RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|255764478|ref|YP_003065205.2| aminopeptidase protein
[Candidatus Liberibacter asiaticus str. psy62]
         (418 letters)



>gnl|CDD|145308 pfam02073, Peptidase_M29, Thermophilic metalloprotease (M29). 
          Length = 404

 Score =  494 bits (1275), Expect = e-140
 Identities = 171/401 (42%), Positives = 250/401 (62%), Gaps = 2/401 (0%)

Query: 16  LEKLAKVALQVGVNIQEGQHLIVMAPVSALPLARLITKHAYMLGAGLVSVFYKDSEATLM 75
           LEK A++ ++VGVN+Q+GQ +++ APV A PL R + + AY  GA  V V + D E T  
Sbjct: 6   LEKYAELLVKVGVNVQKGQTVLISAPVEAAPLVRALVEEAYEAGAKNVVVEWSDDEITRA 65

Query: 76  LYKYGADYAFDRVADWFCEGLAKAYSDNTALLSISGDNPLLLVNEDSDKVSRVNQAYLKA 135
             ++  +  F+   +W  EG+ +   +  A +SI G+NP LL + D ++++   +A   A
Sbjct: 66  RLEHAPEEQFEEFPEWEAEGMLELAEEGDAFISIRGENPDLLADVDPERIAAYQKARGPA 125

Query: 136 YKPALERISNFDINWSIVPFPSCAWAEIVYPDDPVPIAIAKLANTIFSVSRAHCIDPIAA 195
            KP      +  ++W +V +P+ AWA+ V+P   +  A+  L + IF   R    DP+AA
Sbjct: 126 LKPRRSATMSNKVSWCVVAYPTPAWAQKVFPQAGM--AVEALWDFIFKAVRLDEEDPVAA 183

Query: 196 WAEHNNFLHQKSQWLSQRDFAEIRFSGPNTSLKVGLAEGHRWSGGSSIAQNGIMCNPNIP 255
           W  H+  L +K   L+++ F ++ +  P T L V L   H W+GG S  ++G+    N+P
Sbjct: 184 WEAHDEKLKKKVDILNEKRFKKLHYKAPGTDLTVSLPGRHAWNGGGSKNKDGVEFIANMP 243

Query: 256 TEEVFTAPHARRVEGYATSTKPLVYQGMLIENIRVRFDQGRVVEASASKGEEMLNKILDI 315
           TEEVFTAP    VEG  TSTKPL YQG LIE IR+ F+ G+VV+ASA KGEE+L K+LD 
Sbjct: 244 TEEVFTAPVKDSVEGTVTSTKPLSYQGNLIEGIRLTFEDGKVVDASAEKGEEVLKKLLDT 303

Query: 316 DEGARRLGEVALVPHSSLLSKMNTLFYDTLFDENAASHIAFGQCYSKCFKKPDNALDNWL 375
           DEGAR LGEVALVP+ S +S +  +FY+TLFDENA+ H+A G+ Y +C +      D  L
Sbjct: 304 DEGARYLGEVALVPNPSPISNIGIIFYNTLFDENASCHLALGRAYPECIEGGKEMSDEEL 363

Query: 376 EERGGNSSITHIDWMIGSGDMNVDGLTKNGVLVPIMRGGEW 416
           +  GGN S  H+D+MIGSG++++DG+TK+G   PI R G +
Sbjct: 364 KAGGGNDSAVHVDFMIGSGEIDIDGITKDGTREPIFRNGNF 404


>gnl|CDD|32463 COG2309, AmpS, Leucyl aminopeptidase (aminopeptidase T) [Amino acid
           transport and metabolism].
          Length = 385

 Score =  355 bits (913), Expect = 1e-98
 Identities = 162/405 (40%), Positives = 227/405 (56%), Gaps = 26/405 (6%)

Query: 16  LEKLAKVALQVGVNIQEGQHLIVMAPVSALPLARLITKHAYMLGAGLVSVFYKDSEATLM 75
           LEK A++ ++VG+N+Q GQ +++ APV ALPL RLI K AY  GA  V V   D E    
Sbjct: 4   LEKYAELLVKVGINLQPGQKVVISAPVDALPLVRLIVKEAYEAGARPVKVCLGDPEVARA 63

Query: 76  LYKYGADYAFDRVADWFCEGLAKAYSDNTALLSISGDNPLLLVNEDSDKVSRVNQAYLKA 135
           +Y    D  F+ + +W    + +A ++  A L I+ +   LL  ED  KV+   +A  KA
Sbjct: 64  VYTLAPDEEFEEIPEWEAAAMEEADANGAARLPINTEG--LLDEEDPAKVAAAQKAGAKA 121

Query: 136 YKPALERISNFDINWSIVPFPSCAWAEIVYPDDPVPIAIAKLANTIFSVSRAHCIDPIAA 195
            KP    IS+  ++W++V +P+ +WA+ V+P+     A+AKL + IF   R         
Sbjct: 122 VKPVRISISSNKVSWTVVRYPAPSWAKRVFPE-----AVAKLEDFIFRAVRVD------E 170

Query: 196 WAEHNNFLHQKSQWLSQRDFAEIRFSGPN-TSLKVGLAEGHRWSGGSSIAQNGIMCNPNI 254
           W EH+  L + ++ L++     +  + P  T L  GLA  H W+   S+ + G   N N+
Sbjct: 171 WEEHSALLEKLAEILNEAS--AVHITTPGGTDLTFGLAGRHAWNDAGSVNKGG---NANM 225

Query: 255 PTEEVFTAPHARRVEGYATSTKPLVYQGMLIENIRVRFDQGRVVEASASKGEEMLNKILD 314
           PT EVFTAPH   V G     KPL YQG LIE IR+ F+ G+VVE SA KGEE+L ++LD
Sbjct: 226 PTGEVFTAPHEDSVNGVVVFDKPLSYQGTLIEGIRLTFEDGKVVEISAEKGEEVLKRLLD 285

Query: 315 IDEGARRLGEVALVPHSSLLSKMNTLFYDTLFDENAAS--HIAFGQCYSKCFKKPDNALD 372
            DEGARRLGE+AL P     S +  LFY+ LFDE A+   HIA G  Y    +     + 
Sbjct: 286 TDEGARRLGELALGP----NSPIARLFYNILFDEKASGTVHIAIGSAYPFNVEG-GAEMQ 340

Query: 373 NWLEERGGNSSITHIDWMIGSGDMNVDGLTKNGVLVPIMRGGEWA 417
           N     G N S  H+D MIGS ++ +DG+  +G   P+ R GEWA
Sbjct: 341 NESAIHGDNVSDVHVDSMIGSSEVYIDGVLVDGNGEPVFRKGEWA 385


>gnl|CDD|35304 KOG0081, KOG0081, KOG0081, GTPase Rab27, small G protein
           superfamily [Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 219

 Score = 30.0 bits (67), Expect = 1.3
 Identities = 10/42 (23%), Positives = 23/42 (54%)

Query: 62  LVSVFYKDSEATLMLYKYGADYAFDRVADWFCEGLAKAYSDN 103
           L + F++D+   L+++   ++ +F  V +W  +    AY +N
Sbjct: 83  LTTAFFRDAMGFLLIFDLTSEQSFLNVRNWLSQLQTHAYCEN 124


>gnl|CDD|35519 KOG0298, KOG0298, KOG0298, DEAD box-containing helicase-like
           transcription factor/DNA repair protein [Replication,
           recombination and repair].
          Length = 1394

 Score = 29.2 bits (65), Expect = 2.2
 Identities = 26/115 (22%), Positives = 48/115 (41%), Gaps = 20/115 (17%)

Query: 208 QWLSQRDFAEIRFSGPNTSLKVGLAEGHRWSGGSSIAQ----NGIMCNPNIPTEEV---- 259
           QW       EI      + LKV L  G R +   S  +    + ++   +I   E+    
Sbjct: 434 QWFE-----EIHKHIS-SLLKVLLYFGIRKTFWLSPFELLQYDIVLTTYDILRNELYHTE 487

Query: 260 -FTAPHARRVEG-YATSTKPLVYQGMLIENIRVRFDQGRVVEASASKGEEMLNKI 312
            F +    R +  Y     PL    +++   R+  D+ ++VE+S+S   EM+ ++
Sbjct: 488 DFGSDRQLRHQSRYMRPNSPL----LMVNWWRICLDEAQMVESSSSAAAEMVRRL 538


>gnl|CDD|133327 cd04127, Rab27A, Rab27a subfamily.  The Rab27a subfamily consists
           of Rab27a and its highly homologous isoform, Rab27b.
           Unlike most Rab proteins whose functions remain poorly
           defined, Rab27a has many known functions.  Rab27a has
           multiple effector proteins, and depending on which
           effector it binds, Rab27a has different functions as
           well as tissue distribution and/or cellular
           localization. Putative functions have been assigned to
           Rab27a when associated with the effector proteins Slp1,
           Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin,
           Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1,
           and Munc13-4. Rab27a has been associated with several
           human diseases, including hemophagocytic syndrome
           (Griscelli syndrome or GS), Hermansky-Pudlak syndrome,
           and choroidermia. In the case of GS, a rare, autosomal
           recessive disease, a Rab27a mutation is directly
           responsible for the disorder.  When Rab27a is localized
           to the secretory granules of pancreatic beta cells, it
           is believed to mediate glucose-stimulated insulin
           secretion, making it a potential target for diabetes
           therapy.  When bound to JFC1 in prostate cells, Rab27a
           is believed to regulate the exocytosis of prostate-
           specific markers.  GTPase activating proteins (GAPs)
           interact with GTP-bound Rab and accelerate the
           hydrolysis of GTP to GDP. Guanine nucleotide exchange
           factors (GEFs) interact with GDP-bound Rabs to promote
           the formation of the GTP-bound state.  Rabs are further
           regulated by guanine nucleotide dissociation inhibitors
           (GDIs), which facilitate Rab recycling by masking
           C-terminal lipid binding and promoting cytosolic
           localization. Most Rab GTPases contain a lipid
           modification site at the C-terminus, with sequence
           motifs CC, CXC, or CCX. Lipid binding is essential for
           membrane attachment, a key feature of most Rab proteins.
            Due to the presence of truncated sequences in this CD,
           the lipid modification site is not available for
           annotation.
          Length = 180

 Score = 28.6 bits (64), Expect = 3.5
 Identities = 10/42 (23%), Positives = 22/42 (52%)

Query: 62  LVSVFYKDSEATLMLYKYGADYAFDRVADWFCEGLAKAYSDN 103
           L + F++D+   L+++    + +F  V +W  +    AY +N
Sbjct: 79  LTTAFFRDAMGFLLIFDLTNEQSFLNVRNWMSQLQTHAYCEN 120


>gnl|CDD|147061 pfam04710, Pellino, Pellino.  Pellino is involved in Toll-like
           signalling pathways, and associates with the kinase
           domain of the Pelle Ser/Thr kinase.
          Length = 416

 Score = 28.2 bits (63), Expect = 4.0
 Identities = 15/26 (57%), Positives = 16/26 (61%), Gaps = 2/26 (7%)

Query: 389 WMIGSGDMNVDGLTKNGVLVPIMRGG 414
           W    G+M  DGLT NGVLV   RGG
Sbjct: 171 WQNPDGEM--DGLTTNGVLVMHPRGG 194


>gnl|CDD|35306 KOG0083, KOG0083, KOG0083, GTPase Rab26/Rab37, small G protein
           superfamily [General function prediction only].
          Length = 192

 Score = 28.1 bits (62), Expect = 4.4
 Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 2/47 (4%)

Query: 66  FYKDSEATLMLYKYGADYAFDRVADWFCEGLAKAYSDNTALLSISGD 112
           +Y+D++A L+LY      +FD    W  E     Y+     L + G+
Sbjct: 67  YYRDADALLLLYDIANKASFDNCQAWLSE--IHEYAKEAVALMLLGN 111


>gnl|CDD|145189 pfam01888, CbiD, CbiD.  CbiD is essential for cobalamin
           biosynthesis in both S. typhimurium and B. megaterium,
           no functional role has been ascribed to the protein. The
           CbiD protein has a putative S-AdoMet binding site. It is
           possible that CbiD might have the same role as CobF in
           undertaking the C-1 methylation and deacylation
           reactions required during the ring contraction process.
          Length = 261

 Score = 27.8 bits (62), Expect = 5.6
 Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 6/52 (11%)

Query: 283 MLIENIR--VRFDQGRVVEASASKGEEM----LNKILDIDEGARRLGEVALV 328
           M+ EN++  +R D+G +V  S  +GEE+    LN  L I  G   LG   +V
Sbjct: 123 MIRENLQKALREDEGVMVTISVPEGEELAKKTLNARLGIVGGISILGTTGIV 174


>gnl|CDD|31221 COG1018, Hmp, Flavodoxin reductases (ferredoxin-NADPH reductases)
           family 1 [Energy production and conversion].
          Length = 266

 Score = 27.6 bits (61), Expect = 6.8
 Identities = 9/33 (27%), Positives = 14/33 (42%)

Query: 29  NIQEGQHLIVMAPVSALPLARLITKHAYMLGAG 61
           +++ G  L V AP     L  L  +   +L  G
Sbjct: 87  HLKVGDTLEVSAPAGDFVLDDLPERKLLLLAGG 119


>gnl|CDD|99847 cd06144, REX4_like, DEDDh 3'-5' exonuclease domain of RNA
           exonuclease 4, XPMC2, Interferon Stimulated Gene product
           of 20 kDa, and similar proteins.  This subfamily is
           composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2,
           Interferon (IFN) Stimulated Gene product of 20 kDa
           (ISG20), and similar proteins. REX4 is involved in
           pre-rRNA processing. It controls the ratio between the
           two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene
           which was identified through its ability to correct a
           mitotic defect in fission yeast. The human homolog of
           XPMC2 (hPMC2) may be involved in angiotensin II-induced
           adrenal cell cycle progression and cell proliferation.
           ISG20 is an IFN-induced antiviral exonuclease with a
           strong preference for single-stranded RNA and minor
           activity towards single-stranded DNA. These proteins are
           DEDDh-type DnaQ-like 3'-5' exonucleases containing three
           conserved sequence motifs termed ExoI, ExoII and ExoIII,
           with a specific Hx(4)D conserved pattern at ExoIII.
           These motifs are clustered around the active site and
           contain four conserved acidic residues that serve as
           ligands for the two metal ions required for catalysis.
           REX proteins function in the processing and maturation
           of many RNA species, similar to the function of
           Escherchia coli RNase T.
          Length = 152

 Score = 27.5 bits (62), Expect = 7.4
 Identities = 12/20 (60%), Positives = 16/20 (80%), Gaps = 2/20 (10%)

Query: 16  LEKLAKVALQVGVNIQEGQH 35
           L+KLAK  L  G++IQEG+H
Sbjct: 121 LKKLAKQLL--GLDIQEGEH 138


>gnl|CDD|132926 cd07015, Clp_protease_NfeD, Nodulation formation efficiency D
           (NfeD) is a membrane-bound ClpP-class protease.
           Nodulation formation efficiency D (NfeD; stomatin operon
           partner protein, STOPP; DUF107) is a member of
           membrane-anchored ClpP-class proteases. Currently, more
           than 300 NfeD homologs have been identified - all of
           which are bacterial or archaeal in origin. Majority of
           these genomes have been shown to possess operons
           containing a homologous NfeD/stomatin gene pair, causing
           NfeD to be previously named STOPP (stomatin operon
           partner protein). NfeD homologs can be divided into two
           groups: long and short forms. Long-form homologs have a
           putative ClpP-class serine protease domain while the
           short form homologs do not. Downstream from the
           ClpP-class domain is the so-called NfeD or DUF107
           domain. N-terminal region of the NfeD homolog PH1510
           (1510-N or PH1510-N) from Pyrococcus horikoshii has been
           shown to possess serine protease activity and has a
           Ser-Lys catalytic dyad, preferentially cleaving
           hydrophobic substrates. Difference in oligomeric form
           and catalytic residues between 1510-N (forming a dimer)
           and ClpP (forming a tetradecamer) shows a possible
           functional difference: 1510-N is likely to have a
           regulatory function while ClpP is involved in protein
           quality control.
          Length = 172

 Score = 27.4 bits (60), Expect = 8.1
 Identities = 12/29 (41%), Positives = 15/29 (51%)

Query: 23  ALQVGVNIQEGQHLIVMAPVSALPLARLI 51
           A   G  I  G HLI MAP +++   R I
Sbjct: 72  AASAGTYIALGSHLIAMAPGTSIGACRPI 100


  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
   0.319    0.134    0.407 

Gapped
Lambda     K      H
   0.267   0.0640    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,110,283
Number of extensions: 269024
Number of successful extensions: 567
Number of sequences better than 10.0: 1
Number of HSP's gapped: 560
Number of HSP's successfully gapped: 14
Length of query: 418
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 322
Effective length of database: 4,189,273
Effective search space: 1348945906
Effective search space used: 1348945906
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: 59 (26.7 bits)