RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780591|ref|YP_003065004.1| aminomethyltransferase protein (glycine cleavage) [Candidatus Liberibacter asiaticus str. psy62] (273 letters) >gnl|CDD|30703 COG0354, COG0354, Predicted aminomethyltransferase related to GcvT [General function prediction only]. Length = 305 Score = 173 bits (439), Expect = 5e-44 Identities = 76/287 (26%), Positives = 123/287 (42%), Gaps = 20/287 (6%) Query: 1 MSSVYLSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKI 60 ++ V LS+++ I+V G A FLQ +T DV L + +A+LTPQG++L F + + Sbjct: 14 LTLVLLSDRALIRVSGADAEKFLQGQLTNDVSALAEGQSTLAALLTPQGRVLFDFRLYRR 73 Query: 61 EEDTFILEIDRSKRDSLIDKLLFYKLRSNVIIEIQPI--------NGVVLSWNQEHTFSN 112 D L+ D+S ++L+ +L Y LRS V I + Sbjct: 74 G-DGLYLDTDKSVLEALLKRLKKYALRSKVTIAPSDLVLIGVAGEEAAEALAVDFPALPK 132 Query: 113 SSFIDERFSIADVLLHR-------TWGHNEKIASDIKTYHELRINHGIVDPNTDFLPSTI 165 RF + + + + D + LRI GI D Sbjct: 133 QWRAAGRFLLDLPVPRLLQLVPKLALPQALEASLDQ--WLALRIRAGIPGI-DDATSEDF 189 Query: 166 FPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIRKRPMIITGTDDLPPSGSPILTDDI 225 P + +D L GIS KGCY+GQE V+R ++R ++R +++ LP +G IL Sbjct: 190 IPQEVNLDALGGISFKKGCYVGQETVARAKYRGTNKRRLVLLALDASLPEAGEEILAGGE 249 Query: 226 EIGTLGVVVGKKALAIARIDKVDHAIKKGMALTVHGVRVKASFPHWY 272 E+G G V+ L + ++ + G+A+ V G + P W Sbjct: 250 EVGL-GTVLSAVGLGPVALIRLKVVLDNGLAIDVGGRIANLALPPWV 295 >gnl|CDD|38140 KOG2929, KOG2929, KOG2929, Transcription factor, component of CCR4 transcriptional complex [Transcription]. Length = 348 Score = 134 bits (338), Expect = 3e-32 Identities = 80/307 (26%), Positives = 132/307 (42%), Gaps = 44/307 (14%) Query: 6 LSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARG---------SAILTPQGKIL---- 52 L ++S I+V G + FLQ ++T DV T + +G +A L QG++L Sbjct: 35 LESRSLIRVRGPDTVKFLQGLLTNDV-TRHFPGIQGAPITRNGLYAAFLNTQGRLLYDTI 93 Query: 53 LYFLISKIEEDTFILEIDRSKRDSLIDKLLFYKLRSNVIIEIQPINGVVLSWNQEHTFSN 112 LY + E +LE D S + L Y+LR V E++ I+ + +W E N Sbjct: 94 LYPTPVPVSEPELLLECDGSVVGDFLKHLQKYRLRRKV--EVEKIDHELKTWKVEVLPKN 151 Query: 113 S--SFIDERFSIADVLLHR-----------------TWGHNEKIASDIKTYHELRINHGI 153 S + + E +VL +R + D Y LR G+ Sbjct: 152 SIDANVFEENV-LNVLYNRDPRFSGMGWRLLPQDFAVPTSEQVSEGDESDYRLLRYQQGV 210 Query: 154 VDPNTDFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIRKR--PMIITGTD 211 + + + +P T+ P ++ D LNGIS KGCY+GQE+ +R H +IRKR P + + Sbjct: 211 AEGSQELIPGTLLPLESNFDFLNGISFDKGCYVGQELTARTHHTGVIRKRLFPFRLDLAE 270 Query: 212 DLP-PSGSPILTDDIEIGT---LGVVVGKKALAIARIDKVDHAIKKGMALTVHGVR--VK 265 + P G ++E +G V+ + L + +++ + LT G +K Sbjct: 271 NEPLLVGFTNAPPEVEKKKGRKVGRVISGEGLRGLGLLRLEKFKAQFYKLTTKGENIKIK 330 Query: 266 ASFPHWY 272 P W+ Sbjct: 331 PQKPEWW 337 >gnl|CDD|144970 pfam01571, GCV_T, Aminomethyltransferase folate-binding domain. This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. Length = 212 Score = 58.4 bits (142), Expect = 2e-09 Identities = 24/88 (27%), Positives = 44/88 (50%) Query: 6 LSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTF 65 +S+ I+V G A FLQ ++T DV L A + +L +G I+ + ++ ED F Sbjct: 4 VSHMGKIEVSGPDAAAFLQRLLTNDVSKLKPGQATYTLLLNEKGGIIDDLTVYRLGEDEF 63 Query: 66 ILEIDRSKRDSLIDKLLFYKLRSNVIIE 93 +L ++ + + + L Y + S V + Sbjct: 64 LLVVNAANAEKDLAWLRKYAVFSKVTVA 91 >gnl|CDD|30753 COG0404, GcvT, Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]. Length = 379 Score = 51.4 bits (123), Expect = 3e-07 Identities = 67/317 (21%), Positives = 120/317 (37%), Gaps = 63/317 (19%) Query: 6 LSNQSFIKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTF 65 +S+ ++V G A FLQ ++T DV L AR + +L G I+ ++ ++ ED F Sbjct: 53 VSHMGKVEVSGPDAAAFLQRLLTNDVSKLKPGRARYTLMLNEDGGIIDDLIVYRLGEDRF 112 Query: 66 ILEIDRSKRDSLIDKLLFYKLRSNVIIEIQP---------ING---------VVLSW-NQ 106 L + + + + L ++ ++ + + + G +V + Sbjct: 113 FLVTNAATAEKDLAWLERHQAGPDLDVTLTSVTEDLAVLALQGPKAREVLAKLVDGDLVE 172 Query: 107 EHTFSNSSFIDERFSIADVLLHRT----------WGHNEKIAS------------DIKTY 144 F + V + RT + E A+ +K Sbjct: 173 ALPFFAFKEVTI-GGGVPVRISRTGYTGELGFEIYVPAEDAAAVWDALLEAGEKFGVKPC 231 Query: 145 -----HELRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNI 199 LR+ G+ D TI P +A + + L K +IG+ + R + + + Sbjct: 232 GLGARDTLRLEAGLRLYGQDLDE-TITPLEAGLGWA--VKLDKDDFIGKAALLREKAKGV 288 Query: 200 IRKR-PMIITGTDDLPPSGSPILTDDIEI-------GTLGVVVGKKALAIARIDKVDHAI 251 RK + + + G P+L D E+ GT +G K++A+A +D D+A Sbjct: 289 RRKLVGLKLDDKGPVLRGGEPVLDADGEVEVGEVTSGTFSPTLG-KSIALAYVDS-DYA- 345 Query: 252 KKGMALTVH--GVRVKA 266 K G L V G RV A Sbjct: 346 KPGTELEVEIRGKRVPA 362 >gnl|CDD|37981 KOG2770, KOG2770, KOG2770, Aminomethyl transferase [Amino acid transport and metabolism]. Length = 401 Score = 39.2 bits (91), Expect = 0.001 Identities = 54/305 (17%), Positives = 99/305 (32%), Gaps = 54/305 (17%) Query: 12 IKVCGKSAIPFLQAIITADVLTLPYKIARGSAILTPQGKILLYFLISKIEEDTFILEID- 70 +V GK + FL+++ TAD LP S G I+ +I+K++E+ + + Sbjct: 80 SRVSGKDRVAFLESLTTADFEGLPEGSGTLSVFTNETGGIIDDLIITKVDENELYIVSNA 139 Query: 71 --RSKRDSLIDKLLFYKLRSNVIIEIQPINGVVLSWNQEHT------------------F 110 + K ++L+ F + + ++G L Q Sbjct: 140 GCQEKDEALLKDHFFAWKSKGKDVSWETLDGRSLLALQGPEAAKVLQKLLSKLGDLSKLP 199 Query: 111 SNSSFIDERFSIADVLLHRTW-------------GHNEKIASDI-----------KTYHE 146 S + + + R +A + Sbjct: 200 FGQSQVYDFKGGPGCRVTRGGYTGEDGFEISVPPEGAVDLAETLLANPVVKPAGLGARDS 259 Query: 147 LRINHGIVDPNTDFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSR-IQHRNIIRKRPM 205 LR+ G+ +D T L ++ + G EV+ + ++ I R+R Sbjct: 260 LRLEAGLCLYGSDIDEETTPVEAGLSWVIGKRRRGTYDFPGAEVILKQLKDGGISRRRVG 319 Query: 206 IITGTDDLPPSGSPILTDD-IEIGTL----GVVVGKKALAIARIDKVDHAIKKGMALTVH 260 + SGS I DD ++G + K +A+ + K H K G + V Sbjct: 320 LNLSAKPPARSGSAIFVDDGTKVGQVTSGCPSPTLGKNIAMGYVKKGYH--KIGTKVLV- 376 Query: 261 GVRVK 265 VR K Sbjct: 377 KVRNK 381 >gnl|CDD|143599 cd07575, Xc-1258_like, Xanthomonas campestris XC1258 and related proteins, members of the nitrilase superfamily (putative class 13 nitrilases). Uncharacterized subgroup belonging to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup either represents a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. XC1258 is a homotetramer. Length = 252 Score = 28.7 bits (65), Expect = 1.9 Identities = 10/45 (22%), Positives = 19/45 (42%), Gaps = 3/45 (6%) Query: 41 GSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDKLLFYK 85 SA++ P G+ L ++ +E +D+ +K F K Sbjct: 205 DSAVIDPLGEPLAE---AEEDEGVLTATLDKEALQEFREKFPFLK 246 >gnl|CDD|33284 COG3481, COG3481, Predicted HD-superfamily hydrolase [General function prediction only]. Length = 287 Score = 27.6 bits (61), Expect = 4.1 Identities = 20/62 (32%), Positives = 30/62 (48%), Gaps = 7/62 (11%) Query: 192 SRIQHRNIIRKRPMIITGTDDLPPSGSPILTDDIEIGTLGVVVGKKALAIARIDKVDHAI 251 R QH IIR R + TD P + +P+ D++E G + + I RI V H + Sbjct: 66 GRKQH-KIIRIRLI----TDSDPVTKAPLSMDEMEEEITGYIFSIENAVIQRI--VRHDL 118 Query: 252 KK 253 +K Sbjct: 119 EK 120 >gnl|CDD|145541 pfam02455, Hex_IIIa, Hexon-associated protein (IIIa). The major capsid protein of the adenovirus strain is also known as a hexon. This is a family of hexon-associated proteins (protein IIIa). Length = 491 Score = 27.4 bits (61), Expect = 4.3 Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 8/46 (17%) Query: 42 SAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDKLL-FYKL 86 S++LTP ++LL + + +TF RDS + LL Y+ Sbjct: 154 SSLLTPNTRLLLLLVAPFTDSNTF-------SRDSYLGHLLTLYRE 192 >gnl|CDD|37224 KOG2013, KOG2013, KOG2013, SMT3/SUMO-activating complex, catalytic component UBA2 [Posttranslational modification, protein turnover, chaperones]. Length = 603 Score = 26.9 bits (59), Expect = 6.0 Identities = 24/135 (17%), Positives = 48/135 (35%), Gaps = 22/135 (16%) Query: 95 QPINGVVLSWNQEHTFS---NSSFIDERFSIADVLLHRTWGHNEKIAS---DIKTYHELR 148 +PI+ +V W + + F+ D+ + E+ A + + E R Sbjct: 176 EPIHCIV--WAKHYLFNQLFGEDDDDQYGRHDNADPDNCEDMTEEEAEAFRETEDLKERR 233 Query: 149 INHGIVDPNTDFLPSTIFPHDALMDLLNGISLTKGCYIGQEVVSRIQHRNIIRKRPMIIT 208 + +D N DF P IF + D+ E + ++ R RP+ ++ Sbjct: 234 ESIVEIDKNLDFGPFKIFNKLFIYDI--------------EYLLGMEALWKPRSRPVPLS 279 Query: 209 GTDDLPPSGSPILTD 223 + + S I + Sbjct: 280 IAEVISTSLETINSI 294 >gnl|CDD|144519 pfam00949, Peptidase_S7, Peptidase S7, Flavivirus NS3 serine protease. The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (pfam01002) as a cofactor. Length = 150 Score = 26.9 bits (60), Expect = 6.5 Identities = 18/77 (23%), Positives = 28/77 (36%), Gaps = 18/77 (23%) Query: 185 YIGQEVVSRIQHRNIIRKRP--MIITG------TDDLPP--SGSPILTDDIEI-----GT 229 + G+EV Q+ ++ +P G D P SGSPI + +I Sbjct: 77 WHGEEVQ---QYVENVQTKPGVFKTDGYGLGLIDLDFPGGSSGSPIFNQNGQIVGLYGNG 133 Query: 230 LGVVVGKKALAIARIDK 246 L G IA+ + Sbjct: 134 LVTGNGTYVSGIAQGLR 150 >gnl|CDD|36110 KOG0892, KOG0892, KOG0892, Protein kinase ATM/Tel1, involved in telomere length regulation and DNA repair [Signal transduction mechanisms, Chromatin structure and dynamics, Replication, recombination and repair, Cell cycle control, cell division, chromosome partitioning]. Length = 2806 Score = 26.5 bits (58), Expect = 8.2 Identities = 21/126 (16%), Positives = 41/126 (32%), Gaps = 8/126 (6%) Query: 34 LPYKIARGSAILTPQGKILLYFLISKIEEDTFILEIDRSKRDSLIDKLLFYKLRSNV--- 90 L IAR ++ K+L F +++ I ++ + +K S Sbjct: 2041 LLQNIARAFPVIMLSIKLLCKFSLAQENLKHDIDKLSEAILWQRDEKNEAIISLSESLAK 2100 Query: 91 ----IIEIQPINGVVLSWNQEHTFSNSSFIDERFSI-ADVLLHRTWGHNEKIASDIKTYH 145 I V+ W E NS+ I E++ A L + K +++ Sbjct: 2101 NNSLKEFPSDIYAVLGKWLAETKSENSALISEKYLEKAVSLAEHYDNESCKALIYCQSFA 2160 Query: 146 ELRINH 151 + + Sbjct: 2161 QFCLAK 2166 >gnl|CDD|33244 COG3439, COG3439, Uncharacterized conserved protein [Function unknown]. Length = 137 Score = 26.4 bits (58), Expect = 8.6 Identities = 13/51 (25%), Positives = 23/51 (45%), Gaps = 7/51 (13%) Query: 186 IGQEVVSRIQHRNIIRKR------PMIITGTDDLPPSGSPILTDDIEIGTL 230 G +V + I H ++ P I + P +G+P+L+ + E G L Sbjct: 35 NGFKVFTEIDHAEALKNAGVLDIPPYTILVFCN-PKAGTPLLSKNPEFGLL 84 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 0.323 0.140 0.410 Gapped Lambda K H 0.267 0.0748 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,376,283 Number of extensions: 183526 Number of successful extensions: 385 Number of sequences better than 10.0: 1 Number of HSP's gapped: 381 Number of HSP's successfully gapped: 15 Length of query: 273 Length of database: 6,263,737 Length adjustment: 92 Effective length of query: 181 Effective length of database: 4,275,709 Effective search space: 773903329 Effective search space used: 773903329 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 (25.7 bits)