RPS-BLAST 2.2.22 [Sep-27-2009]

Database: mmdb70 
           33,805 sequences; 4,956,049 total letters

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

Query= gi|254780939|ref|YP_003065352.1| type I signal peptidase
[Candidatus Liberibacter asiaticus str. psy62]
         (248 letters)



>1b12_A Signal peptidase I; serine proteinase, serine-dependant
           hydrolase, signal peptide processing, protein
           translocation, membrane bound proteinase; HET: 1PN;
           1.95A {Escherichia coli} (A:72-99,A:175-215)
          Length = 69

 Score = 58.3 bits (141), Expect = 1e-09
 Identities = 30/103 (29%), Positives = 43/103 (41%), Gaps = 35/103 (33%)

Query: 107 VIGLPGDRISLEKGIIYINGAPVVRHMEGYFSYHYKEDWSSNVPIFQEKLSNGVLYNVLS 166
            +GLPGD+++ +         PV + +                                 
Sbjct: 1   AVGLPGDKVTYD---------PVSKELTIQPGCSS------------------------G 27

Query: 167 QDFLAPSSNISEFLVPKGHYFMMGDNRDKSKDSRWVEVGFVPE 209
           Q +  P   ++ ++VP G YFMMGDNRD S DSR+   GFVPE
Sbjct: 28  QYYQQPGQQLATWIVPPGQYFMMGDNRDNSADSRY--WGFVPE 68


>1b12_A Signal peptidase I; serine proteinase, serine-dependant
           hydrolase, signal peptide processing, protein
           translocation, membrane bound proteinase; HET: 1PN;
           1.95A {Escherichia coli} (A:1-71,A:216-248)
          Length = 104

 Score = 57.2 bits (138), Expect = 2e-09
 Identities = 36/77 (46%), Positives = 54/77 (70%), Gaps = 6/77 (7%)

Query: 30  IRTFLFQPSVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGD 89
           +R+F+++P  IPSGSM+PTLL+GD+I+V KF+YG     +  +            P+RGD
Sbjct: 1   VRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKDPIYQKTLIETGH------PKRGD 54

Query: 90  VVVFRYPKDPSIDYVKR 106
           +VVF+YP+DP +DY+KR
Sbjct: 55  IVVFKYPEDPKLDYIKR 71


>2or0_A Hydroxylase; APC7385, rhodococcus SP. RHA1, structural
           genomics, PSI-2, protein structure initiative, midwest
           center for structural genomics; HET: MSE; 2.10A
           {Rhodococcus SP} (A:109-244)
          Length = 136

 Score = 30.4 bits (68), Expect = 0.25
 Identities = 7/47 (14%), Positives = 17/47 (36%), Gaps = 6/47 (12%)

Query: 176 ISEFLVPKGHYFMMGDNRDK--SKDSRWVEVGF----VPEENLVGRA 216
               ++P+  Y ++ D  D    + +   ++      VP    +  A
Sbjct: 74  SLHVILPRTDYQIVEDTWDVIGLRGTGSKDLIVDGAFVPGYRTLNAA 120


>2uva_G Fatty acid synthase beta subunits; fungal, dehydratase,
           enoyl reductase, ketoacyl synthase, ketoacyl reductase;
           HET: FMN; 3.10A {Thermomyces lanuginosus} PDB: 2uvc_G*
           (G:1106-1261)
          Length = 156

 Score = 27.5 bits (61), Expect = 1.9
 Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 2/22 (9%)

Query: 79  RIFNNQPRRGDVVVFRYPKDPS 100
           R+F   P RG  V    P DP+
Sbjct: 71  RLF--APTRGMYVEITNPDDPA 90


>2fjr_A Repressor protein CI; genetic switch, regulation,
           cooperativity, transcription regulator; 1.95A
           {Enterobacteria phage 186} PDB: 2fkd_A (A:71-189)
          Length = 119

 Score = 27.3 bits (60), Expect = 2.3
 Identities = 8/75 (10%), Positives = 17/75 (22%), Gaps = 26/75 (34%)

Query: 44  SMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDY 103
             +     G    V+K                            G  +V           
Sbjct: 44  DGMAIRSEGKIYFVDK----------------------QASLSDGLWLVDIKGA----IS 77

Query: 104 VKRVIGLPGDRISLE 118
           ++ +  LPG ++ + 
Sbjct: 78  IRELTKLPGRKLHVA 92


>2uv8_G Fatty acid synthase subunit beta (FAS1); fatty acid
           biosynthesis, malonyl/palmitoyl transferase,
           phosphopantetheine, transferase; HET: GVL FMN; 3.10A
           {Saccharomyces cerevisiae} PDB: 2vkz_G* 3hmj_G*
           (G:1103-1260)
          Length = 158

 Score = 27.1 bits (60), Expect = 2.4
 Identities = 12/75 (16%), Positives = 24/75 (32%), Gaps = 16/75 (21%)

Query: 79  RIFNNQPRRGDVVVFRYPKDPSI-----------DYVKRVI--GLPGDRISLEKGIIYIN 125
           ++F  +P +G VV        S            +    VI   L  + I +E  I    
Sbjct: 53  KVF--KPSQGMVVEISNGNTSSKTVVTLSEPVQGELKPTVILKLLKENIIQMEM-IENRT 109

Query: 126 GAPVVRHMEGYFSYH 140
                  +   ++++
Sbjct: 110 MDGKPVSLPLLYNFN 124


>2d29_A Acyl-COA dehydrogenase; structural genomics, NPPSFA,
           national project on protein structural and functional
           analyses; HET: FAD; 1.65A {Thermus thermophilus HB8}
           (A:121-232)
          Length = 112

 Score = 26.9 bits (59), Expect = 3.0
 Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 7/47 (14%)

Query: 175 NISEFLVPKGH-YFMMGDNRDKS--KDSRWVEVGF----VPEENLVG 214
            IS F   +      +G   +K     S   ++      VPEE L+G
Sbjct: 66  GISAFAFFRPERGLKVGRKEEKLGLTASDTAQLILEDLFVPEEALLG 112


>3k3w_B Penicillin G acylase; hydrolase; 3.31A {Alcaligenes
          faecalis} (B:338-440)
          Length = 103

 Score = 26.4 bits (58), Expect = 3.5
 Identities = 10/77 (12%), Positives = 25/77 (32%), Gaps = 10/77 (12%)

Query: 15 DTLKSILQALFFAILIRTFLFQPSVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYN 74
            L  ++     A+  +T          GS+  +  +G  +++         +  P   N
Sbjct: 16 QVLMPVVPESHRAMYSQTGFATQQGPNPGSINLS--MGTKVLLRALVLE--AHPDPKRVN 71

Query: 75 LFNGRIFNNQPRRGDVV 91
          +F  R         +++
Sbjct: 72 VFGER------SSQEIM 82


>1r2j_A Protein FKBI; polyketide synthase, polyketide, acyl-COA
           dehydrogenase, , aldehyde dehydrogenase, oxidoreductase;
           HET: FAD; 2.10A {Streptomyces hygroscopicus} (A:105-209)
          Length = 105

 Score = 25.3 bits (55), Expect = 7.1
 Identities = 5/46 (10%), Positives = 14/46 (30%), Gaps = 7/46 (15%)

Query: 176 ISEFLVPKGHY-FMMGDNRDKS--KDSRWVEVGF----VPEENLVG 214
            +  +VP       +      S  + +   ++      VP   ++ 
Sbjct: 59  GAVVVVPADTPGVRVERVPKPSGCRAAGHADLHLDQVRVPAGAVLA 104


>2vig_A Short-chain specific acyl-COA dehydrogenase,; fatty acid
           metabolism, FAD, polymorphism, flavoprotein,
           mitochondrion, disease mutation; HET: FAD COS; 1.9A
           {Homo sapiens} PDB: 1jqi_A* (A:117-227)
          Length = 111

 Score = 25.4 bits (55), Expect = 7.9
 Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 7/45 (15%)

Query: 177 SEFLVPKGH-YFMMGDNRDKS--KDSRWVEVGF----VPEENLVG 214
           S FLVP       +G   DK   + S    + F    +P+++++G
Sbjct: 67  SAFLVPMPTPGLTLGKKEDKLGIRGSSTANLIFEDCRIPKDSILG 111


>2z1q_A Acyl-COA dehydrogenase; FAD, structural genomics, NPPSFA,
           national project on protein structural and functional
           analyses; HET: FAD; 2.30A {Thermus thermophilus}
           (A:104-248)
          Length = 145

 Score = 25.4 bits (54), Expect = 8.4
 Identities = 9/48 (18%), Positives = 17/48 (35%), Gaps = 7/48 (14%)

Query: 175 NISEFLVPKGHYFMMGDNRDKSKDSRWVEVG-------FVPEENLVGR 215
           + + FLV +    +     +K    +             VP EN++G 
Sbjct: 98  HFTAFLVERDTPGLSFGPEEKKMGIKASSTRQVILEDVKVPVENVLGE 145


>3i23_A Oxidoreductase, GFO/IDH/MOCA family; structural genomics,
           PSI-2, protein structure initiative, northeast
           structural genomics consortium; 2.30A {Enterococcus
           faecalis} PDB: 3fd8_A* 3hnp_A (A:126-349)
          Length = 224

 Score = 25.2 bits (55), Expect = 9.2
 Identities = 6/39 (15%), Positives = 12/39 (30%), Gaps = 5/39 (12%)

Query: 130 VRHMEGYFSYHYKEDWSSNVPIFQEKLSNGVLYNVLSQD 168
           +  +E +  Y+     +      Q    NG  Y +    
Sbjct: 21  INEVETHIDYYRPGSITE-----QGPKENGSFYGLGIHL 54


  Database: mmdb70
    Posted date:  Jun 20, 2010  3:12 AM
  Number of letters in database: 4,956,049
  Number of sequences in database:  33,805
  
Lambda     K      H
   0.325    0.143    0.454 

Gapped
Lambda     K      H
   0.267   0.0610    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 2,091,274
Number of extensions: 98574
Number of successful extensions: 321
Number of sequences better than 10.0: 1
Number of HSP's gapped: 321
Number of HSP's successfully gapped: 21
Length of query: 248
Length of database: 4,956,049
Length adjustment: 86
Effective length of query: 162
Effective length of database: 2,048,819
Effective search space: 331908678
Effective search space used: 331908678
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.4 bits)