RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780762|ref|YP_003065175.1| recombination protein RecR
[Candidatus Liberibacter asiaticus str. psy62]
(201 letters)
>gnl|CDD|178844 PRK00076, recR, recombination protein RecR; Reviewed.
Length = 196
Score = 285 bits (733), Expect = 4e-78
Identities = 93/196 (47%), Positives = 134/196 (68%), Gaps = 1/196 (0%)
Query: 6 TGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGN 65
IE LI+ L ++PG GP+SA+R HL+++ + + LA+A+ K+ CS+CGN
Sbjct: 2 YPPPIEKLIEALRKLPGIGPKSAQRLAFHLLQRDREDVLRLAQALEEAKEKIKHCSVCGN 61
Query: 66 VDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDI 125
+ DPC IC D +RD S+I VVE AD+ A+ER+ LYHVLGG LSPLD IGPED+
Sbjct: 62 LTEQDPCEICSDPRRDQSLICVVESPADVLAIERTGEYRGLYHVLGGLLSPLDGIGPEDL 121
Query: 126 GIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDY 185
I L+ER++ +++E+I A + T+EG+ TAHYI LK + VK+TRLA+G+P+G EL+Y
Sbjct: 122 NIDELLERLD-GEVKEVILATNPTVEGEATAHYIARLLKPLGVKVTRLAHGVPVGGELEY 180
Query: 186 LDDGTIFEAIRSRTVL 201
+D+GT+ A+ R L
Sbjct: 181 VDEGTLSRALEGRREL 196
>gnl|CDD|161960 TIGR00615, recR, recombination protein RecR. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University).
Length = 195
Score = 199 bits (509), Expect = 3e-52
Identities = 82/190 (43%), Positives = 126/190 (66%)
Query: 10 IENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSICGNVDTT 69
I LI+ L ++PG GP+SA+R HL+K+ + LA+A+ + CS+CG +
Sbjct: 6 ISKLIESLKKLPGIGPKSAQRLAFHLLKRDPSEVLRLAQALLEAKENLRTCSVCGAISDQ 65
Query: 70 DPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQS 129
+ C IC D++RD SVI VVED D++ALE++K YHVLGG +SPLD IGPED+ I +
Sbjct: 66 EVCNICSDERRDNSVICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDGIGPEDLTIAA 125
Query: 130 LIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDG 189
L++R++ + ++E+I A + T+EG+ TA YI L+ VK+TR+A G+P+G +L+Y D+
Sbjct: 126 LLKRLQEESVKEVILATNPTVEGEATALYIARLLQPFGVKVTRIASGLPVGGDLEYADEV 185
Query: 190 TIFEAIRSRT 199
T+ A+ R
Sbjct: 186 TLARALEGRR 195
>gnl|CDD|139904 PRK13844, PRK13844, recombination protein RecR; Provisional.
Length = 200
Score = 136 bits (344), Expect = 4e-33
Identities = 70/199 (35%), Positives = 116/199 (58%), Gaps = 1/199 (0%)
Query: 1 MQKKITGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLC 60
M KI +I +I+ L ++P G +S++R L+L+ K + +A ++ + + C
Sbjct: 1 MTSKIFSPKISAVIESLRKLPTIGKKSSQRLALYLLDKSPETAIAIANSLLDATANIKKC 60
Query: 61 SICGNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRI 120
C + D C IC + RD + + ++E + D+ A+E + Y VL G +SPLD I
Sbjct: 61 VYCQALTEDDVCNICSNTNRDDTKLCIIESMLDMIAIEEAGIYRGKYFVLNGRISPLDGI 120
Query: 121 GPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMG 180
GP ++ + L + I +KI E+I AIS T+EG+TTAH+I ++ D+KI+R+ +G+P G
Sbjct: 121 GPSELKLDILQQIIADRKIDEVILAISPTVEGETTAHFI-SQMIAKDIKISRIGFGVPFG 179
Query: 181 SELDYLDDGTIFEAIRSRT 199
EL+YLD T+ A +RT
Sbjct: 180 GELEYLDQQTLLHAFNART 198
>gnl|CDD|128769 smart00493, TOPRIM, topoisomerases, DnaG-type primases, OLD family
nucleases and RecR proteins.
Length = 76
Score = 38.0 bits (89), Expect = 0.001
Identities = 25/83 (30%), Positives = 38/83 (45%), Gaps = 10/83 (12%)
Query: 83 SVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIREL 142
V+I+VE AD ALE++ LGG L + I L++R+ K +E+
Sbjct: 1 KVLIIVEGPADAIALEKAGGFGGNVVALGGHLLKKEII--------KLLKRL--AKKKEV 50
Query: 143 IFAISATIEGQTTAHYIMDKLKG 165
I A EG+ A + + LK
Sbjct: 51 ILATDPDREGEAIAWKLAELLKP 73
>gnl|CDD|131070 TIGR02015, BchY, chlorophyllide reductase subunit Y. This model
represents the Y subunit of the three-subunit enzyme,
(bacterio)chlorophyllide reductase. This enzyme is
responsible for the reduction of the chlorin B-ring and
is closely related to the protochlorophyllide reductase
complex which reduces the D-ring. Both of these
complexes in turn are homologous to nitrogenase.
Length = 422
Score = 29.1 bits (65), Expect = 0.88
Identities = 27/109 (24%), Positives = 42/109 (38%), Gaps = 10/109 (9%)
Query: 8 KEIENLIKILARIPGFGPRSARRATLHLV------KKKEQLLGPLAEAMANIYNKVCLCS 61
K I + + +PGFG + A LV ++E GP+ E + +K L
Sbjct: 111 KRINGVRVLGIDVPGFGVPTHAEAKDVLVSAMLKYARREVSAGPVGEPKSGRDSKPTL-V 169
Query: 62 ICGNVDTTDPCAI-CIDQQRDASVIIVV--EDVADLWALERSKAVNALY 107
+ G + D I + Q V D +L+A S AV L+
Sbjct: 170 LLGEIFPVDAMVIGGVLQPIGVESGPTVPGRDWRELYAALDSSAVAVLH 218
>gnl|CDD|162521 TIGR01763, MalateDH_bact, malate dehydrogenase, NAD-dependent. The
annotation of Botryococcus braunii as lactate
dehydrogenase appears top be in error. This was
initially annotated as MDH by Swiss-Prot and then
changed. The rationale for either of these annotations
is not traceable.
Length = 305
Score = 28.3 bits (63), Expect = 1.6
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 140 RELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTI 191
R+ I I A G TTA + +K D+ + + GIP G LD + +
Sbjct: 1 RKKISVIGAGFVGATTAFRLAEKELA-DLVLLDVVEGIPQGKALDMYEASPV 51
>gnl|CDD|173065 PRK14601, ruvA, Holliday junction DNA helicase RuvA; Provisional.
Length = 183
Score = 26.7 bits (59), Expect = 4.0
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 16 ILARIPGFGPRSARRATLHLVKKKEQL 42
+L ++PG GP+SA+R L K +L
Sbjct: 109 VLKKVPGIGPKSAKRIIAELSDAKTKL 135
>gnl|CDD|163271 TIGR03453, partition_RepA, plasmid partitioning protein RepA.
Members of this family are the RepA (or ParA) protein
involved in replicon partitioning. All known examples
occur in bacterial species with two or more replicons,
on a plasmid or the smaller chromosome. Note that an
apparent exception may be seen as a pseudomolecule from
assembly of an incompletely sequenced genome. Members of
this family belong to a larger family that also includes
the enzyme cobyrinic acid a,c-diamide synthase, but
assignment of that name to members of this family would
be in error.
Length = 387
Score = 26.5 bits (59), Expect = 4.5
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 182 ELDYLDDGTIFEAIR 196
E D ++ T++ AIR
Sbjct: 156 EFDVGENETLYGAIR 170
>gnl|CDD|173066 PRK14602, ruvA, Holliday junction DNA helicase RuvA; Provisional.
Length = 203
Score = 26.6 bits (59), Expect = 5.1
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 14 IKILARIPGFGPRSARRATLHLVKK 38
+ L R+ G G ++A+ L L K
Sbjct: 108 VAALTRVSGIGKKTAQHIFLELKYK 132
>gnl|CDD|178018 PLN02396, PLN02396, hexaprenyldihydroxybenzoate methyltransferase.
Length = 322
Score = 26.2 bits (57), Expect = 5.8
Identities = 17/63 (26%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 111 GGSLS-PLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQ-TTAHYIMDKLKGIDV 168
GG LS PL R+G G+ ++ + +++ ++ + +++TIE TTA + D+ + D
Sbjct: 142 GGLLSEPLARMGATVTGVDAVDKNVKIARLHADMDPVTSTIEYLCTTAEKLADEGRKFDA 201
Query: 169 KIT 171
++
Sbjct: 202 VLS 204
>gnl|CDD|182221 PRK10070, PRK10070, glycine betaine transporter ATP-binding
subunit; Provisional.
Length = 400
Score = 26.1 bits (57), Expect = 5.9
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 13 LIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAE 48
++ + PGFGPRSA L L++ +++ G + E
Sbjct: 284 PNGLIRKTPGFGPRSA----LKLLQDEDREYGYVIE 315
>gnl|CDD|178876 PRK00116, ruvA, Holliday junction DNA helicase RuvA; Reviewed.
Length = 192
Score = 25.9 bits (58), Expect = 6.8
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 14 IKILARIPGFGPRSARR 30
+K L ++PG G ++A R
Sbjct: 107 VKALTKVPGIGKKTAER 123
>gnl|CDD|177561 PHA03232, PHA03232, DNA packaging protein UL32; Provisional.
Length = 586
Score = 25.8 bits (57), Expect = 7.3
Identities = 9/37 (24%), Positives = 13/37 (35%)
Query: 67 DTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAV 103
+ + D + VE AD AL+R V
Sbjct: 65 EDVEADPEDPDGEGHPDTAPFVEAAADTLALDRPCLV 101
>gnl|CDD|162178 TIGR01056, topB, DNA topoisomerase III, bacteria and conjugative
plasmid. This model describes topoisomerase III from
bacteria and its equivalents encoded on plasmids. The
gene is designated topB if found in the bacterial
chromosome, traE on conjugative plasmid RP4, etc. These
enzymes are involved in the control of DNA topology. DNA
topoisomerase III belongs to the type I topoisomerases,
which are ATP-independent.
Length = 660
Score = 25.6 bits (56), Expect = 9.0
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 137 KKIRELIFAISATIEGQTTAHYIMDKLKGID-VKITRL 173
K+ E++ A EG+ A I+D LK D V I RL
Sbjct: 94 NKVDEVVIATDPDREGELIAREILDYLKVTDKVTIKRL 131
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
0.322 0.139 0.398
Gapped
Lambda K H
0.267 0.0741 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,339,164
Number of extensions: 210498
Number of successful extensions: 447
Number of sequences better than 10.0: 1
Number of HSP's gapped: 444
Number of HSP's successfully gapped: 24
Length of query: 201
Length of database: 5,994,473
Length adjustment: 89
Effective length of query: 112
Effective length of database: 4,071,361
Effective search space: 455992432
Effective search space used: 455992432
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: 55 (24.9 bits)