RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254781215|ref|YP_003065628.1| putative phage terminase,
large subunit [Candidatus Liberibacter asiaticus str. psy62]
         (511 letters)



>gnl|CDD|146059 pfam03237, Terminase_6, Terminase-like family.  This family
           represents a group of terminase proteins.
          Length = 380

 Score = 60.9 bits (148), Expect = 8e-10
 Identities = 66/373 (17%), Positives = 95/373 (25%), Gaps = 65/373 (17%)

Query: 82  ISAGRGIGKTTLNAWLVLWLMSTRPGISVICLANSETQLKTTLWAEVSKWL-SLLPNKHW 140
           I   R  GKT   A   L         + I L+ S+ Q +      + +    LL     
Sbjct: 2   ILGSRQSGKTFAFAREALRHALGNGPKNQIILSASKAQARLEFKKGIIEIAGDLLEITFE 61

Query: 141 FEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHH-NTYGMAIINDE 199
            +  +  + P       L+                   E   T  G+   +       DE
Sbjct: 62  EKNGNPIILPNGA---KLYF---------------LGLESETTAQGYRGASIAGIYF-DE 102

Query: 200 ASGTPDVINLGILGFLTERNANRFWIMT----SNPRRLSGKFYEIFNKPLDDWKRFQIDT 255
           A+  P          L  R             S P       Y+ +   LDD  +     
Sbjct: 103 ATWLPKFQES----ELVRRLRATKGKWRKTFFSTPPSPGHWVYDFWTGWLDDKGKRTFIP 158

Query: 256 RTVEG-------IDPSFHEGIIARYGLDSDVTRVEVCGQFPQQDIDSFIPLNIIEEALNR 308
             VE        + P + E + A Y  +       + G++      S       E     
Sbjct: 159 ADVEVTIEDARALGPEYKEELRALYSDE--EFARLLMGEW---VDTSGSIFKRFELERCD 213

Query: 309 EPCPDPYA--PLIMGCDIAE-EGGDNT---VVVLRRGPVIEHL--FDWSKTDLRTTNNKI 360
                P     +I G D A   GGD     V+    G     L                I
Sbjct: 214 VDEERPPEHREVIGGVDPAASRGGDYAALVVIAEVDGDKFYVLAREHERGLSPAEQAAII 273

Query: 361 SGLVEKYRPDAIIIDANNTGARTCDYLEM-LGYHVYRVLGQKRAVDLEFCRNRRTELHVK 419
             L E+Y    I ID    G      L   L    + V                     K
Sbjct: 274 KKLAERYNVIYIYIDDTGGGESVAQLLRRELPGAAFTVRP---------------APKGK 318

Query: 420 MADWLEFASLINH 432
            A  L+ + LI  
Sbjct: 319 NARVLKVSDLIES 331


>gnl|CDD|35312 KOG0089, KOG0089, KOG0089, Methylenetetrahydrofolate
           dehydrogenase/methylenetetrahydrofolate cyclohydrolase
           [Coenzyme transport and metabolism].
          Length = 309

 Score = 32.3 bits (73), Expect = 0.31
 Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 8/62 (12%)

Query: 262 DPSFHEGIIARYGLDSDVTRVEVCGQF-PQQDIDSFIPLNIIEEALNREPCPDPYAPLIM 320
           DPS H GI+ +  +   +    +     P++D+D F PLNI           D   PL +
Sbjct: 94  DPSVH-GILVQLPVPQHIQEQYILNAVSPEKDVDGFHPLNI------GRLALDGREPLFL 146

Query: 321 GC 322
            C
Sbjct: 147 PC 148


>gnl|CDD|99779 cd06182, CYPOR_like, NADPH cytochrome p450 reductase (CYPOR) serves
           as an electron donor in several oxygenase systems and is
           a component of nitric oxide synthases and methionine
           synthase reductases. CYPOR transfers two electrons from
           NADPH to the heme of cytochrome p450 via FAD and FMN.
           CYPOR has a C-terminal ferredoxin reducatase (FNR)- like
           FAD and NAD binding module, an FMN-binding domain, and
           an additional conecting domain (inserted within the FAD
           binding region) that orients the FNR and FMN binding
           domains. Ferredoxin-NADP+ (oxido)reductase is an
           FAD-containing enzyme that catalyzes the reversible
           electron transfer between NADP(H) and electron carrier
           proteins such as ferredoxin and flavodoxin. Isoforms of
           these flavoproteins (i.e. having a non-covalently bound
           FAD as a prosthetic group) are present in chloroplasts,
           mitochondria, and bacteria and participate in a wide
           variety of redox metabolic pathways. The C-terminal
           domain contains most of the NADP(H) binding residues and
           the N-terminal domain interacts non-covalently with the
           isoalloxazine rings of the flavin molecule which lies
           largely in a large gap betweed the two domains.
           Ferredoxin-NADP+ reductase first accepts one electron
           from reduced ferredoxin to form a flavin semiquinone
           intermediate. The enzyme then accepts a second electron
           to form FADH2, which then transfers two electrons and a
           proton to NADP+ to form NADPH..
          Length = 267

 Score = 30.8 bits (70), Expect = 1.0
 Identities = 19/93 (20%), Positives = 32/93 (34%), Gaps = 17/93 (18%)

Query: 230 PRRLSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPS--FHEGIIARYGLDSDVTRVEVCGQ 287
           P  L  ++Y I + P  D     +  R V    P+    +G+ + +          + G 
Sbjct: 43  PNPLQPRYYSIASSPDVDPGEVHLCVRVVSYEAPAGRIRKGVCSNF----------LAGL 92

Query: 288 FPQQDIDSFIPLNIIEEALNREPCPDPYAPLIM 320
                +  FI       A +     DP  P+IM
Sbjct: 93  QLGAKVTVFIR-----PAPSFRLPKDPTTPIIM 120


>gnl|CDD|39672 KOG4471, KOG4471, KOG4471, Phosphatidylinositol 3-phosphate
           3-phosphatase myotubularin MTM1 [Lipid transport and
           metabolism, Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 717

 Score = 30.4 bits (68), Expect = 1.2
 Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 9/48 (18%)

Query: 127 EVSKWLSLLPNKHWFEMQSLSLHPAPWYSD---------VLHCSLGID 165
           + S WLS L + HW E  S  L  A   +D         ++HCS G D
Sbjct: 339 DESNWLSALESTHWLEHISSLLAGAVRIADKVESESRSVLVHCSDGWD 386


>gnl|CDD|29127 cd02052, PEDF, Pigment epithelium-derived factor (PEDF)_like. PEDF
           is non-inhibitory member of the Serpin superfamily. It
           exhibits neurotrophic, neuroprotective and
           antiangiogenic properties and is widely expressed in the
           developing and adult nervous systems. This subgroup
           corresponds to clade F1 of the serpin superfamily..
          Length = 374

 Score = 30.0 bits (67), Expect = 1.7
 Identities = 24/88 (27%), Positives = 34/88 (38%), Gaps = 15/88 (17%)

Query: 233 LSGKFYEIFNKPLDDWKRFQIDTRTVEGIDPSFHEGIIARYGLDSDVTRVEVC--GQFPQ 290
             G++   F+K       F +D +    +          RYGLDSD+     C   Q P 
Sbjct: 173 FKGQWITKFDKRNTVLTDFHLDEQRTVVVPMMSDPNAPVRYGLDSDLN----CKIAQLPL 228

Query: 291 QDIDS---FIP------LNIIEEALNRE 309
               S   F+P      L +IEE+L  E
Sbjct: 229 TGGVSIMFFLPDKVTQNLTLIEESLTSE 256


>gnl|CDD|163676 cd07938, DRE_TIM_HMGL, 3-hydroxy-3-methylglutaryl-CoA lyase,
           catalytic TIM barrel domain.
           3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes
           the cleavage of HMG-CoA to acetyl-CoA and acetoacetate,
           one of the terminal steps in ketone body generation and
           leucine degradation, and is a key enzyme in the pathway
           that supplies metabolic fuel to extrahepatic tissues.
           Mutations in HMGL cause a human autosomal recessive
           disorder called primary metabolic aciduria that affects
           ketogenesis and leucine catabolism and can be fatal due
           to an inability to tolerate hypoglycemia.  HMGL has a
           TIM barrel domain with a catalytic center containing a
           divalent cation-binding site formed by a cluster of
           invariant residues that cap the core of the barrel.  The
           cleavage of HMG-CoA requires the presence of a divalent
           cation like Mg2+ or Mn2+, and the reaction is thought to
           involve general acid/base catalysis.  This family
           belongs to the DRE-TIM metallolyase superfamily.
           DRE-TIM metallolyases include 2-isopropylmalate synthase
           (IPMS), alpha-isopropylmalate synthase (LeuA),
           3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate
           synthase, citramalate synthase, 4-hydroxy-2-oxovalerate
           aldolase, re-citrate synthase, transcarboxylase 5S,
           pyruvate carboxylase, AksA, and FrbC.  These members all
           share a conserved  triose-phosphate isomerase (TIM)
           barrel domain consisting of a core beta(8)-alpha(8)
           motif with the eight parallel beta strands forming an
           enclosed barrel surrounded by eight alpha helices.  The
           domain has a catalytic center containing a divalent
           cation-binding site formed by a cluster of invariant
           residues that cap the core of the barrel.  In addition,
           the catalytic site includes three invariant residues -
           an aspartate (D), an arginine (R), and a glutamate (E) -
           which is the basis for the domain name "DRE-TIM".
          Length = 274

 Score = 29.7 bits (68), Expect = 2.2
 Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 2/28 (7%)

Query: 172 MCRTYSEERPDT-FVGH-HNTYGMAIIN 197
           +     E  PD     H H+T G A+ N
Sbjct: 183 LLEAVLERFPDEKLALHFHDTRGQALAN 210


>gnl|CDD|133424 cd01339, LDH-like_MDH, L-lactate dehydrogenase-like malate
           dehydrogenase proteins.  Members of this subfamily have
           an LDH-like structure and an MDH enzymatic activity.
           Some members, like MJ0490 from Methanococcus jannaschii,
           exhibit both MDH and LDH activities. Tetrameric MDHs,
           including those from phototrophic bacteria, are more
           similar to LDHs than to other MDHs. LDH catalyzes the
           last step of glycolysis in which pyruvate is converted
           to L-lactate. MDH is one of the key enzymes in the
           citric acid cycle, facilitating both the conversion of
           malate to oxaloacetate and replenishing levels of
           oxalacetate by reductive carboxylation of pyruvate. The
           LDH-like MDHs are part of the NAD(P)-binding Rossmann
           fold superfamily, which includes a wide variety of
           protein families including the NAD(P)-binding domains of
           alcohol dehydrogenases, tyrosine-dependent
           oxidoreductases, glyceraldehyde-3-phosphate
           dehydrogenases, formate/glycerate dehydrogenases,
           siroheme synthases, 6-phosphogluconate dehydrogenases,
           aminoacid dehydrogenases, repressor rex, and NAD-binding
           potassium channel domains, among others.
          Length = 300

 Score = 29.4 bits (67), Expect = 2.6
 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 4/31 (12%)

Query: 348 WSKTDLRTTNNKI----SGLVEKYRPDAIII 374
            S+ DL  TN KI    +  ++KY P+AI+I
Sbjct: 82  MSRDDLLGTNAKIVKEVAENIKKYAPNAIVI 112


>gnl|CDD|37048 KOG1837, KOG1837, KOG1837, Uncharacterized conserved protein
            [Function unknown].
          Length = 1621

 Score = 29.2 bits (65), Expect = 2.7
 Identities = 13/59 (22%), Positives = 20/59 (33%), Gaps = 3/59 (5%)

Query: 11   TEQKLFDLMWSDEIKLSFSNFVLHFFP---WGEKGTPLEGFSAPRSWQLEFMEVVDAHC 66
             E+ + +   +  +KLS S F   F P   W E G   +         + F    D   
Sbjct: 1365 LERSVQNKAVAKVLKLSESTFRPLFSPLFDWAEPGLEAKAEQKCLERLISFYHFADYLQ 1423


>gnl|CDD|36305 KOG1089, KOG1089, KOG1089, Myotubularin-related
           phosphatidylinositol 3-phosphate 3-phosphatase MTM6
           [General function prediction only].
          Length = 573

 Score = 28.8 bits (64), Expect = 4.0
 Identities = 33/147 (22%), Positives = 48/147 (32%), Gaps = 33/147 (22%)

Query: 44  PLEGFSAPRSWQLEFMEVVDAHCLNSVNNPNPEVFKGAISAGRGIGKTTLNAWL------ 97
           PL GF A R  + E +       L ++   NP   +G I   R       N         
Sbjct: 220 PLSGFIAKRCREDEKI-------LEAILKANPNSKRGYIVDTRPRTNAMANRAKGGGYEN 272

Query: 98  ------VLWLMSTRPGISVICLANSETQLK---TTLWAEVSKWLSLLPNKHWFEMQSLSL 148
                   +L      I V+   +S  +L          + KWLSLL +  W +     L
Sbjct: 273 EDNYSQWKFLFLGIENIHVV--RSSLQKLLEVCNNFLPTMDKWLSLLESSGWLKHIRAIL 330

Query: 149 HPAPWYSD---------VLHCSLGIDS 166
             A   +          ++HCS G D 
Sbjct: 331 KAAAEIAKCLSSEGASVLVHCSDGWDR 357


>gnl|CDD|112181 pfam03354, Terminase_1, Phage Terminase.  The majority of the
           members of this family are bacteriophage proteins,
           several of which are thought to be terminase large
           subunit proteins. There are also a number of bacterial
           proteins of unknown function.
          Length = 473

 Score = 28.6 bits (64), Expect = 4.4
 Identities = 31/179 (17%), Positives = 65/179 (36%), Gaps = 19/179 (10%)

Query: 82  ISAGRGIGKTTLNAWLVLWLM--STRPGISVICLANSETQLKTTLWAEVSKWLSLLPNKH 139
           +S GR  GK+ L A  VL+ +    +    ++  A +  Q +  L+  V   + L P   
Sbjct: 27  VSVGRKNGKSYLMAIRVLYELLLGGKSNQEILVAATTFKQAE-KLFKYVKNQVKLSPFLS 85

Query: 140 WFEMQSLSLHPAPWYSDVLHCSLGIDSKHYSTMCRTYSEERPDTFVGHHNTYGMAIINDE 199
                 L        S       GI+ K  + + +  S    D + G + +  +AI ++ 
Sbjct: 86  IANENKLL------KSQ----KDGIEMKINNNVFKALSNN-GDQYDGGNPS--LAIFDEM 132

Query: 200 ASGTPDVINLGILGFLTERNANRFWIMTSNPRRLSGKFYE---IFNKPLDDWKRFQIDT 255
                  +   I+  + +++  +   +T+      G + E      + L+       D+
Sbjct: 133 HEFKDRELVSTIVTGMRKQDNPQTIQITTAGPNRGGPYDEEREYIKRILEGDVERDDDS 191


>gnl|CDD|30377 COG0027, PurT, Formate-dependent phosphoribosylglycinamide
           formyltransferase (GAR transformylase) [Nucleotide
           transport and metabolism].
          Length = 394

 Score = 28.3 bits (63), Expect = 5.4
 Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 4/39 (10%)

Query: 358 NKISGLVEKYRPDAII--IDANNTGARTCDYLEMLGYHV 394
           + +  +VE+ +PD I+  I+A  T A     LE  GY V
Sbjct: 65  DALRAVVEREKPDYIVPEIEAIATDA--LVELEEEGYTV 101


>gnl|CDD|110578 pfam01583, APS_kinase, Adenylylsulphate kinase.  Enzyme that
           catalyses the phosphorylation of adenylylsulphate to
           3'-phosphoadenylylsulfate. This domain contains an ATP
           binding P-loop motif.
          Length = 157

 Score = 28.0 bits (63), Expect = 5.7
 Identities = 22/67 (32%), Positives = 27/67 (40%), Gaps = 11/67 (16%)

Query: 386 YLEMLGYHVYRVLGQ----KRAVDLEFCRNRRTELHVKMADWLEFASLINHSGLIQNLKS 441
            L   G  VY + G         DL F    RTE   ++A   E A L   +GLI     
Sbjct: 25  KLFAQGISVYVLDGDNVRHGLNKDLGFSEEDRTENIRRIA---EVAKLFADAGLI----V 77

Query: 442 LKSFIVP 448
           + SFI P
Sbjct: 78  ITSFISP 84


>gnl|CDD|144324 pfam00682, HMGL-like, HMGL-like.  This family contains a diverse
           set of enzymes. These include various aldolases and a
           region of pyruvate carboxylase.
          Length = 237

 Score = 27.7 bits (62), Expect = 7.3
 Identities = 13/36 (36%), Positives = 17/36 (47%), Gaps = 3/36 (8%)

Query: 188 HNTYGMAIINDEA--SGTPDVINLGILGFLTERNAN 221
           HN  GMA+ N  A      D ++  + G L ER  N
Sbjct: 189 HNDLGMAVANSLAAVEAGADRVDGTVNG-LGERAGN 223


>gnl|CDD|147641 pfam05582, Peptidase_U57, YabG peptidase U57.  YabG is a protease
           involved in the proteolysis and maturation of SpoIVA and
           YrbA proteins, conserved with the cortex and/or coat
           assembly by Bacillus subtilis.
          Length = 287

 Score = 27.5 bits (62), Expect = 7.7
 Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 5/38 (13%)

Query: 359 KISGLVEKYRPDAIII---DANNTGARTCDYLEMLGYH 393
           KI  L+EKYRPD ++I   DA        DY ++  Y 
Sbjct: 145 KIESLLEKYRPDILVITGHDAYLKNKG--DYGDLNNYR 180


>gnl|CDD|33745 COG3964, COG3964, Predicted amidohydrolase [General function
           prediction only].
          Length = 386

 Score = 27.6 bits (61), Expect = 8.3
 Identities = 17/65 (26%), Positives = 28/65 (43%)

Query: 317 PLIMGCDIAEEGGDNTVVVLRRGPVIEHLFDWSKTDLRTTNNKISGLVEKYRPDAIIIDA 376
           PL++         D  +  LRRG +I H F+     + T +  +   V + R   +I DA
Sbjct: 187 PLMVHIGEPPVLMDEVLERLRRGDIITHCFNGKPNTILTDDGVVRAEVRRARERGVIFDA 246

Query: 377 NNTGA 381
            +  A
Sbjct: 247 GHGRA 251


  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
   0.320    0.137    0.431 

Gapped
Lambda     K      H
   0.267   0.0793    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 6,680,371
Number of extensions: 361916
Number of successful extensions: 816
Number of sequences better than 10.0: 1
Number of HSP's gapped: 814
Number of HSP's successfully gapped: 18
Length of query: 511
Length of database: 6,263,737
Length adjustment: 98
Effective length of query: 413
Effective length of database: 4,146,055
Effective search space: 1712320715
Effective search space used: 1712320715
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 (21.8 bits)
S2: 60 (26.8 bits)