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)