Query 020327
Match_columns 327
No_of_seqs 127 out of 197
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 08:52:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020327.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020327hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2826 Actin-related protein 100.0 3E-126 6E-131 874.8 22.5 295 1-312 1-300 (301)
2 PF04045 P34-Arc: Arp2/3 compl 100.0 3E-105 6E-110 744.3 16.1 238 53-299 1-241 (241)
3 PTZ00278 ARP2/3 complex subuni 93.0 0.19 4.2E-06 45.5 5.3 120 152-292 53-173 (174)
4 PF05856 ARPC4: ARP2/3 complex 91.3 0.77 1.7E-05 41.7 7.0 118 151-289 50-168 (170)
5 KOG1876 Actin-related protein 76.1 4.3 9.3E-05 36.2 4.4 120 151-290 48-167 (168)
6 PF05856 ARPC4: ARP2/3 complex 39.7 30 0.00065 31.6 3.1 48 50-108 70-125 (170)
7 PTZ00278 ARP2/3 complex subuni 38.3 21 0.00044 32.7 1.8 58 40-108 55-127 (174)
8 COG0415 PhrB Deoxyribodipyrimi 34.9 20 0.00044 37.4 1.4 15 274-288 331-345 (461)
9 cd00577 PCNA Proliferating Cel 31.7 2.5E+02 0.0054 25.1 7.9 52 183-244 193-246 (248)
10 PTZ00483 proliferating cell nu 27.6 3E+02 0.0066 26.5 8.0 104 129-244 145-261 (264)
11 PTZ00113 proliferating cell nu 27.4 3.5E+02 0.0076 26.2 8.4 107 129-247 141-269 (275)
12 PLN00057 proliferating cell nu 27.3 3E+02 0.0064 26.2 7.9 103 128-247 138-257 (263)
13 TIGR00590 pcna proliferating c 23.0 4.7E+02 0.01 24.7 8.3 100 129-245 139-255 (259)
14 TIGR02170 thyX thymidylate syn 22.8 31 0.00067 31.6 0.3 35 263-297 55-90 (209)
15 TIGR03829 YokU_near_AblA uncha 22.4 69 0.0015 26.4 2.2 48 68-130 40-87 (89)
16 KOG0898 40S ribosomal protein 20.5 88 0.0019 28.0 2.6 23 276-298 44-74 (152)
17 TIGR02765 crypto_DASH cryptoch 20.3 54 0.0012 33.0 1.4 16 274-289 345-360 (429)
No 1
>KOG2826 consensus Actin-related protein Arp2/3 complex, subunit ARPC2 [Cytoskeleton]
Probab=100.00 E-value=2.6e-126 Score=874.79 Aligned_cols=295 Identities=32% Similarity=0.610 Sum_probs=279.3
Q ss_pred CcccccccHHHHHHHHHhhhcc---CCCcccceEEeecCceEEEEecCCCCCceEEEEEeeCCCCCccccccCCCccHHH
Q 020327 1 MLLLQSHSRFLLEALLNRVQNV---DKATEVDYHWVEFDDVRYHVQVTMKNPHIVLLSVSLPVPPPETIFIGGLPFGAIE 77 (327)
Q Consensus 1 MilLe~~N~ii~~~L~~~~~~~---~kp~~id~~~~DFD~v~yHis~~~~~k~~l~lSislk~~~~~~~~~~~l~~Ga~e 77 (327)
||+||++|+||+++|.++++++ .+|+++|++++|||||+|||||+++||++|+||||+|||+ .++ .||+++
T Consensus 1 Mi~Le~nN~iI~etL~~kf~~~~~g~~P~sid~~vaDFDgv~yhiSnp~gdktkillSislK~y~--elq----~~Ga~~ 74 (301)
T KOG2826|consen 1 MILLEPNNRIIEETLNEKFENARAGGKPESIDVTVADFDGVLYHISNPNGDKTKILLSISLKFYK--ELQ----LHGADD 74 (301)
T ss_pred CceeccccHHHHHHHHHHHHHHhccCCCcceeEEEeccCceEEEccCCCCCceEEEEEEehhhHH--HHH----HcCHHH
Confidence 9999999999999999999884 4899999999999999999999999999999999999954 344 499999
Q ss_pred HHHHhhcccccccCCCCCCcceEEEEcCCCCCCChhhHHHHHHHHHhHHHHHhhhHHHHHHHHHhccCcccccCcceEEe
Q 020327 78 AIKAAYGNVVQILDPPRDGFNLTLKLNLSKLPPNEENKHALLVKIASVREVVLGAPLRVVLKHLASKTVASDIDQLLALV 157 (327)
Q Consensus 78 ~Lk~~Yg~~~~i~~~pE~GYdvTL~iDL~~lp~~~e~~~~li~~~s~lKrn~laApF~~~f~~l~~~~~~~~~~~~~~i~ 157 (327)
+||++||.|+ ..||+|||+||+|||++||++.++ +++.+++|||||+||+|+++|+ .|..+.++.+.++||
T Consensus 75 LLk~~yg~~~---~epE~Gyn~slli~L~~lpa~~~~---l~~~i~~lkrn~~as~F~k~f~---~Q~~~~e~~~r~~I~ 145 (301)
T KOG2826|consen 75 LLKRVYGSYL---SEPEPGYNVSLLIDLAELPADKES---LAKTISLLKRNCFASVFEKYFQ---FQEAGVEGEKRAVIH 145 (301)
T ss_pred HHHHHhcccc---CCCCCCccEEEEEEHHhCchhHHH---HHHHHHHhhhhHHHHHHHHHHh---cchhhhhhhheeEEE
Confidence 9999999997 679999999999999999999664 9999999999999999999997 455556677889999
Q ss_pred ccCCceEEEeecCCeeEEEEeceecCCccchhhhHHHHHHHHHhhhcCCCCCCCccCCC-CCCcccCCCCCcccCCCeeE
Q 020327 158 HRPKESFFLIPQAEKVTVVFPMRFNDSIDTVLATSFLQEFVEARRTAGLNNAPLCMWSS-SPPLELKGVPSETLSANAGF 236 (327)
Q Consensus 158 YR~dE~iyi~~~~DrVTVIFst~F~D~~D~vigkvFLQEFvdaRr~~~~~~APqVl~S~-~PPlEL~~~~~~~~~~n~gy 236 (327)
||+||+|||+|++|||||||||+|+|+||+||||||||||+||||+ +|+|||||||+ ||||||++++++++|+|+||
T Consensus 146 YRddEti~i~~k~DRVTvvFsTiF~de~D~I~GKVFlQEf~e~Rra--~qtAPqVLfShrePPLElkd~~~~~vgdn~gy 223 (301)
T KOG2826|consen 146 YRDDETIYIEPKNDRVTVVFSTIFRDEDDVIIGKVFLQEFVEGRRA--SQTAPQVLFSHREPPLELKDLYDARVGDNIGY 223 (301)
T ss_pred eccCceEEEecCCCeEEEEEEEeeccCCceeehHHHHHHHHHHHhh--hccccHHHhhcCCCCchhhhcCCcccccccce
Confidence 9999999999999999999999999999999999999999999997 89999999996 99999999999999999999
Q ss_pred EEEEeeccccCccchhhhhHHHhhhccccceeeeccchhhHHHHHHhHHHHHHHHhhhCCCccc-cccccccchhhh
Q 020327 237 VTFVIFPRHVEGKKLDRTVWNLSTFHAYVSYHVKCSEGFMHTRMRRRVESMIRTLDRAKPDAEK-LKKSTSNKSFKR 312 (327)
Q Consensus 237 VTFvLFprH~~~~~~~~ti~~l~~FR~YlhYHIKcSKaYmHsRMR~Rv~~~lkvLnRAkpe~~~-ekkT~sGr~f~~ 312 (327)
|||||||||++++.+++||++|++|||||||||||||||||||||+||++|||||||||||++. ||||+|||+|++
T Consensus 224 iTFVLFpRH~~k~~rd~tI~~i~~FRdylHyHIKcSKaYmHsRMR~k~~dFlKVLNRArpd~~~~erkT~tGrtf~~ 300 (301)
T KOG2826|consen 224 ITFVLFPRHTNKETRDNTINLIHLFRDYLHYHIKCSKAYMHSRMRAKTSDFLKVLNRARPDVEDEERKTFTGRTFVY 300 (301)
T ss_pred EEEEEecccCCchhccchhHHHHHHHHHhhhhhhhhHHHHHHHHHHhHHHHHHHHhhcCCCccchhhccccCceEec
Confidence 9999999999999999999999999999999999999999999999999999999999999754 999999999986
No 2
>PF04045 P34-Arc: Arp2/3 complex, 34 kD subunit p34-Arc; InterPro: IPR007188 Arp2/3 protein complex has been implicated in the control of actin polymerisation in cells. The human complex consists of seven subunits, which include the actin related Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc []. This family represents the p34-Arc subunit.; GO: 0030833 regulation of actin filament polymerization, 0005856 cytoskeleton; PDB: 2P9L_D 2P9I_D 2P9U_D 3DXM_D 2P9N_D 1TYQ_D 3DXK_D 1K8K_D 2P9S_D 1U2V_D ....
Probab=100.00 E-value=2.6e-105 Score=744.25 Aligned_cols=238 Identities=42% Similarity=0.795 Sum_probs=202.0
Q ss_pred EEEEeeCCCCCccccccCCCccHHHHHHHhhcccccccCCCCCCcceEEEEcCCCCCCChhhHHHHHHHHHhHHHHHhhh
Q 020327 53 LLSVSLPVPPPETIFIGGLPFGAIEAIKAAYGNVVQILDPPRDGFNLTLKLNLSKLPPNEENKHALLVKIASVREVVLGA 132 (327)
Q Consensus 53 ~lSislk~~~~~~~~~~~l~~Ga~e~Lk~~Yg~~~~i~~~pE~GYdvTL~iDL~~lp~~~e~~~~li~~~s~lKrn~laA 132 (327)
+|||++|| |.++. +||+.|+|+++||++++ ++||+|||+||.|||++||++++++.++|+++|+||||||||
T Consensus 1 lvSi~~~~--~~~l~----~~G~~e~l~~~Yg~~~~--~~pe~Gy~~tL~idl~~lp~~~~~~~~~i~~is~LKr~~~aa 72 (241)
T PF04045_consen 1 LVSISLKC--WKELQ----QYGAEEYLKREYGSYVQ--TPPESGYDVTLVIDLEKLPADEEDREELIKKISLLKRNCLAA 72 (241)
T ss_dssp EEEEE-TT--HHHHH----TTTHHHHHHHHCCCCE---ES--TTSSEEEEEETTS-----SSHHHHHHHHHTHHHHHCCH
T ss_pred CeEEEech--HHHHH----HcCHHHHHHHhcccccc--CCCCCCccEEEEEEcccCCchhhhHHHHHHHHHHHHHHHHHH
Confidence 68999999 77777 59999999999999985 689999999999999999998888999999999999999999
Q ss_pred HHHHHHHHHhccCcccccCcceEEeccCCceEEEeecCCeeEEEEeceecCCccchhhhHHHHHHHHHhhhcCCCCCCCc
Q 020327 133 PLRVVLKHLASKTVASDIDQLLALVHRPKESFFLIPQAEKVTVVFPMRFNDSIDTVLATSFLQEFVEARRTAGLNNAPLC 212 (327)
Q Consensus 133 pF~~~f~~l~~~~~~~~~~~~~~i~YR~dE~iyi~~~~DrVTVIFst~F~D~~D~vigkvFLQEFvdaRr~~~~~~APqV 212 (327)
||+++|+.+++++..+.++++++|+||+||+|||+|++|||||||||+|+|+||+||||||||||+||||+++ |+||||
T Consensus 73 pF~~~f~~~~~~~~~~~~~~~~~i~YR~~E~iyi~~~~DrVTVIFst~F~D~~D~vigkvFLQEFvdaRr~~~-~~APqv 151 (241)
T PF04045_consen 73 PFEKAFDEQASLSEEPPGEKPAVIHYRDDETIYIKPSKDRVTVIFSTRFKDEDDRVIGKVFLQEFVDARRRSR-QTAPQV 151 (241)
T ss_dssp HHHHHHCHHHCT-----TTT-EEEEECTTEEEEEEEESSEEEEEEEEE-SSCCHHHHHHHHHHHHHTGGGT---TTS-EE
T ss_pred HHHHHHHHHHhCCccccCCceEEEEeCCCceEEEEeCCCEEEEEEEEEEcCCCCeEeeHHHHHHHHHhccccC-CCCCce
Confidence 9999999888876555567899999999999999999999999999999999999999999999999999975 999999
Q ss_pred cCCC-CCCcccCCCCCcc-cCCCeeEEEEEeecccc-CccchhhhhHHHhhhccccceeeeccchhhHHHHHHhHHHHHH
Q 020327 213 MWSS-SPPLELKGVPSET-LSANAGFVTFVIFPRHV-EGKKLDRTVWNLSTFHAYVSYHVKCSEGFMHTRMRRRVESMIR 289 (327)
Q Consensus 213 l~S~-~PPlEL~~~~~~~-~~~n~gyVTFvLFprH~-~~~~~~~ti~~l~~FR~YlhYHIKcSKaYmHsRMR~Rv~~~lk 289 (327)
+||+ +||+||+|+++++ .++|+|||||||||||+ +++++++|||+|++|||||||||||||||||||||+||++|||
T Consensus 152 lfS~~~PPlEl~~~~~~~~~~~n~gyvTFvLfprH~~~~~~~~~ti~~l~~FR~YlhYHIKcsKaymHsRMR~Rv~~~lk 231 (241)
T PF04045_consen 152 LFSHREPPLELRGVPGARNLGDNVGYVTFVLFPRHFVTPERRDNTIWHLQTFRNYLHYHIKCSKAYMHSRMRKRVESFLK 231 (241)
T ss_dssp EEECSS--CGGTT-TT----STTEEEEEEEEEHHHGHSTTTHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred eccCCCCChhHcCCCCccccCCCeEEEEEEEeccccCcchhHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence 9997 9999999998887 89999999999999995 5889999999999999999999999999999999999999999
Q ss_pred HHhhhCCCcc
Q 020327 290 TLDRAKPDAE 299 (327)
Q Consensus 290 vLnRAkpe~~ 299 (327)
||||||||.+
T Consensus 232 vLnrAkpe~~ 241 (241)
T PF04045_consen 232 VLNRAKPEEE 241 (241)
T ss_dssp HHHCTS----
T ss_pred HHHhcCcCCC
Confidence 9999999953
No 3
>PTZ00278 ARP2/3 complex subunit; Provisional
Probab=92.96 E-value=0.19 Score=45.52 Aligned_cols=120 Identities=20% Similarity=0.351 Sum_probs=98.5
Q ss_pred cceEEeccCCceEEEeecCCeeEEEEeceecCCccchhhhHHHHHHHHHhhhcCCCCCCCccCCCCCCcccCCCCCcccC
Q 020327 152 QLLALVHRPKESFFLIPQAEKVTVVFPMRFNDSIDTVLATSFLQEFVEARRTAGLNNAPLCMWSSSPPLELKGVPSETLS 231 (327)
Q Consensus 152 ~~~~i~YR~dE~iyi~~~~DrVTVIFst~F~D~~D~vigkvFLQEFvdaRr~~~~~~APqVl~S~~PPlEL~~~~~~~~~ 231 (327)
.++.|..-++|.+.|.|+-+.|.|.|...-.|+-++++++-|+. |.-.|-. +=+| ||-.|-
T Consensus 53 ~pl~I~Rne~E~clIE~SiNSvRiSi~ikqaDeie~iL~~kf~~-Fl~~RAe-----~F~I---------LRrkPv---- 113 (174)
T PTZ00278 53 NPIYIVRSEKEKCLIEPSINSVRISFSFKKSDELDVIIARKFVS-FLAQRAE-----QFVI---------LRRKPI---- 113 (174)
T ss_pred CcEEEEEcCCceEEEEcccceEEEEEEehhhChHHHHHHHHHHH-HHHhhhh-----ceeE---------EeecCc----
Confidence 56888888999999999999999999999999999999999987 5554432 1122 222221
Q ss_pred CCeeE-EEEEeeccccCccchhhhhHHHhhhccccceeeeccchhhHHHHHHhHHHHHHHHh
Q 020327 232 ANAGF-VTFVIFPRHVEGKKLDRTVWNLSTFHAYVSYHVKCSEGFMHTRMRRRVESMIRTLD 292 (327)
Q Consensus 232 ~n~gy-VTFvLFprH~~~~~~~~ti~~l~~FR~YlhYHIKcSKaYmHsRMR~Rv~~~lkvLn 292 (327)
.|| |||.+.--|++.--+.+-|+.|.+|=.=.---|.--|-.+-+|=|.=.++|++-++
T Consensus 114 --~GYDISFLItn~H~e~m~k~kLidFIi~FmeeiDkeIsemKL~~NaRaR~~A~~fl~~f~ 173 (174)
T PTZ00278 114 --PGYDISFLITNFHTENMFKHKLIDFIIDFMEDIDKDISDMKLNVNTRARIAAPEFFKALA 173 (174)
T ss_pred --CCCChhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhc
Confidence 244 88999999998766789999999999999999999999999999999999998764
No 4
>PF05856 ARPC4: ARP2/3 complex 20 kDa subunit (ARPC4); InterPro: IPR008384 This family consists of several eukaryotic ARP2/3 complex 20 kDa subunit (P20-ARC) proteins. The Arp2/3 protein complex has been implicated in the control of actin polymerisation in cells. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3 it has been suggested that the complex promotes actin assembly in lamellipodia and may participate in lamellipodial protrusion [].; GO: 0030041 actin filament polymerization, 0005856 cytoskeleton; PDB: 3DWL_K 1K8K_F 1U2V_F 2P9S_F 2P9U_F 2P9N_F 3DXK_F 1TYQ_F 3RSE_F 2P9I_F ....
Probab=91.26 E-value=0.77 Score=41.70 Aligned_cols=118 Identities=20% Similarity=0.329 Sum_probs=85.0
Q ss_pred CcceEEeccCCceEEEeecCCeeEEEEeceecCCccchhhhHHHHHHHHHhhhcCCCCCCCccCCCCCCcccCCCCCccc
Q 020327 151 DQLLALVHRPKESFFLIPQAEKVTVVFPMRFNDSIDTVLATSFLQEFVEARRTAGLNNAPLCMWSSSPPLELKGVPSETL 230 (327)
Q Consensus 151 ~~~~~i~YR~dE~iyi~~~~DrVTVIFst~F~D~~D~vigkvFLQEFvdaRr~~~~~~APqVl~S~~PPlEL~~~~~~~~ 230 (327)
-.++.|...+.|.++|.|+-+.|.|.+.....|+-++++.+-|+. |.-.|-. +=+|| |-.|-.
T Consensus 50 l~pl~I~Rne~E~clIE~SiNSvRvSi~ikq~Deie~iL~~kf~r-Fl~~RAe-----~F~IL---------RRkPv~-- 112 (170)
T PF05856_consen 50 LNPLVISRNEKEKCLIEPSINSVRVSIKIKQADEIERILCHKFTR-FLMQRAE-----NFFIL---------RRKPVE-- 112 (170)
T ss_dssp ---EEEESSSS-EEEEEEBSSEEEEEEE----SCHHHHHHHHHHH-HHHHCTT-----TSTTB----------SS--T--
T ss_pred cCceeeccCCCceEEEEcccceEEEEEEecccChHHHHHHHHHHH-HHHhhhh-----hheee---------eecCcC--
Confidence 357888888999999999999999999999999999999999976 5555432 11222 222211
Q ss_pred CCCeeE-EEEEeeccccCccchhhhhHHHhhhccccceeeeccchhhHHHHHHhHHHHHH
Q 020327 231 SANAGF-VTFVIFPRHVEGKKLDRTVWNLSTFHAYVSYHVKCSEGFMHTRMRRRVESMIR 289 (327)
Q Consensus 231 ~~n~gy-VTFvLFprH~~~~~~~~ti~~l~~FR~YlhYHIKcSKaYmHsRMR~Rv~~~lk 289 (327)
|| |||.+.-.|++.--+.+-|+.|.+|=.=+---|.--|-.+-+|=|.=.++|++
T Consensus 113 ----GYDISFLIt~~h~e~m~k~kLidFIi~FmeeiDkeIs~mKl~~naRaR~~A~~fl~ 168 (170)
T PF05856_consen 113 ----GYDISFLITNFHTEQMGKHKLIDFIITFMEEIDKEISEMKLSLNARARIVAEEFLK 168 (170)
T ss_dssp ----TSSEEEEEECCHHHHSTHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHC
T ss_pred ----CCceeeeeechhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence 44 89999999998766789999999998777777777788888888877777764
No 5
>KOG1876 consensus Actin-related protein Arp2/3 complex, subunit ARPC4 [Cytoskeleton]
Probab=76.10 E-value=4.3 Score=36.24 Aligned_cols=120 Identities=18% Similarity=0.278 Sum_probs=93.9
Q ss_pred CcceEEeccCCceEEEeecCCeeEEEEeceecCCccchhhhHHHHHHHHHhhhcCCCCCCCccCCCCCCcccCCCCCccc
Q 020327 151 DQLLALVHRPKESFFLIPQAEKVTVVFPMRFNDSIDTVLATSFLQEFVEARRTAGLNNAPLCMWSSSPPLELKGVPSETL 230 (327)
Q Consensus 151 ~~~~~i~YR~dE~iyi~~~~DrVTVIFst~F~D~~D~vigkvFLQEFvdaRr~~~~~~APqVl~S~~PPlEL~~~~~~~~ 230 (327)
..+++|.-.+.|.+-|.|+-..|.+.....=.|+-.+|+.+-|++ |...|-. |=+||-. .|-.
T Consensus 48 l~pv~isRNe~Ek~LIE~SiNSvRiSi~vKQaDEiE~IL~~KF~r-Fl~~RAe-----~F~iLRR---------kPv~-- 110 (168)
T KOG1876|consen 48 LTPVVISRNEQEKVLIEPSINSVRISIAVKQADEIERILCHKFTR-FLMMRAE-----AFFILRR---------KPVQ-- 110 (168)
T ss_pred hCceEeecccccceeEecccceEEEEEeecchHHHHHHHHHHHHH-HHHHhhh-----hheeeee---------CCcC--
Confidence 467888888899999999999998888888889999999999988 7766643 3444433 2211
Q ss_pred CCCeeEEEEEeeccccCccchhhhhHHHhhhccccceeeeccchhhHHHHHHhHHHHHHH
Q 020327 231 SANAGFVTFVIFPRHVEGKKLDRTVWNLSTFHAYVSYHVKCSEGFMHTRMRRRVESMIRT 290 (327)
Q Consensus 231 ~~n~gyVTFvLFprH~~~~~~~~ti~~l~~FR~YlhYHIKcSKaYmHsRMR~Rv~~~lkv 290 (327)
+-+|+|.+-.-|.+.-..-+-++.+.-|-.=..--|.-+|.++..|-|--.++|++.
T Consensus 111 ---gy~IsfLItn~hte~m~k~Klvdf~iefmeeidkeiSemkl~~n~rar~~ae~fl~~ 167 (168)
T KOG1876|consen 111 ---GYDISFLITNFHTEQMYKHKLVDFIIEFMEEIDKEISEMKLFLNARARQVAEEFLKR 167 (168)
T ss_pred ---ccchhhhhhccchHHHHhchhHHHHHHHHHHHhhhhhhhccccchhhHHhHHHHHhc
Confidence 123899999999875444567777888887788899999999999999999999874
No 6
>PF05856 ARPC4: ARP2/3 complex 20 kDa subunit (ARPC4); InterPro: IPR008384 This family consists of several eukaryotic ARP2/3 complex 20 kDa subunit (P20-ARC) proteins. The Arp2/3 protein complex has been implicated in the control of actin polymerisation in cells. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3 it has been suggested that the complex promotes actin assembly in lamellipodia and may participate in lamellipodial protrusion [].; GO: 0030041 actin filament polymerization, 0005856 cytoskeleton; PDB: 3DWL_K 1K8K_F 1U2V_F 2P9S_F 2P9U_F 2P9N_F 3DXK_F 1TYQ_F 3RSE_F 2P9I_F ....
Probab=39.75 E-value=30 Score=31.61 Aligned_cols=48 Identities=10% Similarity=0.207 Sum_probs=27.5
Q ss_pred ceEEEEEeeCCCCCccccccCCCccHHHHHHHhhcccc-------cc-cCCCCCCcceEEEEcCCCC
Q 020327 50 HIVLLSVSLPVPPPETIFIGGLPFGAIEAIKAAYGNVV-------QI-LDPPRDGFNLTLKLNLSKL 108 (327)
Q Consensus 50 ~~l~lSislk~~~~~~~~~~~l~~Ga~e~Lk~~Yg~~~-------~i-~~~pE~GYdvTL~iDL~~l 108 (327)
|-+.|||.+|- .++ .+..|-++|-.++ .| .-.|=+|||+|.+|.-..+
T Consensus 70 NSvRvSi~ikq-------~De----ie~iL~~kf~rFl~~RAe~F~ILRRkPv~GYDISFLIt~~h~ 125 (170)
T PF05856_consen 70 NSVRVSIKIKQ-------ADE----IERILCHKFTRFLMQRAENFFILRRKPVEGYDISFLITNFHT 125 (170)
T ss_dssp SEEEEEEE-----------SC----HHHHHHHHHHHHHHHCTTTSTTB-SS--TTSSEEEEEECCHH
T ss_pred ceEEEEEEecc-------cCh----HHHHHHHHHHHHHHhhhhhheeeeecCcCCCceeeeeechhh
Confidence 67889998884 122 3345555554443 22 3468899999999987754
No 7
>PTZ00278 ARP2/3 complex subunit; Provisional
Probab=38.34 E-value=21 Score=32.73 Aligned_cols=58 Identities=14% Similarity=0.145 Sum_probs=35.3
Q ss_pred EEEecCCCCC-------ceEEEEEeeCCCCCccccccCCCccHHHHHHHhhc--------ccccccCCCCCCcceEEEEc
Q 020327 40 YHVQVTMKNP-------HIVLLSVSLPVPPPETIFIGGLPFGAIEAIKAAYG--------NVVQILDPPRDGFNLTLKLN 104 (327)
Q Consensus 40 yHis~~~~~k-------~~l~lSislk~~~~~~~~~~~l~~Ga~e~Lk~~Yg--------~~~~i~~~pE~GYdvTL~iD 104 (327)
-+|+-+++++ |-+.|||.+|- . ++ .+..|-++|- .+.-..-.|=+|||+|.+|.
T Consensus 55 l~I~Rne~E~clIE~SiNSvRiSi~ikq---a----De----ie~iL~~kf~~Fl~~RAe~F~ILRrkPv~GYDISFLIt 123 (174)
T PTZ00278 55 IYIVRSEKEKCLIEPSINSVRISFSFKK---S----DE----LDVIIARKFVSFLAQRAEQFVILRRKPIPGYDISFLIT 123 (174)
T ss_pred EEEEEcCCceEEEEcccceEEEEEEehh---h----Ch----HHHHHHHHHHHHHHhhhhceeEEeecCcCCCChhhhhh
Confidence 4566555444 67888888884 2 22 2233334443 33322346889999999998
Q ss_pred CCCC
Q 020327 105 LSKL 108 (327)
Q Consensus 105 L~~l 108 (327)
-...
T Consensus 124 n~H~ 127 (174)
T PTZ00278 124 NFHT 127 (174)
T ss_pred hhhH
Confidence 7765
No 8
>COG0415 PhrB Deoxyribodipyrimidine photolyase [DNA replication, recombination, and repair]
Probab=34.89 E-value=20 Score=37.40 Aligned_cols=15 Identities=53% Similarity=0.935 Sum_probs=14.0
Q ss_pred hhhHHHHHHhHHHHH
Q 020327 274 GFMHTRMRRRVESMI 288 (327)
Q Consensus 274 aYmHsRMR~Rv~~~l 288 (327)
+|||.|||-=|++||
T Consensus 331 G~MHNR~RMivAsFL 345 (461)
T COG0415 331 GYMHNRMRMIVASFL 345 (461)
T ss_pred CCcchHHHHHHHHHH
Confidence 799999999999987
No 9
>cd00577 PCNA Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds. PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY].
Probab=31.69 E-value=2.5e+02 Score=25.09 Aligned_cols=52 Identities=25% Similarity=0.432 Sum_probs=33.7
Q ss_pred CCccchhhhHHHHHHHHHhhhcCCCCCCCccCC--CCCCcccCCCCCcccCCCeeEEEEEeecc
Q 020327 183 DSIDTVLATSFLQEFVEARRTAGLNNAPLCMWS--SSPPLELKGVPSETLSANAGFVTFVIFPR 244 (327)
Q Consensus 183 D~~D~vigkvFLQEFvdaRr~~~~~~APqVl~S--~~PPlEL~~~~~~~~~~n~gyVTFvLFpr 244 (327)
++....|.--||.++..+ +..+..|... ..-|+-|+... .+.|+++|.|.|+
T Consensus 193 ~~~~~~fn~~yL~~~l~~-----~~~s~~v~i~~~~~~p~~i~~~~-----~~~~~~~f~lap~ 246 (248)
T cd00577 193 EPVSSTYSLKYLKDFTKA-----APLSDKVTLSFGSDGPLSLEFKI-----ADGGHLTFYLAPK 246 (248)
T ss_pred CceEEEEhHHHHHHHhhh-----cccCCeEEEEEcCCCCEEEEEEc-----CCCcEEEEEEccc
Confidence 455555555555555444 5546677654 34588888753 2389999999996
No 10
>PTZ00483 proliferating cell nuclear antigen; Provisional
Probab=27.57 E-value=3e+02 Score=26.45 Aligned_cols=104 Identities=21% Similarity=0.219 Sum_probs=62.8
Q ss_pred HhhhHHHHHHHHHhccCcccccCcceEEeccCCceEEEeecCCe--eEEEEe-------ceecCCccchhhhHHHHHHHH
Q 020327 129 VLGAPLRVVLKHLASKTVASDIDQLLALVHRPKESFFLIPQAEK--VTVVFP-------MRFNDSIDTVLATSFLQEFVE 199 (327)
Q Consensus 129 ~laApF~~~f~~l~~~~~~~~~~~~~~i~YR~dE~iyi~~~~Dr--VTVIFs-------t~F~D~~D~vigkvFLQEFvd 199 (327)
+-++.|.++.+.++.=+ ..+.|.- .++.+++.+++|. ..+.++ +.-+++..-.|+--+|-.|..
T Consensus 145 m~s~~f~~i~kdl~~vs------D~v~i~~-~~~~v~f~a~Gd~~~~~~~l~~~~~~v~~~~~~~v~~~fsl~YL~~f~K 217 (264)
T PTZ00483 145 MNSKKFQEFAKYLHSIG------DTVSISM-KKDEMRLETEGEGIKASKQFHNDVGDVRVTSTESLSQEFATRYLVLFSK 217 (264)
T ss_pred EEHHHHHHHHHHHHHcC------CEEEEEE-ECCEEEEEEeecCcEEEEEEccCCCceEEEecCcchheehHHHHHHhhc
Confidence 44778888877655321 2355555 4666887777763 444443 112233345567777888876
Q ss_pred HhhhcCCCCCCCcc--CCCCCCcccCCCCC--cccCCCeeEEEEEeecc
Q 020327 200 ARRTAGLNNAPLCM--WSSSPPLELKGVPS--ETLSANAGFVTFVIFPR 244 (327)
Q Consensus 200 aRr~~~~~~APqVl--~S~~PPlEL~~~~~--~~~~~n~gyVTFvLFpr 244 (327)
| .+-|..|. ++.+-|+.|.=--+ ....++.||++|-|=||
T Consensus 218 a-----~~lsd~V~i~l~~~~Pl~ley~i~~~~~~~~~~G~l~fyLAPr 261 (264)
T PTZ00483 218 A-----TSLADEVSINLSAGIPLSVKFNFKDPLTDLQDSSFINFYLAPN 261 (264)
T ss_pred c-----ccCCCeEEEEEcCCCCEEEEEEecccccCCCCceEEEEEEccc
Confidence 5 34467774 66778887654210 01125789999999997
No 11
>PTZ00113 proliferating cell nuclear antigen; Provisional
Probab=27.38 E-value=3.5e+02 Score=26.20 Aligned_cols=107 Identities=17% Similarity=0.238 Sum_probs=65.9
Q ss_pred HhhhHHHHHHHHHhccCcccccCcceEEeccCCceEEEeecCCe--eEEEEe-------------ceecCCccchhhhHH
Q 020327 129 VLGAPLRVVLKHLASKTVASDIDQLLALVHRPKESFFLIPQAEK--VTVVFP-------------MRFNDSIDTVLATSF 193 (327)
Q Consensus 129 ~laApF~~~f~~l~~~~~~~~~~~~~~i~YR~dE~iyi~~~~Dr--VTVIFs-------------t~F~D~~D~vigkvF 193 (327)
+-++.|+++.+.++.=+ ..++|.- +++.+++.+++|. +.+.+. +..+.+.-..|+--.
T Consensus 141 m~s~~f~~i~rdl~~vg------d~V~i~~-~~~~v~f~a~Gd~g~~~i~l~~~~~~~~~~~~~~~~v~~~~~~~ysl~Y 213 (275)
T PTZ00113 141 LSSKELTNICRQMNEFS------DTVKIEI-DSNSIKFTTQGDLGDGEVVLKPRPPTSEDDCGVTIKVRKPIKQSYATKY 213 (275)
T ss_pred EEHHHHHHHHHHHHHcC------CEEEEEE-eCCEEEEEEeccCcEEEEEEecCCCCCCccceEEEEecCceeeEEhHHH
Confidence 45778888887665421 2345554 4567888887774 333332 233455566888888
Q ss_pred HHHHHHHhhhcCCCCCCCc--cCCCCCCcccCCCCC-----cccCCCeeEEEEEeeccccC
Q 020327 194 LQEFVEARRTAGLNNAPLC--MWSSSPPLELKGVPS-----ETLSANAGFVTFVIFPRHVE 247 (327)
Q Consensus 194 LQEFvdaRr~~~~~~APqV--l~S~~PPlEL~~~~~-----~~~~~n~gyVTFvLFprH~~ 247 (327)
|-.|..|. +-|..| .|+.+-|+.|.=--+ .+-..+.||++|.|=||=-.
T Consensus 214 L~~f~Ka~-----~ls~~V~l~l~~d~Pl~ley~i~~~~~~~~~~~~~G~l~fyLAPkie~ 269 (275)
T PTZ00113 214 LNMFAKSG-----CLSDVVTLGLSDNRPIEVKYEIKDTSPDARHTHKLGEVKFFLAPKMDD 269 (275)
T ss_pred HHHhhccc-----cCCCeEEEEEcCCCCEEEEEEeccccccccccCCccEEEEEEcCccCc
Confidence 88888663 335666 466788887654200 01112579999999998643
No 12
>PLN00057 proliferating cell nuclear antigen; Provisional
Probab=27.32 E-value=3e+02 Score=26.20 Aligned_cols=103 Identities=17% Similarity=0.287 Sum_probs=64.7
Q ss_pred HHhhhHHHHHHHHHhccCcccccCcceEEeccCCceEEEeecCC--eeEEEEe-----------ce--ecCCccchhhhH
Q 020327 128 VVLGAPLRVVLKHLASKTVASDIDQLLALVHRPKESFFLIPQAE--KVTVVFP-----------MR--FNDSIDTVLATS 192 (327)
Q Consensus 128 n~laApF~~~f~~l~~~~~~~~~~~~~~i~YR~dE~iyi~~~~D--rVTVIFs-----------t~--F~D~~D~vigkv 192 (327)
.+.++.|+++.+.+..=+ ..+.|.- +++.+++.+.+| .+.+.++ .. -+++....++--
T Consensus 138 ~m~s~~f~~~~kdl~~vs------d~v~i~~-~~~~~~f~~~Gd~g~~~~~l~~~~~~~~~~~~~~i~~~e~~~~~y~l~ 210 (263)
T PLN00057 138 RMPSAEFQRICKDLSSIG------DTVVISV-TKEGVKFSTSGDIGTANIVLRQNTTVDKPEEKTVIEMQEPVSLTFALR 210 (263)
T ss_pred EEEHHHHHHHHHHHHHcC------CEEEEEE-eCCEEEEEEEecCcEEEEEEecCCCCCCccceEEEEecCceEEEEhHH
Confidence 355778888887666311 2355555 455677777764 4555553 11 123335557777
Q ss_pred HHHHHHHHhhhcCCCCCCCcc--CCCCCCcccCCCCCcccCCCeeEEEEEeeccccC
Q 020327 193 FLQEFVEARRTAGLNNAPLCM--WSSSPPLELKGVPSETLSANAGFVTFVIFPRHVE 247 (327)
Q Consensus 193 FLQEFvdaRr~~~~~~APqVl--~S~~PPlEL~~~~~~~~~~n~gyVTFvLFprH~~ 247 (327)
.|-.|+.| .+-|-.|. ++.+-|+.|+=- . ++.|+++|.|=||=-+
T Consensus 211 YL~~~~Ka-----~~ls~~V~i~~~~~~Pl~l~y~----l-~~~g~l~f~LAPri~~ 257 (263)
T PLN00057 211 YLNSFTKA-----TPLSDTVTLSLSKELPVVVEYK----I-AEMGYIRYYLAPKIEE 257 (263)
T ss_pred HHHHhhcc-----ccCCCeEEEEEcCCCCEEEEEE----e-CCCeEEEEEEcCCCCC
Confidence 77777755 34566774 556889988763 2 3589999999998543
No 13
>TIGR00590 pcna proliferating cell nuclear antigen (pcna). All proteins in this family for which functions are known form sliding DNA clamps that are used in DNA replication processes. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.99 E-value=4.7e+02 Score=24.73 Aligned_cols=100 Identities=15% Similarity=0.273 Sum_probs=64.8
Q ss_pred HhhhHHHHHHHHHhccCcccccCcceEEeccCCceEEEeecCC--eeEEEEece-------------ecCCccchhhhHH
Q 020327 129 VLGAPLRVVLKHLASKTVASDIDQLLALVHRPKESFFLIPQAE--KVTVVFPMR-------------FNDSIDTVLATSF 193 (327)
Q Consensus 129 ~laApF~~~f~~l~~~~~~~~~~~~~~i~YR~dE~iyi~~~~D--rVTVIFst~-------------F~D~~D~vigkvF 193 (327)
+.++.|.++.+.+..=+ ..+.|.- +++.+++.+.+| ++.+.++-. -+++....++--.
T Consensus 139 m~s~~f~~~~kdl~~v~------d~v~i~~-~~~~~~f~~~Gd~g~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~y~l~Y 211 (259)
T TIGR00590 139 MPSSEFARICRDLSQFS------DSVVISC-TKEGVKFSAKGDIGSGNVKLKQTSDTDKEEEAVTIEMKEPVTLTFAIKY 211 (259)
T ss_pred EEHHHHHHHHHHHHHcC------CEEEEEE-eCCEEEEEEEecccEEEEEEecCCCCCCCcceEEEEecCceeeeeeHHH
Confidence 45788888888766421 2355555 346677777774 566666532 2233345677778
Q ss_pred HHHHHHHhhhcCCCCCCCcc--CCCCCCcccCCCCCcccCCCeeEEEEEeeccc
Q 020327 194 LQEFVEARRTAGLNNAPLCM--WSSSPPLELKGVPSETLSANAGFVTFVIFPRH 245 (327)
Q Consensus 194 LQEFvdaRr~~~~~~APqVl--~S~~PPlEL~~~~~~~~~~n~gyVTFvLFprH 245 (327)
|-.|..| .+-|-+|. ++.+-|+.|+=- . .+.|+++|.|=||=
T Consensus 212 L~~~~Ka-----~~ls~~V~l~~~~~~Pl~l~y~----i-~~~g~l~f~lAPri 255 (259)
T TIGR00590 212 LNLFTKA-----TPLSDRVTLSMSNDVPLVVEYK----I-KDMGFLRFFLAPKI 255 (259)
T ss_pred HHHhhhh-----ccCCCeEEEEEcCCCCEEEEEE----e-CCCeEEEEEEcCcc
Confidence 8888766 34466664 556889988763 1 24699999999983
No 14
>TIGR02170 thyX thymidylate synthase, flavin-dependent. Two forms of microbial thymidylate synthase are known: ThyA (2.1.1.45) and ThyX (2.1.1.148). This model describes ThyX, a homotetrameric flavoprotein. Both enzymes convert dUMP to dTMP. Under oxygen-limiting conditions, thyX can complement a thyA mutation.
Probab=22.81 E-value=31 Score=31.64 Aligned_cols=35 Identities=26% Similarity=0.227 Sum_probs=30.6
Q ss_pred cccceeee-ccchhhHHHHHHhHHHHHHHHhhhCCC
Q 020327 263 AYVSYHVK-CSEGFMHTRMRRRVESMIRTLDRAKPD 297 (327)
Q Consensus 263 ~YlhYHIK-cSKaYmHsRMR~Rv~~~lkvLnRAkpe 297 (327)
..++++|+ ||++-.|.=||.|+.+|.+.=.|-...
T Consensus 55 ~~~tF~i~g~sr~~~~ql~RHR~~s~~~~S~RY~~~ 90 (209)
T TIGR02170 55 ASFTFHVKGASRSVAAQLTRHRIASYSVQSQRYVLL 90 (209)
T ss_pred eEEEEEEEeecHHHHHHHHHHhcCceeecccccccC
Confidence 57899999 999999999999999988877776654
No 15
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=22.41 E-value=69 Score=26.38 Aligned_cols=48 Identities=15% Similarity=0.191 Sum_probs=33.3
Q ss_pred ccCCCccHHHHHHHhhcccccccCCCCCCcceEEEEcCCCCCCChhhHHHHHHHHHhHHHHHh
Q 020327 68 IGGLPFGAIEAIKAAYGNVVQILDPPRDGFNLTLKLNLSKLPPNEENKHALLVKIASVREVVL 130 (327)
Q Consensus 68 ~~~l~~Ga~e~Lk~~Yg~~~~i~~~pE~GYdvTL~iDL~~lp~~~e~~~~li~~~s~lKrn~l 130 (327)
.||-.|=.++.+++.=.- =++||-.+||..-. ..+|.+.=.+||||.|
T Consensus 40 ~CGe~y~~dev~~eIE~~--------------l~l~~~~~~p~~~~-y~~lm~~~~~lk~nyf 87 (89)
T TIGR03829 40 HCGMEYQDDTTVKEIEDQ--------------LLLVDTKKLPDETT-YEELMKMPRLLKRNYF 87 (89)
T ss_pred CCCcEeecHHHHHHHHhh--------------hEEeecccCCcccc-HHHHhhcHHHHhhccc
Confidence 455556666666655433 35689999997633 4558888899999987
No 16
>KOG0898 consensus 40S ribosomal protein S15 [Translation, ribosomal structure and biogenesis]
Probab=20.48 E-value=88 Score=27.96 Aligned_cols=23 Identities=43% Similarity=0.723 Sum_probs=19.2
Q ss_pred hHHHHHHhHH--------HHHHHHhhhCCCc
Q 020327 276 MHTRMRRRVE--------SMIRTLDRAKPDA 298 (327)
Q Consensus 276 mHsRMR~Rv~--------~~lkvLnRAkpe~ 298 (327)
+++|+|+|++ ++||=|.+||-+.
T Consensus 44 ~~ar~rrR~~RGL~~k~~~liKklrkAkk~A 74 (152)
T KOG0898|consen 44 FPARQRRRLNRGLTRKPHSLIKKLRKAKKEA 74 (152)
T ss_pred HHHHHHHHHHcccccchHHHHHHHHHHHhhc
Confidence 3688888887 7999999999773
No 17
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=20.25 E-value=54 Score=32.98 Aligned_cols=16 Identities=44% Similarity=0.706 Sum_probs=14.4
Q ss_pred hhhHHHHHHhHHHHHH
Q 020327 274 GFMHTRMRRRVESMIR 289 (327)
Q Consensus 274 aYmHsRMR~Rv~~~lk 289 (327)
+|||-|||-=|++||-
T Consensus 345 G~mhnr~Rm~vAsFl~ 360 (429)
T TIGR02765 345 GFMSNRGRQNVASFLV 360 (429)
T ss_pred CCCCHHHHHHHHHHHH
Confidence 6999999999999874
Done!