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)