=202 Identities=11% Similarity=0.020 Sum_probs=126.6
Q ss_pred HHHHHHHHHHHHHHHHHHHCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 68999999999999998718478998568999899999999989999999999999987278876689999999999866
Q T0627 19 AWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFGRHPGEDMARRWLMRNI 98 (261)
Q Consensus 19 ~~s~~L~~~~~~~w~~~~~HPF~~~l~~G~L~~e~f~~yl~Qdy~yl~~f~r~la~~~~~~~~~~~~~~~~~~~~~~~~~ 98 (261)
.++++|.+++++.=+.+-+++|.+.+..|.++++.+..+|.+.|.+....-..+...... +.... ..
T Consensus 2 ~l~~~Lr~~T~~~H~~~E~~~~~~~~~~~~~~~~~Y~~~L~~~y~~y~~lE~~l~~~~~~-~~~~~------------~~ 68 (205)
T PF01126_consen 2 ALSERLREATRDLHEEAEALVFMKDLFAGRLSRDDYARLLRQFYFVYEALEEALDRHADD-PLLAL------------FY 68 (205)
T ss_dssp SHHHHHHHHTHHHHHHHHTSHHHHHHH---SSHHHHHHHHHHHHHHHHHHHHHHHHTTTS-TTTGG------------GS
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHH------------HC
T ss_conf 088999998999999998403499987278768999999999999999999999862357-41000------------01
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 43267999999999871899888720457778999999999974278899999999999850158999999876654203
Q T0627 99 RVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDSLAVAMAATNYAIEGATGEWSAVVCSTGVYAEA 178 (261)
Q Consensus 99 ~~e~~h~~l~~~~~~~~Gi~~e~l~~~~p~p~t~ay~~~l~~~a~~~~~~~~laA~~~~~E~~~~~~~~~~~~~~~~~~~ 178 (261)
..+.......++.+..++. ++.....+|+|++..|+.++..++.. ++...+|. +|++|+....-+..+.+... ..
T Consensus 69 ~~~l~R~~~l~~DL~~l~g-~~~~~~~~~~~a~~~~~~~i~~~~~~-~p~~llg~-~Yv~ygs~L~Gg~ii~~~~~--~~ 143 (205)
T PF01126_consen 69 FPELRRSPALEADLAYLYG-PDWRDDIEPSPATQAYVPRIREVAEE-SPALLLGH-AYVRYGSDLGGGQIIRRIAA--RA 143 (205)
T ss_dssp -GHHHTHHHHHHHHHHHGG-TTHHHHCHHHHHHHHHHHHHHHHHHH-SGGGHHHH-HHHHHHHHHT-HHHHHHHHH--HH
T ss_pred CCCHHHHHHHHHHHHHHHC-CCCHHCCCCCHHHHHHHHHHHHHCCC-CHHHHHHH-HHHHHHHHHHHHHHHHHHHH--HH
T ss_conf 4446668999999999857-87021147886689999999987036-99999999-99999998537999999999--86
Q ss_pred CCCCCCHHHHHHHHHHCCCCH-HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 577665688999996248535-689999999999975379998999999999999999999999
Q T0627 179 FAEETRKKSMKWLKMHAQYDD-AHPWEALEIICTLVGNKPSLQLQAELRQAVTKSYDYMYLFLE 241 (261)
Q Consensus 179 ~~~~~~~~~~~w~~~h~~~D~-~h~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~s~~~e~~f~D 241 (261)
+..........|+..+...+. .+-......++++ ..++.+++++++.+..+..+....+.
T Consensus 144 ~~l~~~~~~~~f~~~~~~~~~~~~~~~f~~~L~~~---~l~~~~~~~ii~eA~~aF~~~~~~~~ 204 (205)
T PF01126_consen 144 LGLPDGFGGLAFYGFGGIPDTGAFWRAFRAALDAL---ELTEEERDEIIEEAKAAFRLNNAWFR 204 (205)
T ss_dssp HT-BGGB-GGGGGS-TT-SSHHHHHHHHHHHHHHS------HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCC---CCCHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 18999866520046777253999999999998668---99999999999999999999999962
No 4
>PF11583 AurF: P-aminobenzoate N-oxygenase AurF; PDB: 3chi_B 3chh_A 2jcd_B 3chu_A 3cht_B.
Probab=95.77 E-value=0.044 Score=28.76 Aligned_cols=138 Identities=14% Similarity=0.073 Sum_probs=78.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCCCHHHHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999866432679999999998718998887204577789999999999742788-9999999999985015899999
Q T0627 90 ARRWLMRNIRVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSSSDS-LAVAMAATNYAIEGATGEWSAV 168 (261)
Q Consensus 90 ~~~~~~~~~~~e~~h~~l~~~~~~~~Gi~~e~l~~~~p~p~t~ay~~~l~~~a~~~~-~~~~laA~~~~~E~~~~~~~~~ 168 (261)
........+.+|..|..+|.++++..|-. -.+...++.+........+........ ....+++++ +.|.........
T Consensus 114 ~~~~a~~~~~DE~rH~~mf~~~~~r~~~~-~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l-v~E~~i~~~~~~ 191 (304)
T PF11583_consen 114 AKQYALTEIADEARHALMFARFINRTGAL-RGLEDLPPMYPPRRLLRALARLAPAWQRPLVFFAFAL-VGEEIIDAYQRQ 191 (304)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT----S--HHHHHHHHHHHTS-SHHHHHHHHHH----HHHHSBHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHH-HHHHHHHHHHHH
T ss_conf 99999999999999999999999998541-3766578878825889989875332121199999999-999999999998
Q ss_pred HHHHHHHHCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9876654203577665688999996248535689999999999975379998999999999999999999
Q T0627 169 VCSTGVYAEAFAEETRKKSMKWLKMHAQYDDAHPWEALEIICTLVGNKPSLQLQAELRQAVTKSYDYMYL 238 (261)
Q Consensus 169 ~~~~~~~~~~~~~~~~~~~~~w~~~h~~~D~~h~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~s~~~e~~ 238 (261)
+.. +..+.+--..-++.|..++-.|+.=+.+.+......- ++.++.-....+..++..+..
T Consensus 192 ~~~--------d~~i~P~vr~v~~iH~~DEaRH~~f~~~~l~~~~~~l-~~~~r~~~~~~l~~~~~~~~~ 252 (304)
T PF11583_consen 192 IAR--------DERIQPLVRQVMRIHVRDEARHIAFAREVLRRRYPRL-SPAERAILAEILPEALRLFVA 252 (304)
T ss_dssp HHT---------SSS-HHHHHHHHHHHHHHHH---HHHHHHHHHHHHS--HHHHHHHHHHHHHHHHHHHB
T ss_pred HHC--------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHH
T ss_conf 743--------7887959999999999999989999999999999869-999999999999999999998
No 5
>PF05974 DUF892: Domain of unknown function (DUF892); InterPro: IPR010287 This group consists of several hypothetical bacterial proteins of unknown function.; PDB: 2gs4_B 2gyq_A.
Probab=59.64 E-value=3.5 Score=16.67 Aligned_cols=84 Identities=6% Similarity=-0.075 Sum_probs=65.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCCCHH
Q ss_conf 89999999998999999999999998727887668999999999986643267999999999871899888720457778
Q T0627 51 PQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFGRHPGEDMARRWLMRNIRVELNHADYWVNWCAAHDVTLEDLHDQRVAPE 130 (261)
Q Consensus 51 ~e~f~~yl~Qdy~yl~~f~r~la~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~h~~l~~~~~~~~Gi~~e~l~~~~p~p~ 130 (261)
.+.|...|..-|..-+...+.+...+.++.+++.+. .+...+.+.+.|....++.++.+|.+|.. .++++
T Consensus 3 ~e~f~~~L~d~y~aE~q~~~~l~~~~~~a~~peLk~------~l~~H~~eT~~qi~rLe~i~~~lg~~p~~----~~c~~ 72 (159)
T PF05974_consen 3 EELFIDELRDLYSAEKQALKALPKMAKAAEDPELKS------ALEQHLEETEQQIERLEQIFERLGEDPSG----KKCDA 72 (159)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHH------HHHHHHHHHHHHHHHHHHHHHCST------------TT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHH------HHHHHHHHHHHHHHHHHHHHHHCCCCCCC----CCCHH
T ss_conf 889999999999999999999999998868999999------99998999999999999999875799877----87269
Q ss_pred HHHHHHHHHHHHCC
Q ss_conf 99999999997427
Q T0627 131 LHALSHWCWQTSSS 144 (261)
Q Consensus 131 t~ay~~~l~~~a~~ 144 (261)
...++.-...+...
T Consensus 73 m~gl~~e~~~~~~~ 86 (159)
T PF05974_consen 73 MEGLIAEGQELIEE 86 (159)
T ss_dssp T---HHHHHHHHCT
T ss_pred HHHHHHHHHHHHHC
T ss_conf 99999999999861
No 6
>PF02840 Prp18: Prp18 domain; InterPro: IPR004098 The splicing factor Prp18 is required for the second step of pre-mRNA splicing. PRP18 appears to be primarily associated with the U5 snRNP. The structure of a large fragment of the Saccharomyces cerevisiae Prp18 is known . This fragment is fully active in yeast splicing in vitro and includes the sequences of Prp18 that have been evolutionarily conserved. The core structure consists of five alpha-helices that adopt a novel fold. The most highly conserved region of Prp18, a nearly invariant stretch of 19 aa, forms part of a loop between two alpha-helices and may interact with the U5 small nuclear ribonucleoprotein particles .; GO: 0008380 RNA splicing, 0005681 spliceosome; PDB: 1dvk_A.
Probab=56.91 E-value=3.7 Score=16.48 Aligned_cols=42 Identities=17% Similarity=0.360 Sum_probs=30.7
Q ss_pred HHHHHHHCCCCCHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 478998568999899999-----999989999999999999987278
Q T0627 39 ELYQQMRDAKLSPQIMRQ-----YLIGGWPVVEQFAVYMAKNLTKTR 80 (261)
Q Consensus 39 PF~~~l~~G~L~~e~f~~-----yl~Qdy~yl~~f~r~la~~~~~~~ 80 (261)
|.+..|..++||.+.+.. +..|.--|+++.-.|+-+++++++
T Consensus 45 PL~~~Lr~~~l~~dil~~L~~Iv~~~~~r~y~~A~d~Yl~LaIGNa~ 91 (144)
T PF02840_consen 45 PLFKKLRKRTLPEDILDSLAEIVYHLQKRDYVKANDAYLKLAIGNAA 91 (144)
T ss_dssp HHHHHHHCT-S-HHHHHHHHHHHHHHCCCGHHHHHHHHHHHH-----
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 99999997799999999999999999973799999999998425788
No 7
>PF04305 DUF455: Protein of unknown function (DUF455); InterPro: IPR007402 This is a family of uncharacterised proteins.
Probab=36.78 E-value=7.9 Score=14.38 Aligned_cols=113 Identities=14% Similarity=0.053 Sum_probs=73.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCCCHHHHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999866432679999999998718998887204577789999999999742--788999999999998501589999
Q T0627 90 ARRWLMRNIRVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALSHWCWQTSS--SDSLAVAMAATNYAIEGATGEWSA 167 (261)
Q Consensus 90 ~~~~~~~~~~~e~~h~~l~~~~~~~~Gi~~e~l~~~~p~p~t~ay~~~l~~~a~--~~~~~~~laA~~~~~E~~~~~~~~ 167 (261)
.....+....+|-.|..|+.+-+..+|...-+ .|+- +.|++.+. ..+++.-+|.+--..|.--.+...
T Consensus 100 f~~Dw~~va~dEarHf~ll~~rL~~lG~~yGd------~Pah----~gLw~~~~~t~~d~l~RmAlvp~~lEarGLD~~p 169 (253)
T PF04305_consen 100 FYRDWLRVADDEARHFRLLSERLEELGFDYGD------FPAH----DGLWEAAEKTADDLLARMALVPRVLEARGLDATP 169 (253)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC------CHHH----HHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCH
T ss_conf 99999999999999999999999983899777------4044----6999999985369999999879999861799988
Q ss_pred HHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf 998766542035776656889999962485356899999999999753799
Q T0627 168 VVCSTGVYAEAFAEETRKKSMKWLKMHAQYDDAHPWEALEIICTLVGNKPS 218 (261)
Q Consensus 168 ~~~~~~~~~~~~~~~~~~~~~~w~~~h~~~D~~h~~e~~~~i~~~~~~~~~ 218 (261)
.+.+.... ..|..+.+-++.=-.++..|+.-+..-+..+|.....
T Consensus 170 ~~~~kl~~------~GD~~sa~iL~~I~~DEI~HV~~G~rWf~~lc~~~~~ 214 (253)
T PF04305_consen 170 FMIEKLRS------AGDNESAAILDIILRDEIGHVAIGNRWFRYLCERRGL 214 (253)
T ss_pred HHHHHHHH------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 99999997------7988899999999999999998889999999987699
No 8
>PF09441 Abp2: ARS binding protein 2
Probab=34.28 E-value=8.6 Score=14.13 Aligned_cols=59 Identities=5% Similarity=0.058 Sum_probs=32.8
Q ss_pred HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCCCHHHHHHH
Q ss_conf 72788766899999999998664326799999999987189988872045777899999
Q T0627 77 TKTRFGRHPGEDMARRWLMRNIRVELNHADYWVNWCAAHDVTLEDLHDQRVAPELHALS 135 (261)
Q Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~e~~h~~l~~~~~~~~Gi~~e~l~~~~p~p~t~ay~ 135 (261)
.++|..+....|.....+...-.-+..++..|.+..-.+|+.+.+++..+-..-.+.|.
T Consensus 42 Fr~pPkSdGk~Fs~~~L~~LIrkl~~kelkTW~qLa~~LGVepp~~ek~QStQKvQQYa 100 (175)
T PF09441_consen 42 FRSPPKSDGKSFSIFTLFELIRKLDRKELKTWIQLAIELGVEPPDVEKKQSTQKVQQYA 100 (175)
T ss_pred HCCCCCCCCCEEHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHH
T ss_conf 65998557860009999999999878888899999999488998732102289999999
No 9
>PF05138 PaaA_PaaC: Phenylacetic acid catabolic protein; InterPro: IPR007814 This family includes proteins such as PaaA and PaaC that are part of a catabolic pathway of phenylacetic acid . These proteins may form part of a dioxygenase complex.; PDB: 1otk_A.
Probab=34.24 E-value=8.6 Score=14.12 Aligned_cols=68 Identities=15% Similarity=-0.043 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC---CCCHHHHHCC
Q ss_conf 9999999998999999999999998727887668999999999986643267999999999871---8998887204
Q T0627 52 QIMRQYLIGGWPVVEQFAVYMAKNLTKTRFGRHPGEDMARRWLMRNIRVELNHADYWVNWCAAH---DVTLEDLHDQ 125 (261)
Q Consensus 52 e~f~~yl~Qdy~yl~~f~r~la~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~h~~l~~~~~~~~---Gi~~e~l~~~ 125 (261)
..+..|+.+-..=--.-..-++-.+.++|..+.. +.+......+.+|..++-+.+..+ |.+.+++...
T Consensus 16 ~~L~~~l~~laD~elila~r~~ew~~~AP~Leed------iAl~nialDelGhAr~ly~~a~el~G~G~~~d~la~~ 86 (263)
T PF05138_consen 16 AALIRYLLRLADDELILAQRLSEWCGHAPSLEED------IALANIALDELGHARLLYRLAEELEGDGRDEDDLAFL 86 (263)
T ss_dssp -HHHHHHHH---HHHHHHHH--------SSHHHH------HHHHH--------HHHHHHHHHHH------HHHHHHS
T ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHCCCCHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf 9999999998043988614776898609988999------9999999999999999999999971579977889987
No 10
>PF00268 Ribonuc_red_sm: Ribonucleotide reductase, small chain; InterPro: IPR000358 Ribonucleotide reductase (1.17.4.1 from EC) , catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides: 2'-deoxyribonucleoside diphosphate + oxidized thioredoxin + H_2O = ribonucleoside diphosphate + reduced thioredoxin It provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, bacteriophage and viruses, 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 and bacteriophage, 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. Ribonucleotide reductase is an oligomeric enzyme composed of a large subunit (700 to 1000 residues) and a small subunit (300 to 400 residues) - class II RNRs are less complex, using the small molecule B12 in place of the small chain . The small chain binds two iron atoms (three Glu, one Asp, and two His are involved in metal binding) and contains an active site tyrosine radical. The regions of the sequence that contain the metal-binding residues and the active site tyrosine are conserved in ribonucleotide reductase small chain from prokaryotes, eukaryotes and viruses. We have selected one of these regions as a signature pattern. It contains the active site residue as well as a glutamate and a histidine involved in the binding of iron.; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0009186 deoxyribonucleoside diphosphate metabolic process; PDB: 2o1z_B 2p1i_D 1sms_B 1jk0_B 2ani_A 1syy_A 1mrr_A 1piy_A 1yfd_A 1biq_A ....
Probab=27.76 E-value=11 Score=13.43 Aligned_cols=213 Identities=15% Similarity=0.080 Sum_probs=111.7
Q ss_pred CCCCHHHHHHHHHHHH-HHHHHHHCHHHHHHHCC-CCCHHHHHHHHHHHHHHHH----HHHH-HHHHHHHHCCCHHHHHH
Q ss_conf 7762689999999999-99998718478998568-9998999999999899999----9999-99999872788766899
Q T0627 15 SSYPAWAQQLINDCSP-AKARVVEHELYQQMRDA-KLSPQIMRQYLIGGWPVVE----QFAV-YMAKNLTKTRFGRHPGE 87 (261)
Q Consensus 15 ~~~p~~s~~L~~~~~~-~w~~~~~HPF~~~l~~G-~L~~e~f~~yl~Qdy~yl~----~f~r-~la~~~~~~~~~~~~~~ 87 (261)
..+| |...+++.... .| .-.+.||-+++.+= +||++.-..|. .-.-++. .-.+ ++..+....+.++....
T Consensus 14 ~~y~-~~~~~y~~~~~~fW-~peEi~~s~D~~dw~~Ls~~Er~~~~-~~l~~l~~~D~~v~~~~~~~i~~~~~~~E~~~~ 90 (281)
T PF00268_consen 14 IKYP-WAWDLYKKMEANFW-IPEEIDLSKDIKDWKKLSPEEREAYK-RILAFLTQLDSIVTRNILPNISPYITAPEVRAF 90 (281)
T ss_dssp -SSH-HHHHHHHHHHHT----GGGS-GGGHHHHHHHS-HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHBSSHHHHHH
T ss_pred CCCH-HHHHHHHHHHHCCC-CCHHCCCHHHHHHHHHCCHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
T ss_conf 7877-99999999986799-83406804009999869999999999-999999999999998779999987876999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHH----CCCCCHHHHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHH
Q ss_conf 999999998664326799999999987189988872----04577789999999999742788-9999999999985015
Q T0627 88 DMARRWLMRNIRVELNHADYWVNWCAAHDVTLEDLH----DQRVAPELHALSHWCWQTSSSDS-LAVAMAATNYAIEGAT 162 (261)
Q Consensus 88 ~~~~~~~~~~~~~e~~h~~l~~~~~~~~Gi~~e~l~----~~~p~p~t~ay~~~l~~~a~~~~-~~~~laA~~~~~E~~~ 162 (261)
+ ......|..|.+.|-..++.++.++++.. ...-.|..+.-.+++.......+ +...+++. .++|++.
T Consensus 91 l------~~q~~~E~iH~~sYs~il~tl~~~~~~~~~~~~~~~~~~~l~~k~~~i~~~~~~~~~~~~~lv~~-~~lEgi~ 163 (281)
T PF00268_consen 91 L------AFQAFMEAIHAESYSYILDTLGPDPEEREEIFNWIEEDPELQKKAEFINRWYEDDDNFAEKLVAS-VFLEGIL 163 (281)
T ss_dssp H------HHHHHHHHHHHHHHHHHHHHHSSSHHHHHHHHHHHHHSHHHHHHHHHHHHHHSSSSHHHHHHHHH-HHHHHTT
T ss_pred H------HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH
T ss_conf 9------99999999999999999998459857899999999867899989999986303244789999999-9999999
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89999998766542035776656889999962485356899999999999753799989999999999999999999999
Q T0627 163 GEWSAVVCSTGVYAEAFAEETRKKSMKWLKMHAQYDDAHPWEALEIICTLVGNKPSLQLQAELRQAVTKSYDYMYLFLER 242 (261)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~h~~~D~~h~~e~~~~i~~~~~~~~~~~~~~~~~~~~~~s~~~e~~f~D~ 242 (261)
-.-+-...-....++.... --...+|+. .++--|+.-...++..+... ....++.+.+.++.++++|..|.+.
T Consensus 164 fys~F~~~~~l~~~g~m~g--~~~~i~~I~---RDE~~H~~~~~~l~~~l~~e--~~~~~~~i~~l~~~a~e~E~~~~~~ 236 (281)
T PF00268_consen 164 FYSGFAYFLYLARQGKMPG--LAEIIKLIL---RDESLHGEFGIYLFRTLKEE--NKPEQEEIYELFREAVELEIEYIDD 236 (281)
T ss_dssp TTHHHHHHHHHHHTTSSHH--HHHHHHHHH---HHHHHHHHHHHHHHHTHSCT--SHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHCCCCHH--HHHHHHHHH---HHHHHHHHHHHHHHHHHHCC--CCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9899999999998698566--999999999---88889999999999997635--7632999999999999999999998
Q ss_pred HH
Q ss_conf 99
Q T0627 243 CI 244 (261)
Q Consensus 243 ~y 244 (261)
++
T Consensus 237 ~~ 238 (281)
T PF00268_consen 237 IL 238 (281)
T ss_dssp TS
T ss_pred HC
T ss_conf 65
No 11
>PF03970 Herpes_UL37_1: Herpesvirus UL37 tegument protein; InterPro: IPR005655 UL37 interacts with UL36, which is thought to be an important early step in tegumentation during virion morphogenesis in the cytoplasm .; GO: 0019068 virus assembly
Probab=26.46 E-value=12 Score=13.28 Aligned_cols=57 Identities=11% Similarity=0.129 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH
Q ss_conf 77626899999999999999871847899856899989999999998999999999999998727887668
Q T0627 15 SSYPAWAQQLINDCSPAKARVVEHELYQQMRDAKLSPQIMRQYLIGGWPVVEQFAVYMAKNLTKTRFGRHP 85 (261)
Q Consensus 15 ~~~p~~s~~L~~~~~~~w~~~~~HPF~~~l~~G~L~~e~f~~yl~Qdy~yl~~f~r~la~~~~~~~~~~~~ 85 (261)
++.++|......+++..-- -|+ +++++++.+.++.-=. .-.+.++.+..+...++..
T Consensus 23 ~~~~~~~~~~~~~~ra~I~-----~Fl--lS~~~i~~~~~~~~w~-------~l~~~~c~~y~~~~~Peaa 79 (270)
T PF03970_consen 23 TDAEPWPPAVAAKLRAAIA-----KFL--LSTDTISIEEARATWR-------PLFKVLCRAYKATGTPEAA 79 (270)
T ss_pred CCCCCCCHHHHHHHHHHHH-----HHH--HCCCCCCHHHHHHHHH-------HHHHHHHHHHHHCCCHHHH
T ss_conf 9888872778999999999-----999--7389878888999899-------9999999998631994999
Done!