RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780717|ref|YP_003065130.1| zinc uptake ABC transporter [Candidatus Liberibacter asiaticus str. psy62] (294 letters) >gnl|CDD|34180 COG4531, ZnuA, ABC-type Zn2+ transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]. Length = 318 Score = 242 bits (618), Expect = 1e-64 Identities = 111/313 (35%), Positives = 173/313 (55%), Gaps = 24/313 (7%) Query: 2 KNFLIILIFLFFILSSVARAGSLQVVVSIKPIHSIVSCIMQGIGTPALLVKGASSPHEYS 61 K L+ +F + S+ A A + VV SIKP+ I S I G+G P +L+ G +SPH+YS Sbjct: 6 KTLLLSALFALLLGSAPAAA-AAAVVTSIKPLGFIASAIADGVGEPEVLLPGGASPHDYS 64 Query: 62 LRISEAMMLENADIIFWLGAEMESFLVKPLHSLNKQSNVVTLSHSPDLHRILLRDNHSHF 121 LR S+ L++AD++ W+G ++E+FL KPL L + VVTL+ P + +L R+ H H Sbjct: 65 LRPSDVKRLQSADLVVWVGPDLEAFLDKPLSGL-PGAKVVTLADLPGVKPLLFREAHDHE 123 Query: 122 HDSEAD--------------------DLHLWLNPLNVQYIAHVIAMELIKKDPRNKIIYE 161 + + D+HLWL+P + +A IA +L + DP+N Y+ Sbjct: 124 EEHDHGHDHAGADHKGDHDHHHEGEYDMHLWLSPAIAKAVAAAIAKKLAELDPQNAAKYD 183 Query: 162 KNEEEFKNQLSQLDKELHSILQPVEKKKIIVFHEAYRYFASHYNLSIV-TFPMSHSVFMG 220 N ++F+ QL+ LDK++ L PV+ K VFH+AY YF + Y L + F +S V G Sbjct: 184 ANLKDFEAQLAALDKKVGEELAPVKGKPFFVFHDAYGYFENAYGLKPLGHFTVSPEVQPG 243 Query: 221 AASLRNIRSKIISDKISCLFYGPEFDSKIIRSITNDTGVMSAILDPEGMLIAEGPELYFQ 280 A L IR+++ K +C+F P+F K++ ++ T V S LDP G I G + YF Sbjct: 244 AKRLAEIRTQLKEQKATCVFAEPQFRPKVVETVAEGTSVRSGTLDPLGTNIKLGKDSYFN 303 Query: 281 LMRSMSNSIAKNC 293 + +++NS +C Sbjct: 304 FLSNLANSY-ASC 315 >gnl|CDD|29738 cd01019, ZnuA, Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a single helix and bind their specific ligands in the cleft between these domains. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).. Length = 286 Score = 223 bits (570), Expect = 4e-59 Identities = 99/281 (35%), Positives = 142/281 (50%), Gaps = 19/281 (6%) Query: 26 VVVSIKPIHSIVSCIMQGIGTPALLVKGASSPHEYSLRISEAMMLENADIIFWLGAEMES 85 V+ SIKP+ I + IM G+G +LV +SPH+Y LR S+A L+ AD++ W+G ++E+ Sbjct: 6 VLTSIKPLGFIAAAIMGGVGEVEVLVPPGASPHDYELRPSDARKLQEADLVVWIGPDLEA 65 Query: 86 FLVKPLHSLNKQSNVVTLSHSPDLHRILLRDNHSHFHDSEAD---------------DLH 130 FL K L K+ V+TL+ DL L D SH D H Sbjct: 66 FLDKVLQGR-KKGKVLTLAKLIDLK--TLEDGASHGDHEHDHEHAHGEHDGHEEGGLDPH 122 Query: 131 LWLNPLNVQYIAHVIAMELIKKDPRNKIIYEKNEEEFKNQLSQLDKELHSILQPVEKKKI 190 LWL+P N +A +A +L DP N Y N E F +L++LD + L PV+ K Sbjct: 123 LWLSPENAAEVAQAVAEKLSALDPDNAATYAANLEAFNARLAELDATIKERLAPVKTKPF 182 Query: 191 IVFHEAYRYFASHYNLSIV-TFPMSHSVFMGAASLRNIRSKIISDKISCLFYGPEFDSKI 249 VFH+AY YF Y L+ F + + GA L IR +I +C+F P+F KI Sbjct: 183 FVFHDAYGYFEKRYGLTQAGVFTIDPEIDPGAKRLAKIRKEIKEKGATCVFAEPQFHPKI 242 Query: 250 IRSITNDTGVMSAILDPEGMLIAEGPELYFQLMRSMSNSIA 290 ++ TG LDP G LI G Y +R++++S+A Sbjct: 243 AETLAEGTGAKVGELDPLGGLIELGKNSYVNFLRNLADSLA 283 >gnl|CDD|144773 pfam01297, SBP_bac_9, Periplasmic solute binding protein family. This family includes periplasmic solute binding proteins such as TroA that interacts with an ATP-binding cassette transport system in Treponema pallidum. Length = 272 Score = 216 bits (553), Expect = 5e-57 Identities = 86/272 (31%), Positives = 128/272 (47%), Gaps = 9/272 (3%) Query: 26 VVVSIKPIHSIVSCIMQGIGTPALLVKGASSPHEYSLRISEAMMLENADIIFWLGAEMES 85 VV SI P+ +V I LV + PH Y S+ L AD++ + GA +E Sbjct: 1 VVASIPPLADLVKAIGGDKVEVTSLVPPGADPHTYEPTPSDIKKLAKADLVVYNGAGLEP 60 Query: 86 FLVKPLHSLNKQSNVVTLSHSPDLHRIL---LRDNHSHFHDSEADDLHLWLNPLNVQYIA 142 +L K L SL + VV LS +L + D D H+WL+P N + +A Sbjct: 61 WLDKLLASLANKVKVVDLSEGIELLDAPGHEHDHDEHDHDDHGHGDPHIWLDPKNAKAMA 120 Query: 143 HVIAMELIKKDPRNKIIYEKNEEEFKNQLSQLDKELHSILQPVEKKKIIVFHEAYRYFAS 202 IA L + DP N YEKN F +L +LD E+ + L P+ K++I FH+A+ YFA Sbjct: 121 EAIADALSELDPENAATYEKNAAAFLKKLDELDAEIKAKLAPIPGKRVITFHDAFGYFAK 180 Query: 203 HYNLSIVTFPM-SHSVFMGAASLRNIRSKIISDKISCLFYGPEFDSKIIRSITNDTG--V 259 Y L + S A L + I + +F P+F K+ ++ +TG V Sbjct: 181 AYGLEQIAILGESPESEPSPADLAELIKLIKEHNVKVIFVEPQFSPKLAETLAEETGAKV 240 Query: 260 MSAILDPEGMLIAEGPELYFQLMRSMSNSIAK 291 + LDP G EG + Y +LMR +++A+ Sbjct: 241 VPLYLDPLGS---EGGDTYLELMRHNLDTLAE 269 >gnl|CDD|31146 COG0803, LraI, ABC-type metal ion transport system, periplasmic component/surface adhesin [Inorganic ion transport and metabolism]. Length = 303 Score = 149 bits (378), Expect = 7e-37 Identities = 71/295 (24%), Positives = 128/295 (43%), Gaps = 9/295 (3%) Query: 4 FLIILIFLFFILSSVARAGSLQVVVSIKPIHSIVSCIMQGIGTPALLVKGASSPHEYSLR 63 +++L +S + L+VV + PI +V I LV + PH Y Sbjct: 13 LILLLAGCGTSAASDGDSAKLKVVTTFPPIADVVKNIAGDKVDVVSLVPPGADPHSYEPT 72 Query: 64 ISEAMMLENADIIFWLGAEMESFLVKPLHSLNKQSNVVTLSHSPDLHRILLRDNHSHFHD 123 S+ L AD+I + G +E +L K L S +K+ +V ++ + + Sbjct: 73 PSDIAKLRKADLIVYNGLGLEPWLEKLLESADKKKVLVI-----EVSDGIELLPLPGEEE 127 Query: 124 SEADDLHLWLNPLNVQYIAHVIAMELIKKDPRNKIIYEKNEEEFKNQLSQLDKELHSILQ 183 +D H+WL+P N + A IA L++ DP NK YEKN E + +L++LD+E + L Sbjct: 128 EGVNDPHVWLDPKNAKIYAENIADALVELDPENKETYEKNAEAYLKKLNKLDEEAKAKLS 187 Query: 184 PV-EKKKIIVFHEAYRYFASHYNL-SIVTFPMSHSVFMGAASLRNIRSKIISDKISCLFY 241 + ++ ++ H A+ Y A Y L + +S L + I I +F Sbjct: 188 KIPAQRDVVTSHGAFGYLARDYGLKQVAIAGISPEAEPSPKDLAKLVDLIKKKNIKAIFV 247 Query: 242 GPEFDSKIIRSITNDTGV-MSAILDPEGMLIAEGPE-LYFQLMRSMSNSIAKNCS 294 SK ++ +TGV + +L + + + Y +M++ ++I + Sbjct: 248 ESNVSSKSAETLAKETGVKILGLLYLDSLGDKDSKGDTYISMMKANLDTIVEGLK 302 >gnl|CDD|29736 cd01017, AdcA, Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).. Length = 282 Score = 133 bits (337), Expect = 5e-32 Identities = 76/273 (27%), Positives = 122/273 (44%), Gaps = 12/273 (4%) Query: 21 AGSLQVVVSIKPIHSIVSCIMQGIGTPALLVKGASSPHEYSLRISEAMMLENADIIFWLG 80 +G L+VV + P++ I L++ + PH++ + + +AD+ + G Sbjct: 1 SGKLKVVTTFYPLYEFTKAIGGDKADVKLIIPAGTEPHDFEPSPKDIARIADADVFVYNG 60 Query: 81 AEMESFLVKPLHSL-NKQSNVVTLSHSPDLHRILLRDN---HSHFHDSEADDLHLWLNPL 136 ME++ K L SL NK+ VV S L + ++ HSH H D H+WL+P+ Sbjct: 61 LGMETWAEKVLKSLQNKKLKVVEASKGIKLLKAGGAEHDHDHSHSHHHGDYDPHVWLSPV 120 Query: 137 NVQYIAHVIAMELIKKDPRNKIIYEKNEEEFKNQLSQLDKELHSILQPVEKKKIIVFHEA 196 I LIK DP NK YEKN + +L LD+E + L + K + H A Sbjct: 121 LAIQQVENIKDALIKLDPDNKEYYEKNAAAYAKKLEALDQEYRAKLAKAKGKTFVTQHAA 180 Query: 197 YRYFASHYNL---SIVTFPMSHSVFMGAASLRNIRSKIISDKISCLFYGPEFDSKIIRSI 253 + Y A Y L +IV +S V L + + + +F+ SKI ++ Sbjct: 181 FGYLARRYGLKQIAIVG--VSPEVEPSPKQLAELVEFVKKSDVKYIFFEENASSKIAETL 238 Query: 254 TNDTGVMSAILDP-EGMLIAE--GPELYFQLMR 283 +TG +L+P E + E + YF LM+ Sbjct: 239 AKETGAKLLVLNPLETLTKEEIDDGKDYFSLMK 271 >gnl|CDD|29737 cd01018, ZntC, Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).. Length = 266 Score = 123 bits (309), Expect = 7e-29 Identities = 68/250 (27%), Positives = 110/250 (44%), Gaps = 9/250 (3%) Query: 23 SLQVVVSIKPIHSIVSCIMQGIGTPALLVKGASSPHEYSLRISEAMMLENADIIFWLGAE 82 V VSI+P V I +LV S+PH Y + + L AD+ F +G Sbjct: 2 KPTVAVSIEPQKYFVEKIAGDTVDVVVLVPPGSNPHTYEPKPQQMKKLSEADLYFRIGLG 61 Query: 83 MESFLVKPLHSLNKQSNVVTLSHSPDLHRILLRDNHSHFHDSEAD------DLHLWLNPL 136 E ++ S N + VV +S L I + D+H H H D H+WL+P Sbjct: 62 FEEVWLERFRSNNPKMQVVNMSKGITL--IPMADHHHHHHGEHEHHHHGNYDPHIWLSPA 119 Query: 137 NVQYIAHVIAMELIKKDPRNKIIYEKNEEEFKNQLSQLDKELHSILQPVEKKKIIVFHEA 196 N + +A I L + DP+N Y+ N + +L LD E+ +IL ++++ +V+H A Sbjct: 120 NAKIMAENIYEALAELDPQNATYYQANLDALLAELDALDSEIRTILSKLKQRAFMVYHPA 179 Query: 197 YRYFASHYNLSIVTFPMSHSVFMGAASLRNIRSKIISDKISCLFYGPEFDSKIIRSITND 256 + YFA Y L+ + A L+ + + +F P+F +K +I + Sbjct: 180 WGYFARDYGLTQIPIEEEG-KEPSPADLKRLIDLAKEKGVRVVFVQPQFSTKSAEAIARE 238 Query: 257 TGVMSAILDP 266 G +DP Sbjct: 239 IGAKVVTIDP 248 >gnl|CDD|29740 cd01137, PsaA, Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).. Length = 287 Score = 120 bits (302), Expect = 5e-28 Identities = 67/285 (23%), Positives = 122/285 (42%), Gaps = 19/285 (6%) Query: 16 SSVARAGSLQVVVSIKPIHSIVSCIMQGIGTPAL----LVKGASSPHEYSLRISEAMMLE 71 S A L+VV + SI++ I + I + +V + PHEY S+ L Sbjct: 10 SPATAASKLKVVATF----SILADIARNIAGDRVNVTSIVPPGADPHEYEPTPSDIKKLS 65 Query: 72 NADIIFWLGAEMESFLVKPLHSLNKQSNVVTLSHSPDLHRILLRDNHSHFHDSEADDLHL 131 AD+I + G +E +L + + + K VV +S D + H D H Sbjct: 66 KADLILYNGLNLEPWLERLVKNAGKDVPVVAVSEGIDPIPL------EEGHYKGKPDPHA 119 Query: 132 WLNPLNVQYIAHVIAMELIKKDPRNKIIYEKNEEEFKNQLSQLDKELHSILQ--PVEKKK 189 W++P N IA L + DP N Y+KN +K +L LD+ + P EK+K Sbjct: 120 WMSPKNAIIYVKNIAKALSEADPANAETYQKNAAAYKAKLKALDEWAKAKFATIPAEKRK 179 Query: 190 IIVFHEAYRYFASHYNL-SIVTFPMSHSVFMGAASLRNIRSKIISDKISCLFYGPEFDSK 248 ++ A+ YFA Y L +P++ + + ++ +K+ +F + + Sbjct: 180 LVTSEGAFSYFAKAYGLKEAYLWPINTEEEGTPKQVATLIEQVKKEKVPAVFVESTVNDR 239 Query: 249 IIRSITNDTGV-MSAILDPEGMLIAEGP-ELYFQLMRSMSNSIAK 291 +++ + +TG + L + + GP + Y +M ++I + Sbjct: 240 LMKQVAKETGAKIGGQLYTDSLSEKGGPADTYLDMMEHNLDTIVE 284 >gnl|CDD|29748 cd01145, TroA_c, Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.. Length = 203 Score = 80.5 bits (198), Expect = 5e-16 Identities = 47/193 (24%), Positives = 88/193 (45%), Gaps = 14/193 (7%) Query: 24 LQVVVSIKPIHSIVSCIMQGIGTPALLVKGASSPHEYSLRISEAMMLENADIIFWLGAEM 83 L VVV+ + +V + + L PH+Y L+ S+ + AD++ G E+ Sbjct: 3 LNVVVTFPDLKDLVREVAGDAVIVSALTPPGVDPHQYQLKPSDIAKMRKADLVVTSGHEL 62 Query: 84 ESFLVKPLHSLNKQSNV-------VTLSHSPDLHRILLRDNHSHFHDSEADDLHLWLNPL 136 E F K L L+ S V + S + + + D H + H+WL+P Sbjct: 63 EGFEPK-LAELSSNSKVQPGIKILIEDSDTVGMVDRAMGDYHGK------GNPHVWLDPN 115 Query: 137 NVQYIAHVIAMELIKKDPRNKIIYEKNEEEFKNQLSQLDKELHSILQPVEKKKIIVFHEA 196 N +A +A LI+ DP + Y++N F +L++L +E + ++ +++ +H + Sbjct: 116 NAPALAKALADALIELDPSEQEEYKENLRVFLAKLNKLLREWERQFEGLKGIQVVAYHPS 175 Query: 197 YRYFASHYNLSIV 209 Y+Y A + +V Sbjct: 176 YQYLADWLGIEVV 188 >gnl|CDD|29735 cd01016, TroA, Metal binding protein TroA. These proteins have been shown to function as initial receptors in ABC transport of Zn2+ and possibly Fe3+ in many eubacterial species. The TroA proteins belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).. Length = 276 Score = 77.2 bits (190), Expect = 4e-15 Identities = 55/258 (21%), Positives = 101/258 (39%), Gaps = 16/258 (6%) Query: 24 LQVVVSIKPIHSIVSCIMQGIGTPALLVKGASSPHEYSLRISEAMMLENADIIFWLGAEM 83 VV + I V I L+ PH Y + L+NAD++F+ G + Sbjct: 2 PNVVTTTGMIADAVENIGGDHVEVTGLMGPGVDPHLYKATAGDVEKLQNADVVFYNGLHL 61 Query: 84 ESFLVKPLHSLNKQSNVVTLSHSPDLHRILLRDNHSHFHDSEADDLHLWLNPLNVQYIAH 143 E + L L +V+ L + D +++L + + D H+W + +Y Sbjct: 62 EGKMSDVLSKLGSSKSVIALEDTLDRSQLILDEEEGTY------DPHIWFDVKLWKYAVK 115 Query: 144 VIAMELIKKDPRNKIIYEKNEEEFKNQLSQLDKELHSILQ--PVEKKKIIVFHEAYRYFA 201 +A L +K P +K ++ N E + +L LD + P +++ ++ H+A+ YF Sbjct: 116 AVAEVLSEKLPEHKDEFQANSEAYVEELDSLDAYAKKKIAEIPEQQRVLVTAHDAFGYFG 175 Query: 202 SHYNLSIVTFP-MSHSVFMGAASLRNIRSKIISDKISCLFYGPEFDSKIIRSITNDTGVM 260 Y + +S G + + I+ KI +F + K I ++ Sbjct: 176 RAYGFEVKGLQGISTDSEAGLRDINELVDLIVERKIKAIFVESSVNQKSIEALQ------ 229 Query: 261 SAILDPEGMLIAEGPELY 278 + G + G ELY Sbjct: 230 -DAVKARGHDVQIGGELY 246 >gnl|CDD|29739 cd01020, TroA_b, Metal binding protein TroA_b. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).. Length = 264 Score = 71.5 bits (175), Expect = 3e-13 Identities = 45/239 (18%), Positives = 88/239 (36%), Gaps = 20/239 (8%) Query: 22 GSLQVVVSIKPIHSIVSCIMQGIGTPALLVKGAS-SPHEYSLRISEAMMLENADIIFWLG 80 G + VV S S+ + ++ PH++ ++A + ADI+ + G Sbjct: 1 GKINVVASTNFWGSVAEAVGGDHVEVTSIITNPDVDPHDFEPTPTDAAKVSTADIVVYNG 60 Query: 81 AEMESFLVKPLHSLNKQSNVVTLSHSPDLHRILLRDNHSHFHDSEADDLHLWLNPLNVQY 140 + ++ K L I++ + D E D+ HLW +P + Sbjct: 61 GGYDPWMTKLLA--------------DTKDVIVIAADLDGHDDKEGDNPHLWYDPETMSK 106 Query: 141 IAHVIAMELIKKDPRNKIIYEKNEEEFKNQLSQLDKELHSILQPVEKKKIIVFHEAYRYF 200 +A+ +A L+K DP NK Y+ N ++F L L ++ + + + + Y Sbjct: 107 VANALADALVKADPDNKKYYQANAKKFVASLKPLAAKIAELSAKYKGAPVAATEPVFDYL 166 Query: 201 ASHYNLSIVTFPMSHSVFMG-----AASLRNIRSKIISDKISCLFYGPEFDSKIIRSIT 254 + T + A + ++ I + +I L P+ S +IT Sbjct: 167 LDALGMKERTPKGYTATTESETEPSPADIAAFQNAIKNRQIDALIVNPQQASSATTNIT 225 >gnl|CDD|38741 KOG3533, KOG3533, KOG3533, Inositol 1,4,5-trisphosphate receptor [Signal transduction mechanisms]. Length = 2706 Score = 31.1 bits (70), Expect = 0.37 Identities = 14/34 (41%), Positives = 22/34 (64%) Query: 170 QLSQLDKELHSILQPVEKKKIIVFHEAYRYFASH 203 QL++ +KEL L+P ++KK + EA Y+A H Sbjct: 2140 QLARHNKELQIWLKPSDEKKDDLTREALNYYAEH 2173 >gnl|CDD|164574 CHL00198, accA, acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional. Length = 322 Score = 30.9 bits (70), Expect = 0.40 Identities = 12/42 (28%), Positives = 21/42 (50%) Query: 146 AMELIKKDPRNKIIYEKNEEEFKNQLSQLDKELHSILQPVEK 187 EL K P+N + + F+ +L L KE+ L P+++ Sbjct: 22 VEELSKLAPKNDKVINNKLKSFQRKLRILKKEIFYSLTPLQR 63 >gnl|CDD|73072 cd02666, Peptidase_C19J, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.. Length = 343 Score = 30.0 bits (67), Expect = 0.79 Identities = 23/121 (19%), Positives = 40/121 (33%), Gaps = 2/121 (1%) Query: 83 MESFLVKPLHSLNKQSNVVTLSHSPDLHRILLR--DNHSHFHDSEADDLHLWLNPLNVQY 140 E FL + K +V L DL+ L R D S + + L + Sbjct: 165 TERFLSLLVDVGKKGREIVVLLEPKDLYDALDRYFDYDSLTKLPQRSQVQAQLAQPLQRE 224 Query: 141 IAHVIAMELIKKDPRNKIIYEKNEEEFKNQLSQLDKELHSILQPVEKKKIIVFHEAYRYF 200 + + EL + + + + + Q EL + +EK+ + YR Sbjct: 225 LISMDRYELPSSIDDIDELIREAIQSESSLVRQAQNELAELKHEIEKQFDDLKSYGYRLH 284 Query: 201 A 201 A Sbjct: 285 A 285 >gnl|CDD|146070 pfam03251, Tymo_45kd_70kd, Tymovirus 45/70Kd protein. Tymoviruses are single stranded RNA viruses. This family includes a protein of unknown function that has been named based on its molecular weight. Tymoviruses such as the ononis yellow mosaic tymovirus encode only three proteins. Of these two are overlapping this protein overlaps a larger ORF that is thought to be the polymerase. Length = 458 Score = 28.5 bits (64), Expect = 1.9 Identities = 13/38 (34%), Positives = 15/38 (39%), Gaps = 3/38 (7%) Query: 90 PLHSLNKQSNVVTLSHSPD---LHRILLRDNHSHFHDS 124 P+H L K S V LHR L H H+S Sbjct: 158 PVHELPKPSTPVLQPRRSPRKQLHRPLSLPRSLHLHNS 195 >gnl|CDD|39667 KOG4466, KOG4466, KOG4466, Component of histone deacetylase complex (breast carcinoma metastasis suppressor 1 protein in human) [Cell cycle control, cell division, chromosome partitioning, Transcription]. Length = 291 Score = 28.4 bits (63), Expect = 2.4 Identities = 11/38 (28%), Positives = 19/38 (50%) Query: 146 AMELIKKDPRNKIIYEKNEEEFKNQLSQLDKELHSILQ 183 A E + K E E+ +K++L+QL +L + Q Sbjct: 19 ANEESEMSNLEKQFSELKEQMYKDKLAQLQAQLEELGQ 56 >gnl|CDD|35801 KOG0581, KOG0581, KOG0581, Mitogen-activated protein kinase kinase (MAP2K) [Signal transduction mechanisms]. Length = 364 Score = 27.6 bits (61), Expect = 4.0 Identities = 16/74 (21%), Positives = 33/74 (44%), Gaps = 12/74 (16%) Query: 157 KIIYEKNEEEFKNQLSQLDKELHSILQPVEKKKIIVFHEAYRYFASHYNLSIVTFPMSHS 216 K+I + + Q+ + EL IL+ + I+ F+ A ++++ +SI Sbjct: 110 KVILLNIDPALQKQILR---EL-EILRSCQSPYIVGFYGA--FYSNGEEISICM------ 157 Query: 217 VFMGAASLRNIRSK 230 +M SL +I + Sbjct: 158 EYMDGGSLDDILKR 171 >gnl|CDD|31181 COG0839, NuoJ, NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]. Length = 166 Score = 27.5 bits (61), Expect = 4.9 Identities = 11/44 (25%), Positives = 24/44 (54%) Query: 6 IILIFLFFILSSVARAGSLQVVVSIKPIHSIVSCIMQGIGTPAL 49 +I F++ + +A A +L VV++ P++S + + + AL Sbjct: 2 MIETLAFYLFAVLAIAFALGVVLAKNPVYSALYLALTLLSIAAL 45 >gnl|CDD|146639 pfam04108, APG17, Autophagy protein Apg17. Apg17 is required for activating Apg1 protein kinases. Length = 410 Score = 27.3 bits (61), Expect = 5.4 Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 5/42 (11%) Query: 147 MELIKKDPRN--KIIYEKNEEEFKNQLSQLDK---ELHSILQ 183 + L+ K R+ I E + F + +QLD L S L Sbjct: 53 LRLLYKIVRSTALIRTEWGQSVFVDLQNQLDAADARLESTLD 94 >gnl|CDD|36238 KOG1020, KOG1020, KOG1020, Sister chromatid cohesion protein SCC2/Nipped-B [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning, Replication, recombination and repair]. Length = 1692 Score = 26.9 bits (59), Expect = 6.4 Identities = 27/146 (18%), Positives = 47/146 (32%), Gaps = 11/146 (7%) Query: 155 RNKIIYEKNEEEFKNQLSQLDKELHSILQPVEKKKIIVFHEA---YRYFASHYNLS-IVT 210 E E K LS++ + S P + +A Y A + S Sbjct: 756 LAYEKVITVENELKYILSKIKDKEKSGRGPKLNSRFADDDDAKLIVFYLAHARSFSQSFD 815 Query: 211 FPMSHSVFMGAASLRNIRSK------IISDKISCLFYGPEFDSKII-RSITNDTGVMSAI 263 + + + + +R+K +I + + P+ + R + V A Sbjct: 816 PYLKLILSVLGENAIALRTKALKCLSMIVEADPSVLSRPDVQEAVHGRLNDSSASVREAA 875 Query: 264 LDPEGMLIAEGPELYFQLMRSMSNSI 289 LD G + PEL FQ + I Sbjct: 876 LDLVGRFVLSIPELIFQYYDQIIERI 901 >gnl|CDD|30582 COG0233, Frr, Ribosome recycling factor [Translation, ribosomal structure and biogenesis]. Length = 187 Score = 26.7 bits (59), Expect = 7.3 Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 4/47 (8%) Query: 146 AMELIKKDPRNKIIYE----KNEEEFKNQLSQLDKELHSILQPVEKK 188 A + IKK ++K I E K EEE + + K++ +L+ EK+ Sbjct: 137 ANDKIKKLEKDKEISEDEVKKAEEEIQKLTDEYIKKIDELLKDKEKE 183 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.322 0.136 0.392 Gapped Lambda K H 0.267 0.0717 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,535,589 Number of extensions: 189334 Number of successful extensions: 724 Number of sequences better than 10.0: 1 Number of HSP's gapped: 701 Number of HSP's successfully gapped: 29 Length of query: 294 Length of database: 6,263,737 Length adjustment: 93 Effective length of query: 201 Effective length of database: 4,254,100 Effective search space: 855074100 Effective search space used: 855074100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 57 (25.8 bits)