Query psy16836
Match_columns 319
No_of_seqs 115 out of 360
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 23:16:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16836.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16836hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03095 PTPA: Phosphotyrosyl 100.0 2E-131 3E-136 942.4 23.0 287 29-317 1-289 (299)
2 KOG2867|consensus 100.0 3E-126 6E-131 909.9 21.4 297 20-317 7-303 (367)
3 cd04087 PTPA Phosphotyrosyl ph 100.0 1E-123 2E-128 873.6 25.4 266 51-317 1-266 (266)
4 COG5057 LAG1 Phosphotyrosyl ph 100.0 2E-115 4E-120 818.7 19.7 293 24-317 6-299 (353)
5 COG3657 Uncharacterized protei 71.9 3.8 8.3E-05 34.0 2.8 14 151-164 53-66 (100)
6 PRK15410 DgsA anti-repressor M 50.4 43 0.00093 32.3 6.2 104 75-211 144-250 (260)
7 PRK15322 invasion protein OrgB 42.7 45 0.00099 31.2 4.8 50 110-159 71-148 (210)
8 cd00454 Trunc_globin Truncated 41.0 1.9E+02 0.004 23.2 7.8 60 108-172 15-87 (116)
9 COG3228 Uncharacterized protei 35.8 72 0.0016 30.8 5.1 98 78-208 152-252 (266)
10 cd03572 ENTH_epsin_related ENT 34.6 87 0.0019 26.8 5.0 82 11-127 6-91 (122)
11 PRK00109 Holliday junction res 33.0 1.2E+02 0.0026 26.1 5.7 96 6-113 11-108 (138)
12 PF04915 DltD_N: DltD N-termin 29.3 13 0.00028 28.5 -0.8 27 216-244 25-51 (62)
13 PF03091 CutA1: CutA1 divalent 28.6 41 0.00089 27.8 2.0 33 83-115 61-99 (102)
14 PF03652 UPF0081: Uncharacteri 27.9 11 0.00024 32.4 -1.6 97 6-113 8-106 (135)
15 cd02986 DLP Dim1 family, Dim1- 27.2 22 0.00048 30.2 0.2 27 134-160 55-90 (114)
16 PF14745 WASH-7_N: WASH comple 25.4 4.5E+02 0.0097 27.9 9.4 131 76-219 159-330 (567)
17 PRK11027 hypothetical protein; 24.5 84 0.0018 26.8 3.2 54 156-219 53-107 (112)
18 PF02251 PA28_alpha: Proteasom 22.9 93 0.002 23.8 2.8 32 110-145 10-41 (64)
19 COG3085 Uncharacterized protei 22.9 91 0.002 26.3 3.0 55 157-220 54-108 (112)
20 PF08336 P4Ha_N: Prolyl 4-Hydr 21.9 42 0.00092 28.4 0.9 16 193-208 109-124 (134)
21 PRK10645 divalent-cation toler 21.2 1.4E+02 0.0031 25.1 3.9 37 79-115 67-109 (112)
22 COG2517 Predicted RNA-binding 20.7 3.2E+02 0.007 25.6 6.3 33 79-122 65-97 (219)
No 1
>PF03095 PTPA: Phosphotyrosyl phosphate activator (PTPA) protein; InterPro: IPR004327 Phosphotyrosyl phosphatase activator (PTPA) proteins stimulate the phosphotyrosyl phosphatase (PTPase) activity of the dimeric form of protein phosphatase 2A (PP2A). PTPase activity in PP2A (in vitro) is relatively low when compared to the better recognised phosphoserine/ threonine protein phosphorylase activity. The specific biological role of PTPA is unknown, Basal expression of PTPA depends on the activity of a ubiquitous transcription factor, Yin Yang 1 (YY1). The tumour suppressor protein p53 can inhibit PTPA expression through an unknown mechanism that negatively controls YY1 [].; GO: 0019211 phosphatase activator activity; PDB: 2HV7_H 2HV6_A 2IXM_A 2G62_A 2IXN_B 2IXO_B 2IXP_B.
Probab=100.00 E-value=1.5e-131 Score=942.35 Aligned_cols=287 Identities=52% Similarity=0.928 Sum_probs=269.5
Q ss_pred cccceecCccchhhhhcCHhHHHHHHHHHHHHHhcCCCCCC-CCCCCCHhHHHHHHHHHHHHHhhhhCCCCCC-CCCCCc
Q psy16836 29 IPKRQVLKDSDMKQWENSEAYHEYQGFILSMNEAVRGKAID-TRLEPSNNVMSVFQMLEHFNKLIDETPPIDQ-PQRFGN 106 (319)
Q Consensus 29 ~P~K~I~~~~D~~~f~~S~Ay~~i~~fI~~l~~av~g~~~~-~~~~~S~~v~~l~~iL~~l~~~i~e~PP~~~-p~RFGN 106 (319)
+|+|||.+++||++|++|+||++|+.||++||++|+|++++ ++.+.|++|++++++|++|++||+|+||+++ |+||||
T Consensus 1 ~P~KrI~~~~D~~~f~~S~Ay~~i~~FI~~l~~sV~g~~~~~~~~~~S~~v~~ll~iL~~l~~~i~e~PP~~~~p~RFGN 80 (299)
T PF03095_consen 1 TPVKRILSPEDMEKFKRSQAYADIIGFIQNLNESVKGKKLSTDDYPVSENVQKLLDILDTLEQWIDEIPPVDQGPSRFGN 80 (299)
T ss_dssp --EE---SCCHHHHHHTSHHHHHHHHHHHHHHHHHTT-STTTSTSSSSHHHHHHHHHHHHHHHHHHTS---SS-STTSS-
T ss_pred CCcceECCHhHHHHHcCCHHHHHHHHHHHHHHHHccCCCCCCcccccChHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCC
Confidence 59999999999999999999999999999999999999999 8999999999999999999999999999998 999999
Q ss_pred HHHHHHHHHHHHhHHHHHHHhCCccccccHHHHHHHHHhccCCCcccccCChhHHHHHHHHHHHHhhCCcCCCccchhhH
Q psy16836 107 KAFAQWLNKIGECVETELQKALPEKFHAAIPEISVYLKESFGNSTRIDYGTGHEMAFCMFLLCLFRIGAFSMNDRVAVVN 186 (319)
Q Consensus 107 ~AfR~W~~~l~~~~~~ll~~~l~~~~~~~~~EL~~Yl~~SFGn~tRIDYGTGHEL~Fl~fL~~L~klgil~~~d~~a~vL 186 (319)
+|||+|++||++++++|+++++|+..+++++||+.||.+||||+|||||||||||||+||||||+++|+++.+|..++||
T Consensus 81 ~AfR~w~~~l~~~~~~ll~~~l~~~~~~~~~EL~~Yl~~SFGn~tRiDYGTGHEL~Fl~fL~~L~~lg~l~~~d~~a~vL 160 (299)
T PF03095_consen 81 KAFRTWHDKLEEEAPSLLEDILPSSLCGAIIELSYYLLNSFGNSTRIDYGTGHELSFLAFLCCLFKLGILTEEDYPALVL 160 (299)
T ss_dssp THHHHHHHHHHHHHHHHHHHHSTGGGGGGHHHHHHHHHTSSSBTTTTEEEHHHHHHHHHHHHHHHHTTSSTCHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCccchHHHHHHHHHHHhCcCCCeeeecCcHHHHHHHHHHHHHHHcCCCCccccceeee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhHHHHHHHHHHHHHhhccccCCCCcccccCCcccchhhhhhccccCCCCCCCCccccchhhHhhhcCCCccHHHHHHHH
Q psy16836 187 RIFVRYLDLVRRLQCEYRMEPAGSHGVWSLDDYQFVPFIWGSSQLFGNKDEIEPNMFLLERTVLDHRDKYMFLACIQYIM 266 (319)
Q Consensus 187 ~vF~~Yl~lvR~Lq~~Y~LEPAGSHGvWGLDDy~fLPfi~GsaQL~~~~~~~~P~~i~d~~iv~~~~~~yly~~~I~~I~ 266 (319)
+||.||+++||+||++|+|||||||||||||||||||||||||| +.| +.++|++|+|+++|++|+++|||++||+||+
T Consensus 161 ~vF~~Yl~l~R~Lq~~Y~LEPAGSHGVWGLDDy~fLPfi~GsaQ-~~~-~~~~P~~i~~~~~v~~~~~~yly~~~I~fI~ 238 (299)
T PF03095_consen 161 RVFNRYLELVRRLQSTYRLEPAGSHGVWGLDDYQFLPFIFGSAQ-LDH-PPIKPKSILDPDIVEEYRDDYLYLDCIDFIN 238 (299)
T ss_dssp THHHHHHHHHHHHHHHCT-EECSCCCCCSSSSS-SHHHHHHHHH-TTT-SSGGGGGGGSHHHHHHHTTT-HHHHHHHHHH
T ss_pred eeHHHHHHHHHHHHHheeeccCCCCCCCccccceeecccccccc-ccC-CCCChHHhcCHHHHHHhcccccHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999 788 8999999999999999999999999999999
Q ss_pred HhCccCccccchhhhcccCCCChHHHhHHHHHHHHHhhcCCCccccccccC
Q psy16836 267 KVKTGHFSEHSNQLWNISALPSWSKINQGLLKMYKGEVLAKFPVISTRPCL 317 (319)
Q Consensus 267 ~~K~gpf~ehSp~L~dIs~v~sW~KVn~GliKMY~~EVL~KfpVvQHf~~~ 317 (319)
++|+|||+||||||||||+|++|+|||+||||||++|||+||||||||+|.
T Consensus 239 ~~K~gpf~ehSp~L~~Is~v~~W~KV~~GliKMY~~EVL~KfpVvQHf~FG 289 (299)
T PF03095_consen 239 KVKTGPFREHSPMLWDISGVPSWSKVNSGLIKMYKAEVLGKFPVVQHFWFG 289 (299)
T ss_dssp HHTTS-HHHHSHHHHHHTTSSSHHHHHHHHHHHHHHHTTT-HHHHTTSEBB
T ss_pred HhCCCcHHHHhHHHHhhhcCCCCcchhhHHHHHHHHHHhhcchhhhhhhhh
Confidence 999999999999999999999999999999999999999999999999995
No 2
>KOG2867|consensus
Probab=100.00 E-value=2.6e-126 Score=909.95 Aligned_cols=297 Identities=49% Similarity=0.879 Sum_probs=291.4
Q ss_pred CCCCCCccccccceecCccchhhhhcCHhHHHHHHHHHHHHHhcCCCCCCCCCCCCHhHHHHHHHHHHHHHhhhhCCCCC
Q psy16836 20 AVGPDHVYAIPKRQVLKDSDMKQWENSEAYHEYQGFILSMNEAVRGKAIDTRLEPSNNVMSVFQMLEHFNKLIDETPPID 99 (319)
Q Consensus 20 ~~~~~~~f~~P~K~I~~~~D~~~f~~S~Ay~~i~~fI~~l~~av~g~~~~~~~~~S~~v~~l~~iL~~l~~~i~e~PP~~ 99 (319)
.+.+..+|..|+|||.+.+||..|++|+||++|++||..+|++|+|.+.+...+.|++|+++++||++|++||+|+||++
T Consensus 7 ~~~~~~~~~~PvKrI~~~~Dm~~w~~S~Ay~~i~~fi~~ls~~I~g~~~~~~~p~s~~v~~l~~ild~l~~~i~e~P~~~ 86 (367)
T KOG2867|consen 7 VAFASASFQTPVKRIQSLEDMKDWVESRAYARIIGFINDLSESIKGHRNTYSFPISEQVKRLMDILDQLDHIIDETPPID 86 (367)
T ss_pred ccchhhhcCCcHHHhcCHHHHHHHHHhHHHHHHHHHHHHHHHHhcCCCccccchhHHHHHHHHHHHHHHHHHHHcCCCCC
Confidence 45567789999999999999999999999999999999999999997777888999999999999999999999999999
Q ss_pred CCCCCCcHHHHHHHHHHHHhHHHHHHHhCCccccccHHHHHHHHHhccCCCcccccCChhHHHHHHHHHHHHhhCCcCCC
Q psy16836 100 QPQRFGNKAFAQWLNKIGECVETELQKALPEKFHAAIPEISVYLKESFGNSTRIDYGTGHEMAFCMFLLCLFRIGAFSMN 179 (319)
Q Consensus 100 ~p~RFGN~AfR~W~~~l~~~~~~ll~~~l~~~~~~~~~EL~~Yl~~SFGn~tRIDYGTGHEL~Fl~fL~~L~klgil~~~ 179 (319)
+|+||||+|||+|+++|.++++.++++++|+..+++++||.+||.+||||++||||||||||||+||||||+++|||+.+
T Consensus 87 ~~~Rfgn~AyR~w~~kl~~~~~~ll~~~~p~~~~~~v~El~~Yl~~SFGNs~RIDYGtGHEL~Fl~~L~~L~~~Gil~~~ 166 (367)
T KOG2867|consen 87 GPQRFGNKAYRTWYEKLYEELPKLLDEALPSLKHEAVNELGQYLTESFGNSTRIDYGTGHELNFLFFLCALFKLGILDEN 166 (367)
T ss_pred ChhhhcCHHHHHHHHHHHHHHHHHHHHHcchHHHHHHHHHHHHHHhccCCcccccccchHHHHHHHHHHHHHHccCcccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccchhhHHhHHHHHHHHHHHHHhhccccCCCCcccccCCcccchhhhhhccccCCCCCCCCccccchhhHhhhcCCCccH
Q psy16836 180 DRVAVVNRIFVRYLDLVRRLQCEYRMEPAGSHGVWSLDDYQFVPFIWGSSQLFGNKDEIEPNMFLLERTVLDHRDKYMFL 259 (319)
Q Consensus 180 d~~a~vL~vF~~Yl~lvR~Lq~~Y~LEPAGSHGvWGLDDy~fLPfi~GsaQL~~~~~~~~P~~i~d~~iv~~~~~~yly~ 259 (319)
|..|+||+||+||+++||+||+||+|||||||||||||||||||||||||||+++ ++++|++|+|++||++|+++|||+
T Consensus 167 D~~a~vl~lF~kYlev~R~Lq~tY~lEPAGShGvwgLDD~~FlPfifGsaQL~~~-~~~~P~~~~d~~iv~~~~~~ymyl 245 (367)
T KOG2867|consen 167 DYVALVLRLFNKYLEVMRRLQTTYNLEPAGSHGVWGLDDFQFLPFIFGSAQLCDH-KPLKPKSILDEKIVEEYRDDYMYL 245 (367)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHhccccCCCCCcccccccchhhhhhhHHHHhcC-CCCChhhhccHHHHHHHHhhhhHH
Confidence 9999999999999999999999999999999999999999999999999999999 999999999999999999999999
Q ss_pred HHHHHHHHhCccCccccchhhhcccCCCChHHHhHHHHHHHHHhhcCCCccccccccC
Q psy16836 260 ACIQYIMKVKTGHFSEHSNQLWNISALPSWSKINQGLLKMYKGEVLAKFPVISTRPCL 317 (319)
Q Consensus 260 ~~I~~I~~~K~gpf~ehSp~L~dIs~v~sW~KVn~GliKMY~~EVL~KfpVvQHf~~~ 317 (319)
+||.||+++|+|||+||||||||||+||+|+|||+||||||++|||+||||||||+|.
T Consensus 246 ~cI~fi~k~K~G~f~eHS~~L~~IsaVp~WsKVn~GlikMY~~eVL~k~pvvQHf~FG 303 (367)
T KOG2867|consen 246 SCIDFINKVKTGPFAEHSPQLWSISAVPTWSKVNRGLIKMYDVEVLSKFPVVQHFIFG 303 (367)
T ss_pred HHHHHHHHhcCCchhhhchHHhhhhcCCcHHHHHHHHHHHHHHHHHHhcchHHHHHHh
Confidence 9999999999999999999999999999999999999999999999999999999984
No 3
>cd04087 PTPA Phosphotyrosyl phosphatase activator (PTPA) is also known as protein phosphatase 2A (PP2A) phosphatase activator. PTPA is an essential, well conserved protein that stimulates the tyrosyl phosphatase activity of PP2A. It also reactivates the serine/threonine phosphatase activity of an inactive form of PP2A. Together, PTPA and PP2A constitute an ATPase. It has been suggested that PTPA alters the relative specificity of PP2A from phosphoserine/phosphothreonine substrates to phosphotyrosine substrates in an ATP-hydrolysis-dependent manner. Basal expression of PTPA is controlled by the transcription factor Yin Yang1 (YY1). PTPA has been suggested to play a role in the insertion of metals to the PP2A catalytic subunit (PP2Ac) active site, to act as a chaperone, and more recently, to have peptidyl prolyl cis/trans isomerase activity that specifically targets human PP2Ac.
Probab=100.00 E-value=1.1e-123 Score=873.64 Aligned_cols=266 Identities=53% Similarity=0.960 Sum_probs=263.1
Q ss_pred HHHHHHHHHHHhcCCCCCCCCCCCCHhHHHHHHHHHHHHHhhhhCCCCCCCCCCCcHHHHHHHHHHHHhHHHHHHHhCCc
Q psy16836 51 EYQGFILSMNEAVRGKAIDTRLEPSNNVMSVFQMLEHFNKLIDETPPIDQPQRFGNKAFAQWLNKIGECVETELQKALPE 130 (319)
Q Consensus 51 ~i~~fI~~l~~av~g~~~~~~~~~S~~v~~l~~iL~~l~~~i~e~PP~~~p~RFGN~AfR~W~~~l~~~~~~ll~~~l~~ 130 (319)
+|++||+++|++|+|++++++.++|++|++|+++|++|++||+|+||+++|+||||+|||+|+++|++++++|+++++|+
T Consensus 1 ~i~~fI~~l~~sv~g~~~~~~~~~s~~i~~l~~il~~l~~~i~e~PP~~~~~RfGN~afR~w~~~l~~~~~~ll~~~l~~ 80 (266)
T cd04087 1 DIIAFIQDLSESVQGKPLSDEIPVSENIEKLVEILDQLDALIDETPPIDQPSRFGNKAFRTWHDKLEEELPSLLEELLPE 80 (266)
T ss_pred CHHHHHHHHHHHhcCCcCCCCCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcccCCHHHHHHHHHHHHHHHHHHHHHcCc
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccHHHHHHHHHhccCCCcccccCChhHHHHHHHHHHHHhhCCcCCCccchhhHHhHHHHHHHHHHHHHhhccccCCC
Q psy16836 131 KFHAAIPEISVYLKESFGNSTRIDYGTGHEMAFCMFLLCLFRIGAFSMNDRVAVVNRIFVRYLDLVRRLQCEYRMEPAGS 210 (319)
Q Consensus 131 ~~~~~~~EL~~Yl~~SFGn~tRIDYGTGHEL~Fl~fL~~L~klgil~~~d~~a~vL~vF~~Yl~lvR~Lq~~Y~LEPAGS 210 (319)
..+++++||.+||.+||||+|||||||||||||+||||||+|+|+++.+|..++||+||.||+++||+||++|+||||||
T Consensus 81 ~~~~~~~EL~~Yl~~SFGn~~RiDYGTGHEL~Fl~fL~~L~~lgil~~~d~~~~vL~vF~~Yl~l~R~Lq~~Y~LEPAGS 160 (266)
T cd04087 81 ELDEAVNELSYYLLESFGNSTRIDYGTGHELNFLAFLCCLFKLGILTEEDYGAIVLRVFNRYLELVRRLQLTYRLEPAGS 160 (266)
T ss_pred hhhHHHHHHHHHHHhccCCCcccccCCchHHHHHHHHHHHHHCCCCCcchhhHHHHHHHHHHHHHHHHHHHHhccccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccCCcccchhhhhhccccCCCCCCCCccccchhhHhhhcCCCccHHHHHHHHHhCccCccccchhhhcccCCCChH
Q psy16836 211 HGVWSLDDYQFVPFIWGSSQLFGNKDEIEPNMFLLERTVLDHRDKYMFLACIQYIMKVKTGHFSEHSNQLWNISALPSWS 290 (319)
Q Consensus 211 HGvWGLDDy~fLPfi~GsaQL~~~~~~~~P~~i~d~~iv~~~~~~yly~~~I~~I~~~K~gpf~ehSp~L~dIs~v~sW~ 290 (319)
|||||||||||||||||||||+++ ++++|++|+|+++|++|+++|||++||+||+++|+|||+||||||||||+|++|+
T Consensus 161 HGvWGLDDy~fLPfi~GsaQL~~~-~~~~P~~i~~~~~v~~~~~~ymy~~~I~fI~~vK~gpf~ehSp~L~dIs~v~~W~ 239 (266)
T cd04087 161 HGVWGLDDYQFLPFIFGSAQLINH-KPLKPKSILDPEIVEEYKKDYLYLSCIAFINKVKTGPFAEHSPMLWDISGVPTWS 239 (266)
T ss_pred CCCCcccccccchhhhhHHHhccC-CCCCchhhcCHHHHHHhhhcccHHHHHHHHHHcCCCCccccCHHHHHHhcCCChH
Confidence 999999999999999999999999 9999999999999999999999999999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHhhcCCCccccccccC
Q psy16836 291 KINQGLLKMYKGEVLAKFPVISTRPCL 317 (319)
Q Consensus 291 KVn~GliKMY~~EVL~KfpVvQHf~~~ 317 (319)
|||+||+|||++|||+||||||||+|-
T Consensus 240 Kv~~Gl~KMY~~EVL~KfpvvQHf~FG 266 (266)
T cd04087 240 KVNQGLIKMYKAEVLSKFPVVQHFLFG 266 (266)
T ss_pred HHHHHHHHHHHHHHccccccccccccC
Confidence 999999999999999999999999983
No 4
>COG5057 LAG1 Phosphotyrosyl phosphatase activator [Cell division and chromosome partitioning / Signal transduction mechanisms]
Probab=100.00 E-value=1.7e-115 Score=818.75 Aligned_cols=293 Identities=42% Similarity=0.783 Sum_probs=287.6
Q ss_pred CCccccccceecCccchhhhhcCHhHHHHHHHHHHHHHhcCCCCCCCC-CCCCHhHHHHHHHHHHHHHhhhhCCCCCCCC
Q psy16836 24 DHVYAIPKRQVLKDSDMKQWENSEAYHEYQGFILSMNEAVRGKAIDTR-LEPSNNVMSVFQMLEHFNKLIDETPPIDQPQ 102 (319)
Q Consensus 24 ~~~f~~P~K~I~~~~D~~~f~~S~Ay~~i~~fI~~l~~av~g~~~~~~-~~~S~~v~~l~~iL~~l~~~i~e~PP~~~p~ 102 (319)
..+|..|+|||.+.+||..|+.|.||++|..||..++++|+|.+.++. .+.|..|+.++++|+++..+++|+||+++|+
T Consensus 6 ~~~f~~P~krild~~d~~~f~es~Ay~ri~~fi~~l~~sik~~~~~d~~~~~Sssv~~m~~vL~ri~~I~qe~P~~~~~~ 85 (353)
T COG5057 6 HATFSTPVKRILDMKDMKDFVESEAYARIYNFILDLDESIKGCSDSDYHSEQSSSVNHMMNVLDRIKEITQETPPIPGPQ 85 (353)
T ss_pred cccccCcHHHhccchhhhHhhhhhHHHHHHHHHHHHHHHhcCCCCCcccchhHHHHHHHHHHHHHHHHHHhcCCCCCCch
Confidence 347999999999999999999999999999999999999999998864 5788899999999999999999999999999
Q ss_pred CCCcHHHHHHHHHHHHhHHHHHHHhCCccccccHHHHHHHHHhccCCCcccccCChhHHHHHHHHHHHHhhCCcCCCccc
Q psy16836 103 RFGNKAFAQWLNKIGECVETELQKALPEKFHAAIPEISVYLKESFGNSTRIDYGTGHEMAFCMFLLCLFRIGAFSMNDRV 182 (319)
Q Consensus 103 RFGN~AfR~W~~~l~~~~~~ll~~~l~~~~~~~~~EL~~Yl~~SFGn~tRIDYGTGHEL~Fl~fL~~L~klgil~~~d~~ 182 (319)
||||+|||+||++|.+++++++++.+|+..+++++||..||.+||||++||||||||||||+|||++|+.+|++..+|+.
T Consensus 86 RfGN~Afr~~~~kl~~~~~q~~~~~~p~~~~ea~~el~~Yl~~SfGN~~RiDYGtGHELnFm~~l~~L~~lGif~~~d~~ 165 (353)
T COG5057 86 RFGNPAFRTWHDKLYDTYPQILQEMLPSEYHEAVPELQYYLRNSFGNSIRIDYGTGHELNFMCYLYALYCLGIFGIADYG 165 (353)
T ss_pred hhcChHHHHHHHHHHhhhHHHHHHhccchhhHHHHHHHHHHHhccCceeeeccCCccchhHHHHHHHHHHccCCCccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhHHhHHHHHHHHHHHHHhhccccCCCCcccccCCcccchhhhhhccccCCCCCCCCccccchhhHhhhcCCCccHHHH
Q psy16836 183 AVVNRIFVRYLDLVRRLQCEYRMEPAGSHGVWSLDDYQFVPFIWGSSQLFGNKDEIEPNMFLLERTVLDHRDKYMFLACI 262 (319)
Q Consensus 183 a~vL~vF~~Yl~lvR~Lq~~Y~LEPAGSHGvWGLDDy~fLPfi~GsaQL~~~~~~~~P~~i~d~~iv~~~~~~yly~~~I 262 (319)
|+|+.||.+|+++||.||.+|+|||||||||||||||||||||||||||+++ ++++|++|+|+++|++|+++||||.||
T Consensus 166 a~V~~ifvkY~eimR~Li~~Y~LEPAGSHGVWGLDD~~fLpflfGssQl~~~-~~lkP~~i~~~elv~~~~~s~~Yf~~I 244 (353)
T COG5057 166 ALVFTIFVKYLEIMRLLITKYTLEPAGSHGVWGLDDYFFLPFLFGSSQLCNH-KPLKPREIRDKELVEEYADSNLYFGAI 244 (353)
T ss_pred ceehhhHHHHHHHHHHHHHheecccCccCCcccccccchhhhhcchHHHhcc-CCCCchhhcCHHHHHHhhhcceEEEee
Confidence 9999999999999999999999999999999999999999999999999999 999999999999999999999999999
Q ss_pred HHHHHhCccCccccchhhhcccCCCChHHHhHHHHHHHHHhhcCCCccccccccC
Q psy16836 263 QYIMKVKTGHFSEHSNQLWNISALPSWSKINQGLLKMYKGEVLAKFPVISTRPCL 317 (319)
Q Consensus 263 ~~I~~~K~gpf~ehSp~L~dIs~v~sW~KVn~GliKMY~~EVL~KfpVvQHf~~~ 317 (319)
.|||++|.|||+||||||||||+|++|+|||+||||||++|||+|+||||||+|.
T Consensus 245 ~FiN~~K~g~~~~HSPiL~DIs~Vk~WSKVn~GmIKMY~~EVL~K~PV~QHF~Fg 299 (353)
T COG5057 245 NFINEVKLGPFREHSPILYDISAVKTWSKVNEGMIKMYDVEVLSKLPVVQHFIFG 299 (353)
T ss_pred ehhhhcccCcccccChhhhhhhccccHHHHHHHHHHHHHHHHhhccchhhhhhhc
Confidence 9999999999999999999999999999999999999999999999999999985
No 5
>COG3657 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=71.85 E-value=3.8 Score=33.99 Aligned_cols=14 Identities=43% Similarity=0.605 Sum_probs=11.9
Q ss_pred cccccCChhHHHHH
Q psy16836 151 TRIDYGTGHEMAFC 164 (319)
Q Consensus 151 tRIDYGTGHEL~Fl 164 (319)
.|||||+|+-.-|.
T Consensus 53 LRId~GpGyRvY~~ 66 (100)
T COG3657 53 LRIDHGPGYRVYFQ 66 (100)
T ss_pred heeccCCceEEEEE
Confidence 59999999887765
No 6
>PRK15410 DgsA anti-repressor MtfA; Provisional
Probab=50.40 E-value=43 Score=32.30 Aligned_cols=104 Identities=19% Similarity=0.223 Sum_probs=70.3
Q ss_pred CHhHHHHHHHHHHHHHh-hhhCCCCCCCCCCCcHHHHHHHHHHHHhHHHHHHHhCCccccccHHHHHHHHHhccCCCc-c
Q psy16836 75 SNNVMSVFQMLEHFNKL-IDETPPIDQPQRFGNKAFAQWLNKIGECVETELQKALPEKFHAAIPEISVYLKESFGNST-R 152 (319)
Q Consensus 75 S~~v~~l~~iL~~l~~~-i~e~PP~~~p~RFGN~AfR~W~~~l~~~~~~ll~~~l~~~~~~~~~EL~~Yl~~SFGn~t-R 152 (319)
+-.+....=.||.++.- +|-+||. .+..++.|.+-+.+.-+.+.+++- ..|..+ =
T Consensus 144 NVvIHEFAH~LDm~~G~~adG~PpL------~~~~~~~W~~~~~~~~~~l~~~~~-----------------~~~~~~~~ 200 (260)
T PRK15410 144 NLIIHEVAHKLDMRNGDRASGVPFI------PLREVAGWEHDLHAAMNNIQEEID-----------------LVGENAAS 200 (260)
T ss_pred chhHhHHHhHhhhhcCCCCCCCCCC------CchhHHHHHHHHHHHHHHHHHHHH-----------------hcCCCCCC
Confidence 34566677788888877 8899998 234889999988877666665531 112222 3
Q ss_pred c-ccCChhHHHHHHHHHHHHhhCCcCCCccchhhHHhHHHHHHHHHHHHHhhccccCCCC
Q psy16836 153 I-DYGTGHEMAFCMFLLCLFRIGAFSMNDRVAVVNRIFVRYLDLVRRLQCEYRMEPAGSH 211 (319)
Q Consensus 153 I-DYGTGHEL~Fl~fL~~L~klgil~~~d~~a~vL~vF~~Yl~lvR~Lq~~Y~LEPAGSH 211 (319)
| .||.=++--|+|-++=-| |+. =-.+-.+|=+|-+.|+..|++.|||+-
T Consensus 201 id~YaatnpaEFFAVasE~F----FE~------P~~l~~~~P~LY~~L~~~yrqDP~~~~ 250 (260)
T PRK15410 201 IDAYAASDPAECFAVLSEYF----FSA------PELFAPRFPALYQRFCQFYRQDPLQRL 250 (260)
T ss_pred CCccccCCchhhheeehhhh----hhC------HHHHHHhCHHHHHHHHHHhCCChhHhh
Confidence 3 499999999998765322 111 122334566888999999999999653
No 7
>PRK15322 invasion protein OrgB; Provisional
Probab=42.68 E-value=45 Score=31.25 Aligned_cols=50 Identities=18% Similarity=0.330 Sum_probs=38.4
Q ss_pred HHHHHHHHHhHHHHHHHhC----------------------------CccccccHHHHHHHHHhccCCCcccccCChh
Q psy16836 110 AQWLNKIGECVETELQKAL----------------------------PEKFHAAIPEISVYLKESFGNSTRIDYGTGH 159 (319)
Q Consensus 110 R~W~~~l~~~~~~ll~~~l----------------------------~~~~~~~~~EL~~Yl~~SFGn~tRIDYGTGH 159 (319)
.+|.+++++.+..+++..+ |....+...+|..||.+.+|.+.-|+|+-|.
T Consensus 71 ~~l~~~ie~~~r~lls~~Ld~pd~LL~~le~Wl~~l~~~~~pL~l~lP~~ak~~~~~L~~~l~e~w~~~~~i~yhd~~ 148 (210)
T PRK15322 71 WKWMEKIQIYARELFSAAVDHPETLLTVLDEWLRDFDKPEGQLFLTLPVNAKKDHQKLMVLLMENWPGTFNLKYHQEQ 148 (210)
T ss_pred HHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHhCccccCceeEecChhhhhhHHHHHHHHHHhcCCCeEEEEcCCC
Confidence 3777888887777666655 3334566789999999999989889998765
No 8
>cd00454 Trunc_globin Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct from the three-over-three pattern found in other globins. A subset of these have been demonstrated to form homodimers.
Probab=40.99 E-value=1.9e+02 Score=23.17 Aligned_cols=60 Identities=17% Similarity=0.328 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHhHHHHHHHhCCcc-ccccHHHHHHHHHhccCCCcccccCChhHH------------HHHHHHHHHHh
Q psy16836 108 AFAQWLNKIGECVETELQKALPEK-FHAAIPEISVYLKESFGNSTRIDYGTGHEM------------AFCMFLLCLFR 172 (319)
Q Consensus 108 AfR~W~~~l~~~~~~ll~~~l~~~-~~~~~~EL~~Yl~~SFGn~tRIDYGTGHEL------------~Fl~fL~~L~k 172 (319)
.-.++++++.+. ..+...++.. .......+..||+.-+|.+.+. +|+++ .|=+|+-||..
T Consensus 15 lv~~FY~~i~~d--p~i~~~F~~~~~~~~~~~~~~fl~~~~gg~~~y---~g~~~~~~H~~~~I~~~~f~~~l~~l~~ 87 (116)
T cd00454 15 LVDRFYARVAAD--PRLGPIFPADDLEEHRAKLADFLTQVLGGPGLY---RGHPMLRRHLPFPITEEEFDAWLELLRD 87 (116)
T ss_pred HHHHHHHHHhcC--hHHHHhcCCcchHHHHHHHHHHHHHHcCCCCCC---CCCChhhhhcCCCCCHHHHHHHHHHHHH
Confidence 345677776654 3466666544 5667778889999999988765 56554 36666665443
No 9
>COG3228 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.84 E-value=72 Score=30.75 Aligned_cols=98 Identities=22% Similarity=0.303 Sum_probs=66.3
Q ss_pred HHHHHHHHHHHHHhhhhCCCCCCCCCCCcHHHHHHHHHHHHhHHHH--HHHhCCccccccHHHHHHHHHhccCCCcccc-
Q psy16836 78 VMSVFQMLEHFNKLIDETPPIDQPQRFGNKAFAQWLNKIGECVETE--LQKALPEKFHAAIPEISVYLKESFGNSTRID- 154 (319)
Q Consensus 78 v~~l~~iL~~l~~~i~e~PP~~~p~RFGN~AfR~W~~~l~~~~~~l--l~~~l~~~~~~~~~EL~~Yl~~SFGn~tRID- 154 (319)
+..+--=||..|.=.+-+|+....+ -+-.|-+.|...-+++ ..+++++ +.|-||
T Consensus 152 iHEfAHkLDm~nG~anGvP~l~~r~-----d~~~W~~~l~aayd~~q~~~d~~~~------------------~~t~iD~ 208 (266)
T COG3228 152 IHEFAHKLDMRNGDANGVPFLPLRS-----DVAGWEHDLHAAYDNIQEEIDLVGE------------------RATSIDA 208 (266)
T ss_pred HhHHhhhhhcccCCcCCCCcCcccc-----hHHHHHHHHHHHHHHHHHHHhhccc------------------ccccccc
Confidence 4445555666776677888876444 4668999998877743 3444553 467777
Q ss_pred cCChhHHHHHHHHHHHHhhCCcCCCccchhhHHhHHHHHHHHHHHHHhhccccC
Q psy16836 155 YGTGHEMAFCMFLLCLFRIGAFSMNDRVAVVNRIFVRYLDLVRRLQCEYRMEPA 208 (319)
Q Consensus 155 YGTGHEL~Fl~fL~~L~klgil~~~d~~a~vL~vF~~Yl~lvR~Lq~~Y~LEPA 208 (319)
||--|=.-|+|-+---| |+.- =.+=.+|=.|-++||..|+.+|+
T Consensus 209 Y~AtnPAEfFAV~SE~F----F~aP------~~l~~~~palyq~lq~fY~qdPl 252 (266)
T COG3228 209 YAATNPAEFFAVLSEYF----FSAP------ELLQERFPALYQRLQKFYQQDPL 252 (266)
T ss_pred cccCChHHHHHHHHHHH----hcCH------HHHhHhhHHHHHHHHHHHhhhHH
Confidence 99999888888764322 2211 12335677888999999999996
No 10
>cd03572 ENTH_epsin_related ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the t
Probab=34.63 E-value=87 Score=26.82 Aligned_cols=82 Identities=18% Similarity=0.337 Sum_probs=53.0
Q ss_pred CCCCccCCCCCCCCCccccccceecCccchhhhh--cCHhHHHHHHHHHH-HHHhcCCCCCCCCCCCCHhH-HHHHHHHH
Q psy16836 11 LDLAFSSKNAVGPDHVYAIPKRQVLKDSDMKQWE--NSEAYHEYQGFILS-MNEAVRGKAIDTRLEPSNNV-MSVFQMLE 86 (319)
Q Consensus 11 ~~~~~~~~~~~~~~~~f~~P~K~I~~~~D~~~f~--~S~Ay~~i~~fI~~-l~~av~g~~~~~~~~~S~~v-~~l~~iL~ 86 (319)
.+.|++.++.|+++..+. ++..+. +.....+|+.|+.+ ||. + |+.| .|.+.+|+
T Consensus 6 l~~ATsdd~~p~pgy~~~----------Eia~~t~~s~~~~~ei~d~L~kRL~~--~----------~~hVK~K~Lrilk 63 (122)
T cd03572 6 LSKATSDDDEPTPGYLYE----------EIAKLTRKSVGSCQELLEYLLKRLKR--S----------SPHVKLKVLKIIK 63 (122)
T ss_pred HHHHhcCCCCCCchHHHH----------HHHHHHHcCHHHHHHHHHHHHHHhcC--C----------CCcchHHHHHHHH
Confidence 456788888887776664 333333 33567788888764 443 2 2445 66777777
Q ss_pred HHHHhhhhCCCCCCCCCCCcHHHHHHHHHHHHhHHHHHHHh
Q psy16836 87 HFNKLIDETPPIDQPQRFGNKAFAQWLNKIGECVETELQKA 127 (319)
Q Consensus 87 ~l~~~i~e~PP~~~p~RFGN~AfR~W~~~l~~~~~~ll~~~ 127 (319)
.| .+.|+..|+.|..+--..+..+.+--
T Consensus 64 ~l-------------~~~G~~~f~~~~~~~~~~Ik~~~~f~ 91 (122)
T cd03572 64 HL-------------CEKGNSDFKRELQRNSAQIRECANYK 91 (122)
T ss_pred HH-------------HhhCCHHHHHHHHHhHHHHHHHHHcC
Confidence 65 34588999999988776666655443
No 11
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=32.95 E-value=1.2e+02 Score=26.13 Aligned_cols=96 Identities=13% Similarity=0.168 Sum_probs=65.4
Q ss_pred CCCCCCCCCccCCCCCCCCCccccccceecCccchhhhhcCHhHHHHHHHHHHH--HHhcCCCCCCCCCCCCHhHHHHHH
Q psy16836 6 PGHRRLDLAFSSKNAVGPDHVYAIPKRQVLKDSDMKQWENSEAYHEYQGFILSM--NEAVRGKAIDTRLEPSNNVMSVFQ 83 (319)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~f~~P~K~I~~~~D~~~f~~S~Ay~~i~~fI~~l--~~av~g~~~~~~~~~S~~v~~l~~ 83 (319)
+|..|.+.|-+.... .+..|..-|..... .+....|..+|.+. ..-|.|.|.+.+-..++...++.+
T Consensus 11 ~G~kriGvAv~d~~~-----~~a~pl~~i~~~~~------~~~~~~l~~~i~~~~i~~iVvGlP~~~~G~~~~~~~~v~~ 79 (138)
T PRK00109 11 VGTKRIGVAVSDPLG-----GTAQPLETIKRNNG------TPDWDRLEKLIKEWQPDGLVVGLPLNMDGTEGPRTERARK 79 (138)
T ss_pred eCCCEEEEEEecCCC-----CEEcCEEEEEcCCC------chHHHHHHHHHHHhCCCEEEEeccCCCCCCcCHHHHHHHH
Confidence 577788887554322 35567766655431 13467888888886 567899999877788888888888
Q ss_pred HHHHHHHhhhhCCCCCCCCCCCcHHHHHHH
Q psy16836 84 MLEHFNKLIDETPPIDQPQRFGNKAFAQWL 113 (319)
Q Consensus 84 iL~~l~~~i~e~PP~~~p~RFGN~AfR~W~ 113 (319)
+.++|.... .+|-.-.+-||-.++=+..+
T Consensus 80 f~~~L~~~~-~~~v~~~DEr~TT~~A~~~l 108 (138)
T PRK00109 80 FANRLEGRF-GLPVVLVDERLSTVEAERAL 108 (138)
T ss_pred HHHHHHHHh-CCCEEEEcCCcCHHHHHHHH
Confidence 888887765 44443467788765544444
No 12
>PF04915 DltD_N: DltD N-terminal region; InterPro: IPR006999 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation []. These sequences contain the N-terminal region of DltD.; PDB: 3BMA_C.
Probab=29.31 E-value=13 Score=28.49 Aligned_cols=27 Identities=41% Similarity=0.754 Sum_probs=17.0
Q ss_pred cCCcccchhhhhhccccCCCCCCCCcccc
Q psy16836 216 LDDYQFVPFIWGSSQLFGNKDEIEPNMFL 244 (319)
Q Consensus 216 LDDy~fLPfi~GsaQL~~~~~~~~P~~i~ 244 (319)
|.|-.++|| +|||.|..- +.+.|+...
T Consensus 25 l~~~~yvPf-yGSSEl~r~-D~~HPsvl~ 51 (62)
T PF04915_consen 25 LKDPKYVPF-YGSSELSRF-DPFHPSVLA 51 (62)
T ss_dssp HSSS-EEEE-E-SSTTTS---TTSHHHHH
T ss_pred hcCCCeeee-cCcHHHhcc-CCcCHHHHH
Confidence 467789996 699999887 777676443
No 13
>PF03091 CutA1: CutA1 divalent ion tolerance protein; InterPro: IPR004323 The CutA family of proteins which exhibit ion tolerance are found in a large variety of species []. In E.Coli, two operons on the cutA locus contain genes that encode three proteins, CutA1, CutA2 and CutA3. CutA1 proteins are found in the cytoplasm while CutA2 (50kDa) and CutA3 (24kDa) are located in the inner membrane. Although the role of E. Coli CutA1 is not clear, studies on E. coli cutA locus describe some mutations that lead to an increase in copper sensitivity, thus suggesting a role in ion tolerance []. To date, the structure of CutA proteins from several species have been solved [, ]. The crystal structures of the E.Coli and rat CutA1 proteins show both these proteins to be trimeric in the crystal as well as in solution[].Trimerisation seems to supported by the formation of beta sheets between the subunit. This trimeric structure suggests the protein may be involved in signal transduction due to architectural similarities with PII signal transducer proteins []. Recent studies propose that mammalian CutA1 in the neuronal cell membrane acts as an anchor for acetylcholinesterase (AChE)1 [].; GO: 0010038 response to metal ion; PDB: 1O5J_A 1KR4_A 1VHF_A 3GSD_H 1OSC_A 3OPK_A 4E98_C 1V9B_F 1UKU_A 2E66_C ....
Probab=28.64 E-value=41 Score=27.75 Aligned_cols=33 Identities=27% Similarity=0.647 Sum_probs=25.7
Q ss_pred HHHHHHHHhhhhCCCCCCCC------CCCcHHHHHHHHH
Q psy16836 83 QMLEHFNKLIDETPPIDQPQ------RFGNKAFAQWLNK 115 (319)
Q Consensus 83 ~iL~~l~~~i~e~PP~~~p~------RFGN~AfR~W~~~ 115 (319)
+.+++|.++|.+..|=+.|. -.||.+|.+|...
T Consensus 61 ~~~~~l~~~i~~~HpYe~PeIi~~~i~~~~~~Yl~Wi~~ 99 (102)
T PF03091_consen 61 SRFDELEERIRELHPYEVPEIIALPIDKGNPAYLEWINE 99 (102)
T ss_dssp GGHHHHHHHHHHHSSSSS--EEEEEESEEEHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCCCEEEEEEccccCHHHHHHHHH
Confidence 56788888888888887776 5699999999864
No 14
>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.
Probab=27.89 E-value=11 Score=32.42 Aligned_cols=97 Identities=20% Similarity=0.250 Sum_probs=67.4
Q ss_pred CCCCCCCCCccCCCCCCCCCccccccceecCccchhhhhcCHhHHHHHHHHHHH--HHhcCCCCCCCCCCCCHhHHHHHH
Q psy16836 6 PGHRRLDLAFSSKNAVGPDHVYAIPKRQVLKDSDMKQWENSEAYHEYQGFILSM--NEAVRGKAIDTRLEPSNNVMSVFQ 83 (319)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~f~~P~K~I~~~~D~~~f~~S~Ay~~i~~fI~~l--~~av~g~~~~~~~~~S~~v~~l~~ 83 (319)
+|..|.+.|-+.... .+..|.+.|....+ ......|...|.+- ..-|.|.|...+-..++..+++.+
T Consensus 8 ~G~kriGiAvsd~~~-----~~a~pl~~i~~~~~------~~~~~~l~~li~~~~i~~iVvGlP~~~~G~~~~~~~~v~~ 76 (135)
T PF03652_consen 8 YGTKRIGIAVSDPLG-----IIASPLETIPRRNR------EKDIEELKKLIEEYQIDGIVVGLPLNMDGSESEQARRVRK 76 (135)
T ss_dssp ECSSEEEEEEEETTT-----SSEEEEEEEEECCC------CCCHHHHHHHHHHCCECEEEEEEEBBCTSSC-CCHHHHHH
T ss_pred eCCCeEEEEEecCCC-----CeEeeeEEEECCCC------chHHHHHHHHHHHhCCCEEEEeCCcccCCCccHHHHHHHH
Confidence 355666776554433 36678888886554 56677888888885 788999998887778888899999
Q ss_pred HHHHHHHhhhhCCCCCCCCCCCcHHHHHHH
Q psy16836 84 MLEHFNKLIDETPPIDQPQRFGNKAFAQWL 113 (319)
Q Consensus 84 iL~~l~~~i~e~PP~~~p~RFGN~AfR~W~ 113 (319)
+-+.|.+.+..+|-.-..-||-.++=+.+.
T Consensus 77 f~~~L~~~~~~ipV~~~DEr~TT~~A~~~l 106 (135)
T PF03652_consen 77 FAEELKKRFPGIPVILVDERLTTKEAERRL 106 (135)
T ss_dssp HHHHHHHHH-TSEEEEEECSCSHHCCHCCH
T ss_pred HHHHHHHhcCCCcEEEECCChhHHHHHHHH
Confidence 999998888555544466677655444333
No 15
>cd02986 DLP Dim1 family, Dim1-like protein (DLP) subfamily; DLP is a novel protein which shares 38% sequence identity to Dim1. Like Dim1, it is also implicated in pre-mRNA splicing and cell cycle progression. DLP is located in the nucleus and has been shown to interact with the U5 small nuclear ribonucleoprotein particle (snRNP)-specific 102kD protein (or Prp6). Dim1 protein, also known as U5 snRNP-specific 15kD protein is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 adopts a thioredoxin fold but does not contain the redox active CXXC motif.
Probab=27.18 E-value=22 Score=30.15 Aligned_cols=27 Identities=26% Similarity=0.582 Sum_probs=18.8
Q ss_pred ccHHHHHHHHHhc----c-----CCCcccccCChhH
Q psy16836 134 AAIPEISVYLKES----F-----GNSTRIDYGTGHE 160 (319)
Q Consensus 134 ~~~~EL~~Yl~~S----F-----Gn~tRIDYGTGHE 160 (319)
+-++|++.++.=+ | |...++|||||.-
T Consensus 55 Dev~dva~~y~I~amPtfvffkngkh~~~d~gt~~~ 90 (114)
T cd02986 55 DKVPVYTQYFDISYIPSTIFFFNGQHMKVDYGSPDH 90 (114)
T ss_pred cccHHHHHhcCceeCcEEEEEECCcEEEEecCCCCC
Confidence 3456666665533 1 8889999999963
No 16
>PF14745 WASH-7_N: WASH complex subunit 7, N-terminal
Probab=25.42 E-value=4.5e+02 Score=27.88 Aligned_cols=131 Identities=21% Similarity=0.355 Sum_probs=74.0
Q ss_pred HhHHHHHHHHHHHHHhhhhCCC---------------CCCCCCCC-----cHHHHHHHHHHHHhHH------HHHHHhCC
Q psy16836 76 NNVMSVFQMLEHFNKLIDETPP---------------IDQPQRFG-----NKAFAQWLNKIGECVE------TELQKALP 129 (319)
Q Consensus 76 ~~v~~l~~iL~~l~~~i~e~PP---------------~~~p~RFG-----N~AfR~W~~~l~~~~~------~ll~~~l~ 129 (319)
+.+..++.+|-+++++|+..|- ...|++|| -..|..-..++++..- ..+++..+
T Consensus 159 ~~lg~lL~vlvtlDeIi~~n~~L~~~w~~ykr~l~~v~~np~~f~~~~~~l~~le~ll~~le~~ll~g~iF~~~~eq~fd 238 (567)
T PF14745_consen 159 DHLGELLRVLVTLDEIIEQNPSLRDHWSLYKRMLKSVRHNPSKFGVTEEKLRQLEKLLADLEGQLLDGNIFQRCLEQLFD 238 (567)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHhcChhhcCCCHHHHHHHHHHHHHHHHHhhcchHHHHHHHHhcc
Confidence 4688899999999999996443 23577787 1233444444443221 12333333
Q ss_pred c-------cccccHHHHHHHHHhccCCCcccccCChhHH---HHHHHHHHHHhh--CCcCCCccchhhHHhHHHHHHHHH
Q psy16836 130 E-------KFHAAIPEISVYLKESFGNSTRIDYGTGHEM---AFCMFLLCLFRI--GAFSMNDRVAVVNRIFVRYLDLVR 197 (319)
Q Consensus 130 ~-------~~~~~~~EL~~Yl~~SFGn~tRIDYGTGHEL---~Fl~fL~~L~kl--gil~~~d~~a~vL~vF~~Yl~lvR 197 (319)
. .......|...|+++-|++-.+-. |+--|+ ..++=+|||+-+ .++...|. +++|
T Consensus 239 ~~~~~~v~~n~~l~eef~~~l~~~~~~~e~~l-~~~~e~~~r~~~igl~~L~vl~~~Lf~~~Dk------------kl~K 305 (567)
T PF14745_consen 239 DKGQVSVSKNKRLSEEFAAYLKELLEELEAKL-GEPKELDDRKDFIGLCGLYVLHYHLFPSVDK------------KLFK 305 (567)
T ss_pred cccceeccccHHHHHHHHHHHHHHHHHHHhhc-CCccccccHHHHHHHHHHHHHHHHHccccch------------HHHH
Confidence 1 234457899999999988877764 554443 233444444322 23333231 4566
Q ss_pred HHHHhhccccC---CCCcccccCCc
Q psy16836 198 RLQCEYRMEPA---GSHGVWSLDDY 219 (319)
Q Consensus 198 ~Lq~~Y~LEPA---GSHGvWGLDDy 219 (319)
++-..+.--|+ =-.=.|.-+||
T Consensus 306 ~vwe~~kk~P~v~l~g~v~w~P~~F 330 (567)
T PF14745_consen 306 RVWEVQKKVPAVPLYGNVIWFPDDF 330 (567)
T ss_pred HHHHHhcCCceEEEeccEEechHHH
Confidence 66666666666 11236777764
No 17
>PRK11027 hypothetical protein; Provisional
Probab=24.45 E-value=84 Score=26.75 Aligned_cols=54 Identities=20% Similarity=0.358 Sum_probs=40.4
Q ss_pred CChhHHHHHHHHHHHHhhCCcCCCccchhhHHhHHHHHHHHHHHHHhhccccCCCCc-ccccCCc
Q psy16836 156 GTGHEMAFCMFLLCLFRIGAFSMNDRVAVVNRIFVRYLDLVRRLQCEYRMEPAGSHG-VWSLDDY 219 (319)
Q Consensus 156 GTGHEL~Fl~fL~~L~klgil~~~d~~a~vL~vF~~Yl~lvR~Lq~~Y~LEPAGSHG-vWGLDDy 219 (319)
.|-.|-.||+.+- .+......+=+++.+|++++|+=-+.|.|- |..+ +=+.|||
T Consensus 53 ~t~eE~~Fv~v~~--------g~~~~~s~~Ek~WlKY~~~i~~~kr~~tl~--g~~~~~~~~~d~ 107 (112)
T PRK11027 53 VTEEEKQFVAVCR--------GEREPVTEFEKVWLKYMKRIRRPKRFHTLS--GGKPQVDGVEDY 107 (112)
T ss_pred CCHHHHHHHHHHc--------CCCCCCCHHHHHHHHHHHHhcCCCceEecc--CCCCCCCCcccc
Confidence 4677889998874 233445568899999999999989999994 6555 3457776
No 18
>PF02251 PA28_alpha: Proteasome activator pa28 alpha subunit; InterPro: IPR003185 PA28 activator complex (also known as 11S regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha (PA28alpha) and beta (PA28beta) subunits. The catalytic properties of PA28alpha and PA28beta-activated proteosome are similar [, ]. This entry represents the alpha subunit. The activator complex binds to the 20S proteasome and stimulates peptidase activity in and ATP-independent manner.; GO: 0008537 proteasome activator complex; PDB: 1AVO_K.
Probab=22.88 E-value=93 Score=23.79 Aligned_cols=32 Identities=19% Similarity=0.323 Sum_probs=27.5
Q ss_pred HHHHHHHHHhHHHHHHHhCCccccccHHHHHHHHHh
Q psy16836 110 AQWLNKIGECVETELQKALPEKFHAAIPEISVYLKE 145 (319)
Q Consensus 110 R~W~~~l~~~~~~ll~~~l~~~~~~~~~EL~~Yl~~ 145 (319)
..|.+++..+|+.|+...+|. -+.||...|.+
T Consensus 10 ~~fr~~l~~eAE~Lv~~~fP~----KI~eLd~lLk~ 41 (64)
T PF02251_consen 10 DEFRQSLTKEAENLVSNFFPQ----KIVELDELLKS 41 (64)
T ss_dssp HHHHHHHHHHHHHHHHTHHHH----HHHHHHHHHHS
T ss_pred HHHHHHHHHHHHHHHHhhCcH----HHHHHHHHhcC
Confidence 468899999999999998774 58899999887
No 19
>COG3085 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.87 E-value=91 Score=26.26 Aligned_cols=55 Identities=16% Similarity=0.289 Sum_probs=41.5
Q ss_pred ChhHHHHHHHHHHHHhhCCcCCCccchhhHHhHHHHHHHHHHHHHhhccccCCCCcccccCCcc
Q psy16836 157 TGHEMAFCMFLLCLFRIGAFSMNDRVAVVNRIFVRYLDLVRRLQCEYRMEPAGSHGVWSLDDYQ 220 (319)
Q Consensus 157 TGHEL~Fl~fL~~L~klgil~~~d~~a~vL~vF~~Yl~lvR~Lq~~Y~LEPAGSHGvWGLDDy~ 220 (319)
|--|=.|++++- .+.......=+++.+|...+|+=-+.|.|- .|.--+=|++||-
T Consensus 54 t~eEk~Fvavcr--------ger~aet~~Ek~W~KY~~r~~~~KRfhTLs-g~~~~~~~~eDyt 108 (112)
T COG3085 54 TEEEKLFVAVCR--------GEREAETFAEKVWSKYMTRIRRPKRFHTLS-GGKPQDEGVEDYT 108 (112)
T ss_pred chHHHHHHHHHc--------CCchhhHHHHHHHHHHHHHhcCCceeEecC-CCCCCcccccccc
Confidence 567899999875 234445567789999999999999999996 4444455688873
No 20
>PF08336 P4Ha_N: Prolyl 4-Hydroxylase alpha-subunit, N-terminal region; InterPro: IPR013547 The members found in this entry are eukaryotic proteins, and include all three isoforms of the prolyl 4-hydroxylase alpha subunit. This enzyme (1.14.11.2 from EC) is important in the post-translational modification of collagen, as it catalyses the formation of 4-hydroxyproline. In vertebrates, the complete enzyme is an alpha2-beta2 tetramer; the beta-subunit is identical to protein disulphide isomerase [, , , ]. The function of the N-terminal region featured in this family does not seem to be known. ; GO: 0004656 procollagen-proline 4-dioxygenase activity, 0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen, 0055114 oxidation-reduction process, 0005783 endoplasmic reticulum
Probab=21.86 E-value=42 Score=28.37 Aligned_cols=16 Identities=31% Similarity=0.565 Sum_probs=13.4
Q ss_pred HHHHHHHHHhhccccC
Q psy16836 193 LDLVRRLQCEYRMEPA 208 (319)
Q Consensus 193 l~lvR~Lq~~Y~LEPA 208 (319)
..-+.|||.+|+|.|+
T Consensus 109 ~~~l~RLQ~~Y~L~~~ 124 (134)
T PF08336_consen 109 AEGLLRLQDTYNLDPS 124 (134)
T ss_pred HHHHHHHHHHhCCCHH
Confidence 3457899999999986
No 21
>PRK10645 divalent-cation tolerance protein CutA; Provisional
Probab=21.23 E-value=1.4e+02 Score=25.12 Aligned_cols=37 Identities=16% Similarity=0.454 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhhhhCCCCCCCC------CCCcHHHHHHHHH
Q psy16836 79 MSVFQMLEHFNKLIDETPPIDQPQ------RFGNKAFAQWLNK 115 (319)
Q Consensus 79 ~~l~~iL~~l~~~i~e~PP~~~p~------RFGN~AfR~W~~~ 115 (319)
+-.-+.++.|.+.|.+..|=+.|. =.||++|.+|...
T Consensus 67 KT~~~~~~~l~~~I~~~HpYevPeIi~~~i~~g~~~Yl~Wi~~ 109 (112)
T PRK10645 67 KTTVSHQQALLECLKSHHPYQTPELLVLPVTHGDTDYLSWLNA 109 (112)
T ss_pred EeCHHHHHHHHHHHHHhCCCCCCEEEEEEcccCCHHHHHHHHH
Confidence 334568888999999988877765 5699999999864
No 22
>COG2517 Predicted RNA-binding protein containing a C-terminal EMAP domain [General function prediction only]
Probab=20.67 E-value=3.2e+02 Score=25.58 Aligned_cols=33 Identities=12% Similarity=0.184 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHhhhhCCCCCCCCCCCcHHHHHHHHHHHHhHHH
Q psy16836 79 MSVFQMLEHFNKLIDETPPIDQPQRFGNKAFAQWLNKIGECVET 122 (319)
Q Consensus 79 ~~l~~iL~~l~~~i~e~PP~~~p~RFGN~AfR~W~~~l~~~~~~ 122 (319)
..++++.++.+.+++-.|+. .+|+.+..+.+++
T Consensus 65 e~~~~l~~~a~~ive~l~~e-----------kdw~~~~l~~a~e 97 (219)
T COG2517 65 EQMKDLKEKAEGIVEALGGE-----------KDWSTKFLEQADE 97 (219)
T ss_pred HHHHHHHHHHHHHHHhcCCc-----------chHHHHHHHHHHH
Confidence 56778888888988888887 6888888888754
Done!