RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

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



>gnl|CDD|182787 PRK10861, PRK10861, signal peptidase I; Provisional.
          Length = 324

 Score =  169 bits (429), Expect = 9e-43
 Identities = 90/253 (35%), Positives = 132/253 (52%), Gaps = 66/253 (26%)

Query: 15  DTLKSILQALFFAILIRTFLFQPSVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYN 74
           +T  S+   L   +++R+F+++P  IPSGSM+PTLL+GD+I+V KF+YG      P +  
Sbjct: 62  ETGASVFPVLAIVLIVRSFIYEPFQIPSGSMMPTLLIGDFILVEKFAYGIKD---PITQT 118

Query: 75  LFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVIGLPGDRISLE-------------KGI 121
                I    P+RGD+VVF+YP+DP +DY+KRV+GLPGD+++ +              G 
Sbjct: 119 TL---IETGHPKRGDIVVFKYPEDPKLDYIKRVVGLPGDKVTYDPVSKEVTIQPGCSSGQ 175

Query: 122 IYINGAPVVRHMEGYFSYHYKEDW-----------SSN----VPIFQEKLSNG------- 159
              N  PV       +S     D+           +++    VP+  E   NG       
Sbjct: 176 ACENALPVT------YSNVEPSDFVQTFSRRNGGEATSGFFQVPL-NETKENGIRLSERK 228

Query: 160 -----VLYNVL----SQD-----FLAPSSNISEFLVPKGHYFMMGDNRDKSKDSR-WVEV 204
                V + +L    +QD     +  P   ++ ++VP G YFMMGDNRD S DSR W   
Sbjct: 229 ETLGDVTHRILTVPGAQDQVGMYYQQPGQPLATWVVPPGQYFMMGDNRDNSADSRYW--- 285

Query: 205 GFVPEENLVGRAS 217
           GFVPE NLVG+A+
Sbjct: 286 GFVPEANLVGKAT 298


>gnl|CDD|162773 TIGR02227, sigpep_I_bact, signal peptidase I, bacterial type.  A
           related model finds a simlar protein in many archaea and
           a few bacteria, as well as a microsomal (endoplasmic
           reticulum) protein in eukaryotes.
          Length = 163

 Score =  162 bits (411), Expect = 1e-40
 Identities = 81/206 (39%), Positives = 108/206 (52%), Gaps = 46/206 (22%)

Query: 17  LKSILQALFFAILIRTFLFQPSVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLF 76
           + S+L A+  A+LIRTF+F P  IP GSM PTL  GD I+VNKF+YG S           
Sbjct: 2   ILSLLIAILLALLIRTFVFFPYKIPGGSMEPTLKEGDRILVNKFAYGTS----------- 50

Query: 77  NGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVIGLPGDRISLEKGIIYINGAPVVRHMEGY 136
                   P+RGD+VVF+ P D    YVKRVIGLPGD++    G +YING  +    E Y
Sbjct: 51  -------DPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKVEFRDGKLYINGKKI---DEPY 100

Query: 137 FSYHYKEDWSSNVPIFQEKLSNGVLYNVLSQDFLAPSSNISEFLVPKGHYFMMGDNRDKS 196
              +   D S                          +++     VP GHYF++GDNRD S
Sbjct: 101 LKPNGSLDTSGF-----------------------NTTDFKPVTVPPGHYFVLGDNRDNS 137

Query: 197 KDSRWVEVGFVPEENLVGRASFVLFS 222
            DSR+   GFVP ++++G+ SFV + 
Sbjct: 138 LDSRY--FGFVPIDDIIGKVSFVFYP 161


>gnl|CDD|151062 pfam10502, Peptidase_S26, Peptidase S26.  This is a family of
           serine endopeptidases which function in the processing
           of newly-synthesized secreted proteins. Peptidase S26
           removes the hydrophobic, N-terminal signal peptides as
           proteins are translocated across membranes.
          Length = 138

 Score = 46.5 bits (111), Expect = 6e-06
 Identities = 35/148 (23%), Positives = 57/148 (38%), Gaps = 44/148 (29%)

Query: 85  PRRGDVVVFRYPKD------------PSIDYVKRVIGLPGDRISLEKGIIYINGAPVVRH 132
           P  GD+V    P+               +  +KRV+ LPG R+ +  G++ I+G PV   
Sbjct: 22  PEVGDLVAVCPPEPAAFFAAERGYLPRGVPLLKRVLALPGQRVCIRDGLVTIDGVPVSAA 81

Query: 133 MEGYFSYHYKEDWSSNVPIFQEKLSNGVLYNVLSQDFLAPSSNISEFLVPKGHYFMMGDN 192
           +E       ++     +P +Q                          ++P+G  F+M   
Sbjct: 82  LE-------RDRKGRPLPPWQG-----------------------CRVLPEGELFLMSVT 111

Query: 193 RDKSKDSRWVEVGFVPEENLVGRASFVL 220
              S DSR+   G VP   ++GRA  V 
Sbjct: 112 SPDSFDSRY--FGPVPASAIIGRARPVW 137


>gnl|CDD|131818 TIGR02771, TraF_Ti, conjugative transfer signal peptidase TraF.
           This protein is found in apparent operons encoding
           elements of conjugative transfer systems. This family is
           homologous to a broader family of signal (leader)
           peptidases such as lepB. This family is present in both
           Ti-type and I-type conjugative systems.
          Length = 171

 Score = 41.3 bits (97), Expect = 3e-04
 Identities = 40/155 (25%), Positives = 61/155 (39%), Gaps = 51/155 (32%)

Query: 85  PRRGDVVVFRYPKDPSIDY-------------------VKRVIGLPGDRISLEKGIIYIN 125
             RGD VVF  P +P  +                    +KRV+GLPGDR+++   ++ IN
Sbjct: 47  VERGDYVVFCPPDNPQFEEARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVRADVVAIN 106

Query: 126 GAPVVRHMEGYFSYHYKEDWSSNVPIFQEKLSNGVLYNVLSQDFLAPSSNISEFLVPKGH 185
           G  +       +S     D SS  P                   L P     E ++P G 
Sbjct: 107 GQLLP------YSKPLATD-SSGRP-------------------LPP---FPEGVIPPG- 136

Query: 186 YFMMGDNRDKSKDSRWVEVGFVPEENLVGRASFVL 220
           +F++ D    S DSR+   G +  E ++GR   + 
Sbjct: 137 FFVVHDTSPTSFDSRY--FGPISREQVIGRVKPLF 169


>gnl|CDD|163000 TIGR02754, sod_Ni_protease, nickel-type superoxide dismutase
           maturation protease.  Members of this protein family are
           apparent proteases encoded adjacent to the genes for a
           nickel-type superoxide dismutase. This family belongs to
           the same larger family (see Pfam model pfam00717) as
           signal peptidase I, an unusual serine protease suggested
           to have a Ser/Lys catalytic dyad.
          Length = 90

 Score = 36.3 bits (84), Expect = 0.007
 Identities = 20/66 (30%), Positives = 26/66 (39%), Gaps = 18/66 (27%)

Query: 44  SMIPTLLVGDYIIVNKFSYGYSKYSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDY 103
           SM PTL  GD IIV  +   +                    P  G+VVV R+P  P    
Sbjct: 7   SMSPTLPPGDRIIVVPWLKIF------------------RVPPIGNVVVVRHPLQPYGLI 48

Query: 104 VKRVIG 109
           +KR+  
Sbjct: 49  IKRLAA 54



 Score = 26.6 bits (59), Expect = 5.6
 Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 2/36 (5%)

Query: 181 VPKGHYFMMGDNRDKSKDSRWVEVGFVPEENLVGRA 216
           V     F++GDN   S DSR  ++G VP   L+G+ 
Sbjct: 55  VDDNGLFLLGDNPKASTDSR--QLGPVPRSLLLGKV 88


>gnl|CDD|131283 TIGR02228, sigpep_I_arch, signal peptidase I, archaeal type.  This
           model represents signal peptidase I from most archaea, a
           subunit of the eukaryotic endoplasmic reticulum signal
           peptidase I complex, and an apparent signal peptidase I
           from a small number of bacteria. It is related to but
           does not overlap in hits with TIGR02227, the bacterial
           and mitochondrial signal peptidase I.
          Length = 158

 Score = 30.1 bits (68), Expect = 0.55
 Identities = 24/103 (23%), Positives = 38/103 (36%), Gaps = 27/103 (26%)

Query: 13  GSDTLKSILQALFFAILIRTFLFQPS------VIPSGSMIPTLLVGDYIIVNKFSYGYSK 66
            S+ +  IL  L   +L+   + + S      V+ SGSM PT   GD I+V       + 
Sbjct: 3   ISNVIYFILIILLVILLLYGLVSKASGPDPVVVVLSGSMEPTFNTGDLILVT--GADPND 60

Query: 67  YSFPFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRVIG 109
                              + GDV+ ++ P   +     RVI 
Sbjct: 61  I------------------QVGDVITYKSP-GFNTPVTHRVIE 84


>gnl|CDD|171521 PRK12467, PRK12467, peptide synthase; Provisional.
          Length = 3956

 Score = 28.2 bits (63), Expect = 2.3
 Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 11/51 (21%)

Query: 70   PFSYNLFNGRIFNNQPRRGDVVVFRYPKDPSIDYVKRV---IGLPGDRISL 117
            PFS +   GR++    R GD+   RY  D  I+Y+ R+   + + G RI L
Sbjct: 3464 PFSGS--GGRLY----RTGDLA--RYRADGVIEYLGRIDHQVKIRGFRIEL 3506


>gnl|CDD|132587 TIGR03548, mutarot_permut, cyclically-permuted mutatrotase family
           protein.  Members of this protein family show
           essentially full-length homology, cyclically permuted,
           to YjhT from Escherichia coli. YjhT was shown to act as
           a mutarotase for sialic acid, and by this ability to be
           able to act as a virulence factor. Members of the YjhT
           family (TIGR03547) and this cyclically-permuted family
           have multiple repeats of the beta-propeller-forming
           Kelch repeat.
          Length = 323

 Score = 27.9 bits (62), Expect = 2.5
 Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 4/53 (7%)

Query: 92  VFRYPKDPSIDYVKRVIGLPGDRISLEKGIIYINGAPVVRHMEGYFSYHYKED 144
             ++ KD  + Y        G  +S+E GI YI G+         +     E 
Sbjct: 50  NLKWVKDGQLPYEAAY----GASVSVENGIYYIGGSNSSERFSSVYRITLDES 98


>gnl|CDD|163194 TIGR03260, met_CoM_red_D, methyl-coenzyme M reductase operon
           protein D.  Members of this protein family are protein
           D, a non-structural protein, of the operon for methyl
           coenzyme M reductase, also called coenzyme-B
           sulfoethylthiotransferase (EC 2.8.4.1). That enzyme,
           with alpha, beta, and gamma subunits, catalyzes the last
           step in methanogenesis; it has several modified sites,
           so accessory proteins are expected. Several methanogens
           have encode two such enzymes, designated I and II; this
           model does not separate the isozymes. Proteins in this
           family are expressed at much lower levels than the
           methyl-coenzyme M reductase itself and associate and
           have been shown to form at least transient associations.
           The precise function is unknown.
          Length = 150

 Score = 27.3 bits (61), Expect = 3.7
 Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 5/57 (8%)

Query: 69  FPFSYNLFNGRIFNNQPRRGDVVVFRYPKD-PSIDYVKRVIGLPGDRISLEKGIIYI 124
            PF Y +  G+    +P   D +  +Y +D   ID  +R++GL   R  L + +  I
Sbjct: 97  LPFGYEVRVGKFLRTKPTVTDYI--KYGEDGDKID--ERLLGLVDPRAKLSESVTII 149


>gnl|CDD|117026 pfam08449, UAA, UAA transporter family.  This family includes
           transporters with a specificity for
           UDP-N-acetylglucosamine.
          Length = 303

 Score = 27.2 bits (61), Expect = 3.8
 Identities = 7/26 (26%), Positives = 14/26 (53%), Gaps = 2/26 (7%)

Query: 42  SGSMIPTLLVGDYIIVNKFSYGYSKY 67
           S  +IP +++G  I++    Y   +Y
Sbjct: 98  SCKLIPVMILG--ILIYGKRYSSLQY 121


>gnl|CDD|179163 PRK00911, PRK00911, dihydroxy-acid dehydratase; Provisional.
          Length = 552

 Score = 26.9 bits (61), Expect = 4.7
 Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 2/20 (10%)

Query: 80  IFNNQPRRGDVVVFRY--PK 97
           I   + + GDVVV RY  PK
Sbjct: 414 ILAGKIKAGDVVVIRYEGPK 433


>gnl|CDD|177533 PHA03119, PHA03119, helicase-primase primase subunit; Provisional.
          Length = 1085

 Score = 27.2 bits (60), Expect = 4.7
 Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 10/75 (13%)

Query: 11  IFGSDTLKSILQALFFAILI-RTFLFQPSVIPSGSMIPTLLVGDYIIVNKFSYGYSKYSF 69
           +FGS TLK + + +  A+L+ RTF+         +M P L    +I    +S+G+S    
Sbjct: 810 LFGSSTLKGMARIIQQAVLLERTFV--------ETMGPYLKDFSFIDTGVYSHGHS-LRL 860

Query: 70  PFSYNLFNGRIFNNQ 84
           PF   + +G  FN  
Sbjct: 861 PFFSKVTDGGTFNGL 875


>gnl|CDD|177671 PLN00037, PLN00037, photosystem II oxygen-evolving enhancer protein
           1; Provisional.
          Length = 313

 Score = 26.3 bits (58), Expect = 7.3
 Identities = 11/17 (64%), Positives = 11/17 (64%)

Query: 168 DFLAPSSNISEFLVPKG 184
           DFL PS   S FL PKG
Sbjct: 211 DFLVPSYRGSSFLDPKG 227


>gnl|CDD|183785 PRK12842, PRK12842, putative succinate dehydrogenase; Reviewed.
          Length = 574

 Score = 26.2 bits (58), Expect = 7.3
 Identities = 9/14 (64%), Positives = 9/14 (64%)

Query: 224 GGDTPFSKVWLWIP 237
           GG T FS   LWIP
Sbjct: 45  GGTTAFSGGVLWIP 58


>gnl|CDD|183532 PRK12448, PRK12448, dihydroxy-acid dehydratase; Provisional.
          Length = 615

 Score = 26.3 bits (59), Expect = 7.4
 Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 2/20 (10%)

Query: 80  IFNNQPRRGDVVVFRY--PK 97
           I   + + GDVVV RY  PK
Sbjct: 464 ILGGKVKAGDVVVIRYEGPK 483


>gnl|CDD|182403 PRK10355, xylF, D-xylose transporter subunit XylF; Provisional.
          Length = 330

 Score = 25.9 bits (57), Expect = 9.8
 Identities = 10/19 (52%), Positives = 13/19 (68%), Gaps = 4/19 (21%)

Query: 181 VPKGHYFMMG----DNRDK 195
           VP+G+YF+MG    DN  K
Sbjct: 144 VPQGNYFLMGGSPVDNNAK 162


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.325    0.143    0.454 

Gapped
Lambda     K      H
   0.267   0.0746    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,344,923
Number of extensions: 282023
Number of successful extensions: 701
Number of sequences better than 10.0: 1
Number of HSP's gapped: 694
Number of HSP's successfully gapped: 27
Length of query: 248
Length of database: 5,994,473
Length adjustment: 91
Effective length of query: 157
Effective length of database: 4,028,145
Effective search space: 632418765
Effective search space used: 632418765
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: 56 (25.3 bits)