RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780710|ref|YP_003065123.1| diaminopimelate epimerase
[Candidatus Liberibacter asiaticus str. psy62]
(296 letters)
>gnl|CDD|30602 COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and
metabolism].
Length = 272
Score = 250 bits (641), Expect = 3e-67
Identities = 110/281 (39%), Positives = 155/281 (55%), Gaps = 14/281 (4%)
Query: 6 VDFAKMEGIGNKILVIDMRGCHDNITSDAINALSTDDNTH--FDQIMLIHDFQDASVDAF 63
++F+KM G+GN +V+D D T + AL D + D ++ + + D
Sbjct: 1 MEFSKMHGLGNDFIVVDEFDKKDEETPELARALC-DRHFGIGADGVLFVEPPRSPGADFH 59
Query: 64 IRIINCDGSEVQSCGNGMRCVVRFLTSR--MKRKSFTFETIRGILVAKENRDGSISVDMG 121
+RI N DGSE + CGNG RC RFL R +K+K + ET+ GIL K + D ++SVDMG
Sbjct: 60 LRIFNSDGSEAEMCGNGARCFARFLAERGLVKKKEISVETLAGILKVKVHDDNTVSVDMG 119
Query: 122 EPILDWKLIPLARSFDKMDRDRFHIGPVNHLFLRNPFVVSMGNPHAIFFVEDDLYHYDLA 181
P IPL ++ +++ +G F VSMGNPH + FV DD+ +L
Sbjct: 120 LPSFKPAEIPLL---EEKVEEQYGLGEETVTFY----AVSMGNPHLVIFV-DDVETANLE 171
Query: 182 SFGNLLAKHPMFSEGVNLSIARVTSLESLDLRTWERGVGLTAACGSAACASVVASGCLHK 241
G LL H +F EGVN+ +V S +++ LR +ERG G T ACG+ ACA+ V + L
Sbjct: 172 ELGPLLESHELFPEGVNVGFVQVLSRDAIRLRVYERGAGETLACGTGACAAAVVAARLGL 231
Query: 242 TNRAVSVKMLGGGLLIEW-HDNNHVFMTGEAKKEWEGKLDI 281
+R V+V + GG L IEW D V+MTG A + EGKL I
Sbjct: 232 LDRKVTVHLPGGTLEIEWKDDGKPVYMTGPATRVAEGKLYI 272
>gnl|CDD|145037 pfam01678, DAP_epimerase, Diaminopimelate epimerase.
Diaminopimelate epimerase contains two domains of the
same alpha/beta fold, both contained in this family.
Length = 121
Score = 88.1 bits (219), Expect = 3e-18
Identities = 36/120 (30%), Positives = 51/120 (42%), Gaps = 4/120 (3%)
Query: 158 FVVSMGNPHAIFFVED-DLYHYDLASFGNLLAKHPMFSEGVNLSIARVTSLESLDLRTWE 216
F GNPH + V+D + + G L F N+ +V+ + +R +
Sbjct: 1 FAKMHGNPHDVVVVDDVEGANLLEPELGPALCHRHFFPGADNVLFVQVSGELDIKMRIFN 60
Query: 217 RGVGLTAACGSAACASVVASGCLHK--TNRAVSVKMLGGGLLIEWHDNNHV-FMTGEAKK 273
R T ACG+ A A A+ L T + V V+ GG L IE D+ HV M G A
Sbjct: 61 RDGSETEACGNGAVACFAAAVYLGGLVTKKPVLVETPGGDLEIEVKDDGHVIVMMGPAVL 120
Score = 66.9 bits (164), Expect = 6e-12
Identities = 36/125 (28%), Positives = 57/125 (45%), Gaps = 12/125 (9%)
Query: 8 FAKMEGIGNKILVIDMRGCHDNITSDAINALSTDDNTHF----DQIMLIHDFQDASVDAF 63
FAKM G + ++V+D + + + AL + HF D ++ + + D
Sbjct: 1 FAKMHGNPHDVVVVDDVEGANLLEPELGPALC---HRHFFPGADNVLFVQVSGEL--DIK 55
Query: 64 IRIINCDGSEVQSCGNGM-RCVVRFLTSR--MKRKSFTFETIRGILVAKENRDGSISVDM 120
+RI N DGSE ++CGNG C + + +K ET G L + DG + V M
Sbjct: 56 MRIFNRDGSETEACGNGAVACFAAAVYLGGLVTKKPVLVETPGGDLEIEVKDDGHVIVMM 115
Query: 121 GEPIL 125
G +L
Sbjct: 116 GPAVL 120
>gnl|CDD|145612 pfam02567, PhzC-PhzF, Phenazine biosynthesis-like protein.
PhzC/PhzF is involved in dimerization of two
2,3-dihydro-3-oxo-anthranilic acid molecules to create
PCA by P. fluorescens. This family also contains a
putative thymidilate synthase from Mycobacterium
tuberculosis, though there is no significant sequence
similarity to pfam00303 members. This family appears to
be distantly related to pfam01678, including containing
a weak internal duplication. However members of this
family do not contain the conserved cysteines that are
hypothesized to be active site residues (Bateman A pers
obs).
Length = 280
Score = 34.7 bits (80), Expect = 0.033
Identities = 27/158 (17%), Positives = 45/158 (28%), Gaps = 18/158 (11%)
Query: 83 CVVRFLTSRMKRKSFTFETIRGILVAK---ENRDGSISVDMGEPILDWKLIPLARSFDKM 139
F K+ ET+ GI+ K + +++M P D + +
Sbjct: 75 AHALFEEGGNGNKTLELETLAGIVPVKLVEGDGGAEGAIEMNFPEFDLPAVSR-----ED 129
Query: 140 DRDRFHIGPVNHLFLRNPFVVSMGNPHAIFFVED----DLYHYDLASFGNLLAKHPMFSE 195
D + V S G H ++ DL + +
Sbjct: 130 DALLLAGIGLEFHEALPIAVKSTGLWHVFVPLKSLEALAALDPDLDAAIADCPDDGVIV- 188
Query: 196 GVNLSIARVTSLESLDLRTWERGVGLT--AACGSAACA 231
G S + R + +G+ A GSAA A
Sbjct: 189 GPAASAGSPRDYHA---RMFAPALGIVEDPATGSAAGA 223
>gnl|CDD|132845 cd07206, Pat_TGL3-4-5_SDP1, Triacylglycerol lipase 3, 4, and 5 and
Sugar-Dependent 1 lipase. Triacylglycerol lipases are
involved in triacylglycerol mobilization and
degradation; they are found in lipid particles. TGL4 is
30% homologus to TGL3, whereas TGL5 is 26% homologus to
TGL3. Sugar-Dependent 1 (SDP1) lipase has a patatin-like
acyl-hydrolase domain that initiates the breakdown of
storage oil in germinating Arabidopsis seeds. This
family includes subfamilies of proteins: TGL3, TGL4,
TGL5, and SDP1.
Length = 298
Score = 31.0 bits (71), Expect = 0.38
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 24/62 (38%)
Query: 112 RDGSISVDMGEPILDWKLIPLARSFDKMDRDRFHIGPVNHLFLRNPFVVSMGNPHAIFFV 171
DGS+S D+ P LAR ++ VNH F+VS NPH + F+
Sbjct: 203 VDGSVSDDL--PAKR-----LARLYN-----------VNH------FIVSQTNPHVVPFL 238
Query: 172 ED 173
++
Sbjct: 239 QE 240
>gnl|CDD|38243 KOG3033, KOG3033, KOG3033, Predicted PhzC/PhzF-type epimerase
[General function prediction only].
Length = 286
Score = 29.5 bits (66), Expect = 1.1
Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 72 SEVQSCGNGM--RCVVRFLTSRMKRKSFTFETIRGILVAKENRDGSISVDMGEPILD 126
+EV CG+ V F K F+T+ GIL AK RD S+++ P D
Sbjct: 73 AEVPLCGHATLASAHVLFNEIGNVNKELKFDTLSGILTAK--RDELGSIELNFPEYD 127
>gnl|CDD|132870 cd07232, Pat_PLPL, Patain-like phospholipase. Patatin-like
phospholipase. This family consists of various patatin
glycoproteins from plants and fungi. The patatin protein
accounts for up to 40% of the total soluble protein in
potato tubers. Patatin is a storage protein, but it also
has the enzymatic activity of a lipid acyl hydrolase,
catalyzing the cleavage of fatty acids from membrane
lipids. Members of this family have been found also in
vertebrates.
Length = 407
Score = 29.5 bits (67), Expect = 1.2
Identities = 19/74 (25%), Positives = 25/74 (33%), Gaps = 29/74 (39%)
Query: 103 RGILVAKEN-----RDGSISVDMGEPILDWKLIPLARSFDKMDRDRFHIGPVNHLFLRNP 157
G L+ + +DGS+ D IPL +N LF N
Sbjct: 234 DGTLIPPFSFGSKWKDGSLRTD----------IPLKA--------------LNTLFNVNF 269
Query: 158 FVVSMGNPHAIFFV 171
+VS NPH F
Sbjct: 270 SIVSQVNPHINLFF 283
>gnl|CDD|35339 KOG0116, KOG0116, KOG0116, RasGAP SH3 binding protein rasputin,
contains NTF2 and RRM domains [Signal transduction
mechanisms].
Length = 419
Score = 29.2 bits (65), Expect = 1.5
Identities = 9/42 (21%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 2 QSSMVDFAKMEGIGNKILVIDMRGCHDNITSDAINALSTDDN 43
MV +E I KI+ +D C I++ +++ ++ +
Sbjct: 51 DGKMVSVTGLEAIHEKIMSLDYEVCSVEIST--VDSQASLEK 90
>gnl|CDD|39850 KOG4651, KOG4651, KOG4651, Chondroitin 6-sulfotransferase and
related sulfotransferases [Cell wall/membrane/envelope
biogenesis, Extracellular structures].
Length = 324
Score = 28.8 bits (64), Expect = 2.0
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 9/58 (15%)
Query: 43 NTHFDQIMLIHD----FQDASVDAFIRIINCDGSEVQSCGNGMRCVVRFLTSRMKRKS 96
+ I D F A +D + NC CG MRC+V+ + R+KR++
Sbjct: 144 LKDTVKFAFIRDPFERFVSAYLDKCVNENNCYD-----CGTNMRCIVKKIYKRLKREA 196
>gnl|CDD|112256 pfam03431, RNA_replicase_B, RNA replicase, beta-chain. This family
is of Leviviridae RNA replicases. The replicase is also
known as RNA dependent RNA polymerase.
Length = 539
Score = 27.9 bits (62), Expect = 4.0
Identities = 19/92 (20%), Positives = 31/92 (33%), Gaps = 9/92 (9%)
Query: 185 NLLAKHPMFSEGVNLSIARVTSLESLDLRTWERGVGLTAACGS--AACASVVASG---CL 239
+L+KH FS G++ + + E E T G S +
Sbjct: 46 EILSKHDSFSLGIDTADREAAAWEK--FLAAEARCRQTNQRGYLYDYNEDFNLSWGEAVI 103
Query: 240 HKTNRAVSVKMLGGGLLIEWHDNNHVFMTGEA 271
H R ++ K+LG + H +G A
Sbjct: 104 HTARRLIA-KLLGDSVSF-EPMLRHCRFSGGA 133
>gnl|CDD|30628 COG0280, Pta, Phosphotransacetylase [Energy production and
conversion].
Length = 327
Score = 27.5 bits (61), Expect = 4.8
Identities = 10/38 (26%), Positives = 16/38 (42%)
Query: 85 VRFLTSRMKRKSFTFETIRGILVAKENRDGSISVDMGE 122
V L KRK T E + ++ ++ V +GE
Sbjct: 80 VDRLYELRKRKGVTPEDAQELVREDPTVFAAMMVALGE 117
>gnl|CDD|36540 KOG1326, KOG1326, KOG1326, Membrane-associated protein FER-1 and
related ferlins, contain multiple C2 domains [Cell
wall/membrane/envelope biogenesis].
Length = 1105
Score = 27.2 bits (60), Expect = 5.3
Identities = 7/30 (23%), Positives = 12/30 (40%)
Query: 265 VFMTGEAKKEWEGKLDIKTGKWIKKNEDDE 294
+ + +W+G+ DI K K E
Sbjct: 750 YYSYEVSAIKWKGESDIYDEKEAKTIEVPH 779
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
0.322 0.137 0.420
Gapped
Lambda K H
0.267 0.0625 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,590,098
Number of extensions: 186842
Number of successful extensions: 374
Number of sequences better than 10.0: 1
Number of HSP's gapped: 364
Number of HSP's successfully gapped: 18
Length of query: 296
Length of database: 6,263,737
Length adjustment: 93
Effective length of query: 203
Effective length of database: 4,254,100
Effective search space: 863582300
Effective search space used: 863582300
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 (21.9 bits)
S2: 57 (26.0 bits)