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)