RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780905|ref|YP_003065318.1| glutamate racemase [Candidatus
Liberibacter asiaticus str. psy62]
(271 letters)
>gnl|CDD|31139 COG0796, MurI, Glutamate racemase [Cell envelope biogenesis, outer
membrane].
Length = 269
Score = 216 bits (552), Expect = 5e-57
Identities = 80/259 (30%), Positives = 127/259 (49%), Gaps = 8/259 (3%)
Query: 13 QNSILIFDSGIGGLIVLQKMRFLMPEYHFIYVADDVGFPYGNWEDHALKKRLMFLFSDIL 72
Q I +FDSG+GGL VL+++R +P+ IYV D FPYG + +++R + + +L
Sbjct: 5 QPPIGVFDSGVGGLSVLREIRRQLPDEDIIYVGDTARFPYGEKSEEEIRERTLEIVDFLL 64
Query: 73 DKYQPVLSVIACNTAFTLIKDELRSTFPSMAFLGAVPAIKQAAAYTQSGLISILSTPATL 132
++ VIACNTA + ++LR F + +G +PAIK A A T++G I +++TPAT+
Sbjct: 65 ERG-IKALVIACNTASAVALEDLREKFD-IPVVGVIPAIKPAVALTRNGRIGVIATPATV 122
Query: 133 RRTYTSNLIHSYVSQCHIHLVSSMILASRVEEYACGIKIKEDEIKKEIEGCFIEKEGKRT 192
+ +LI + C + ++ L VEE + ++ +
Sbjct: 123 KSNAYRDLIARFAPDCEVESLACPELVPLVEEG----IRGGPVALEVLKEYLPPLQEAGP 178
Query: 193 DVIVLACTHYPLIVHVFRQLSPWPVDWLDNSDSIARRARCLLPRINTH--QTRVFDDHAL 250
D +VL CTHYPL+ +Q+ V +D+ ARR LL DH
Sbjct: 179 DTLVLGCTHYPLLKPEIQQVLGEHVALIDSGAETARRLARLLSPEGLLAKGADGGPDHRF 238
Query: 251 FLSGKPDIAMRRLMQGFGL 269
F +G PD + L + GL
Sbjct: 239 FTTGDPDEFEQLLKRWLGL 257
>gnl|CDD|144681 pfam01177, Asp_Glu_race, Asp/Glu/Hydantoin racemase. This family
contains aspartate racemase, glutamate racemase,
hydantoin racemase and arylmalonate decarboxylase.
Length = 212
Score = 69.7 bits (171), Expect = 7e-13
Identities = 38/151 (25%), Positives = 65/151 (43%), Gaps = 9/151 (5%)
Query: 81 VIACNTAFTLIKDELRSTFPSMAFLGAVPAIKQAAAYTQSGLISILSTPATLRRTYTSNL 140
VIACNTA L ELR + +G V A +A A + + +L+T T+ S L
Sbjct: 69 VIACNTAHALA-GELREATD-IPVIGIVEAALKALALLGAKRVGVLATYGTI----VSGL 122
Query: 141 IHSYVSQCHIHLVSSMILASRVEEYACGIKIKEDEIKKEIEGCFIEKEGKRTDVIVLACT 200
+++ I +V+ I VE + E+ + + D ++L CT
Sbjct: 123 YQELLAEAGIEVVAPAIRLGIVE--VLELGRIEEASVEALAAALERLAEDGADAVILGCT 180
Query: 201 HYPLIVHVFRQLSPW-PVDWLDNSDSIARRA 230
PL++ + L P V +D++ ++A
Sbjct: 181 ELPLLLELIEALEPELGVPVIDSNQALAWAL 211
>gnl|CDD|173782 cd03362, TOPRIM_TopoIA_TopoIII, TOPRIM_TopoIA_TopoIII: The
topoisomerase-primase (TORPIM) domain found in members
of the type IA family of DNA topoisomerases (Topo IA)
similar to topoisomerase III. Type IA DNA
topoisomerases remove (relax) negative supercoils in the
DNA by: cleaving one strand of the DNA duplex,
covalently linking to the 5' phosphoryl end of the DNA
break and, allowing the other strand of the duplex to
pass through the gap. The TOPRIM domain has two
conserved motifs, one of which centers at a conserved
glutamate and the other one at two conserved aspartates
(DxD). For topoisomerases the conserved glutamate is
believed to act as a general base in strand joining and,
as a general acid in strand cleavage. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 151
Score = 29.5 bits (67), Expect = 1.1
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 167 CGIKIKEDEIKKEIEGCFIEKEGKRTDVIVLAC 199
K+K D+ KK+ ++K KR D IV+A
Sbjct: 75 APFKLKVDKGKKKQFK-VLKKLAKRADEIVIAT 106
>gnl|CDD|37659 KOG2448, KOG2448, KOG2448, Dihydroxy-acid dehydratase [Amino acid
transport and metabolism].
Length = 596
Score = 28.8 bits (64), Expect = 1.5
Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 3/64 (4%)
Query: 79 LSVIACNTAFTLIKDELRSTFPSMAFLGAVPAIKQAAAYTQSGLISILSTPATLRRTYTS 138
L IA + L D+ + + F+ +K + Y L I TP+ L+
Sbjct: 315 LIAIARSVGLELTLDDFQKVSDATPFIAD---LKPSGKYVMEDLHKIGGTPSVLKYLLEL 371
Query: 139 NLIH 142
L+
Sbjct: 372 GLMD 375
>gnl|CDD|173778 cd01028, TOPRIM_TopoIA, TOPRIM_TopoIA: topoisomerase-primase
(TOPRIM) nucleotidyl transferase/hydrolase domain of the
type found in the type IA family of DNA topoisomerases
(TopoIA). This subgroup contains proteins similar to
the Type I DNA topoisomerases: E. coli topisomerases I
and III, eukaryotic topoisomerase III and, ATP-dependent
reverse gyrase found in archaea and thermophilic
bacteria. Type IA DNA topoisomerases remove (relax)
negative supercoils in the DNA. These enzymes cleave one
strand of the DNA duplex, covalently link to the 5'
phosphoryl end of the DNA break and allow the other
strand of the duplex to pass through the gap. Reverse
gyrase is also able to insert positive supercoils in the
presence of ATP and negative supercoils in the presence
of AMPPNP. The TOPRIM domain has two conserved motifs,
one of which centers at a conserved glutamate and the
other one at two conserved aspartates (DxD). For
topoisomerases the conserved glutamate is believed to
act as a general base in strand joining and, as a
general acid in strand cleavage. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 142
Score = 26.8 bits (60), Expect = 6.9
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 1/33 (3%)
Query: 167 CGIKIKEDEIKKEIEGCFIEKEGKRTDVIVLAC 199
K KK+ ++K K+ D IVLA
Sbjct: 67 FEPKYVVIPDKKKQLK-ALKKLAKKADEIVLAT 98
>gnl|CDD|29992 cd01126, TraG_VirD4, The TraG/TraD/VirD4 family are bacterial
conjugation proteins involved in type IV secretion.
These proteins aid the transfer of DNA from the plasmid
into the host bacterial chromosome. They contain an ATP
binding domain. VirD4 is involved in DNA transfer to
plant cells and is required for virulence..
Length = 384
Score = 26.1 bits (57), Expect = 9.8
Identities = 23/93 (24%), Positives = 36/93 (38%), Gaps = 10/93 (10%)
Query: 67 LFSDILDKYQPVLSVIACNTAFTLIKDELRSTFPSMAFLGAVPAIKQAAAYTQSGLIS-- 124
LF+ I+D+ L + DE FP LG + ++A A I
Sbjct: 244 LFNQIIDRLGRSLPGPEEKYRVLFLLDE----FPL---LGKLETFEKAIAIMAGYGIRLL 296
Query: 125 -ILSTPATLRRTYTSNLIHSYVSQCHIHLVSSM 156
I + A L TY S++S C + L ++
Sbjct: 297 LIFQSLAQLEGTYGDAGASSFLSNCGVRLFFAV 329
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
0.326 0.140 0.426
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,423,856
Number of extensions: 184016
Number of successful extensions: 528
Number of sequences better than 10.0: 1
Number of HSP's gapped: 523
Number of HSP's successfully gapped: 12
Length of query: 271
Length of database: 6,263,737
Length adjustment: 92
Effective length of query: 179
Effective length of database: 4,275,709
Effective search space: 765351911
Effective search space used: 765351911
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: 57 (25.8 bits)