RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780762|ref|YP_003065175.1| recombination protein RecR
[Candidatus Liberibacter asiaticus str. psy62]
(201 letters)
>gnl|CDD|30702 COG0353, RecR, Recombinational DNA repair protein (RecF pathway)
[DNA replication, recombination, and repair].
Length = 198
Score = 243 bits (623), Expect = 2e-65
Identities = 87/198 (43%), Positives = 129/198 (65%)
Query: 4 KITGKEIENLIKILARIPGFGPRSARRATLHLVKKKEQLLGPLAEAMANIYNKVCLCSIC 63
+ IE LI L ++PG GP+SA+R HL+++ + + LA+A+ + CS+C
Sbjct: 1 MMYPPPIEKLIDALKKLPGVGPKSAQRLAFHLLQRDREDVERLAKALLEAKENIKHCSVC 60
Query: 64 GNVDTTDPCAICIDQQRDASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPE 123
GN+ +DPC IC D+ RD S + VVE+ D+ ALE++ LYHVLGG LSPLD IGPE
Sbjct: 61 GNLTESDPCDICSDESRDKSQLCVVEEPKDVLALEKTGEFRGLYHVLGGLLSPLDGIGPE 120
Query: 124 DIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSEL 183
D+ I L++R+ I+E+I A + T+EG+ TA YI LK + +K+TRLA G+P+G EL
Sbjct: 121 DLNIDELLQRLAEGSIKEVILATNPTVEGEATALYIARLLKPLGLKVTRLAQGVPVGGEL 180
Query: 184 DYLDDGTIFEAIRSRTVL 201
+Y+D+GT+ A+ R +
Sbjct: 181 EYVDEGTLSRALEGRRKI 198
>gnl|CDD|173775 cd01025, TOPRIM_recR, TOPRIM_recR: topoisomerase-primase (TOPRIM)
nucleotidyl transferase/hydrolase domain of the type
found in Escherichia coli RecR. RecR participates in
the RecFOR pathway of homologous recombinational repair
in prokaryotes. This pathway provides a single-stranded
DNA molecule coated with RecA to allow invasion of a
homologous molecule. The RecFOR system directs the
loading of RecA onto gapped DNA coated with SSB protein.
The TOPRIM domain has two conserved motifs, one of which
centers at a conserved glutamate and the other one at
two conserved aspartates (DxD). In RecR sequences this
glutamate in the first turn of the TOPRIM domain is
semiconserved, the DXD motif is not conserved.
Length = 112
Score = 156 bits (396), Expect = 4e-39
Identities = 54/109 (49%), Positives = 75/109 (68%)
Query: 83 SVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIREL 142
+ + VVE+ D+ A+E S LYHVLGG +SPLD IGP+D+ I L+ERI +++E+
Sbjct: 1 NKLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEV 60
Query: 143 IFAISATIEGQTTAHYIMDKLKGIDVKITRLAYGIPMGSELDYLDDGTI 191
I A + T+EG+ TA YI LK VK+TRLA GIP+G EL+Y D+ T+
Sbjct: 61 ILATNPTVEGEATALYIAKLLKDFGVKVTRLAQGIPVGGELEYADEITL 109
>gnl|CDD|145340 pfam02132, RecR, RecR protein.
Length = 41
Score = 51.7 bits (125), Expect = 1e-07
Identities = 20/41 (48%), Positives = 25/41 (60%)
Query: 41 QLLGPLAEAMANIYNKVCLCSICGNVDTTDPCAICIDQQRD 81
+ LAEA+ KV CS+CGN+ TDPC IC D +RD
Sbjct: 1 EEAERLAEALLEAKEKVRHCSVCGNLTETDPCEICSDPRRD 41
>gnl|CDD|145089 pfam01751, Toprim, Toprim domain. This is a conserved region from
DNA primase. This corresponds to the Toprim domain
common to DnaG primases, topoisomerases, OLD family
nucleases and RecR proteins. Both DnaG motifs IV and V
are present in the alignment, the DxD (V) motif may be
involved in Mg2+ binding and mutations to the conserved
glutamate (IV) completely abolish DnaG type primase
activity. DNA primase EC:2.7.7.6 is a
nucleotidyltransferase it synthesizes the
oligoribonucleotide primers required for DNA replication
on the lagging strand of the replication fork; it can
also prime the leading stand and has been implicated in
cell division. This family also includes the atypical
archaeal A subunit from type II DNA topoisomerases. Type
II DNA topoisomerases catalyse the relaxation of DNA
supercoiling by causing transient double strand breaks.
Length = 89
Score = 43.1 bits (102), Expect = 5e-05
Identities = 22/95 (23%), Positives = 41/95 (43%), Gaps = 7/95 (7%)
Query: 83 SVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERI-EVKKIRE 141
V+I+VE +D AL ++ L G LS + ++ + ++ K E
Sbjct: 1 KVLIIVEGPSDAIALAKAGGYKGNVVALLGHLS------DVIPLTKEQLKLLKKLAKKDE 54
Query: 142 LIFAISATIEGQTTAHYIMDKLKGIDVKITRLAYG 176
+I A EG+ A +++ LK + K+ R+
Sbjct: 55 VILATDPDREGEAIAWKLLELLKPLGKKVRRIFLP 89
>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain. This is a
nucleotidyl transferase/hydrolase domain found in type
IA, type IIA and type IIB topoisomerases, bacterial
DnaG-type primases, small primase-like proteins from
bacteria and archaea, OLD family nucleases from
bacterial and archaea, and bacterial DNA repair proteins
of the RecR/M family. This domain has two conserved
motifs, one of which centers at a conserved glutamate
and the other one at two conserved aspartates (DxD).
This glutamate and two aspartates, cluster together to
form a highly acid surface patch. The conserved
glutamate may act as a general base in nucleotide
polymerization by primases and in strand joining in
topoisomerases and, as a general acid in strand cleavage
by topisomerases and nucleases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 83
Score = 40.1 bits (94), Expect = 5e-04
Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 10/92 (10%)
Query: 83 SVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIREL 142
+I+VE +D AL ++ LGG + L++R+ + +E+
Sbjct: 1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHALNK---------TRELLKRLL-GEAKEV 50
Query: 143 IFAISATIEGQTTAHYIMDKLKGIDVKITRLA 174
I A A EG+ A +++ LK + K+ RL
Sbjct: 51 IIATDADREGEAIALRLLELLKSLGKKVRRLL 82
>gnl|CDD|145942 pfam03059, NAS, Nicotianamine synthase protein. Nicotianamine
synthase EC:2.5.1.43 catalyses the trimerisation of
S-adenosylmethionine to yield one molecule of
nicotianamine. Nicotianamine has an important role in
plant iron uptake mechanisms. Plants adopt two
strategies (termed I and II) of iron acquisition.
Strategy I is adopted by all higher plants except
graminaceous plants, which adopt strategy II. In
strategy I plants, the role of nicotianamine is not
fully determined: possible roles include the formation
of more stable complexes with ferrous than with ferric
ion, which might serve as a sensor of the physiological
status of iron within a plant, or which might be
involved in the transport of iron. In strategy II
(graminaceous) plants, nicotianamine is the key
intermediate (and nicotianamine synthase the key enzyme)
in the synthesis of the mugineic family (the only known
family in plants) of phytosiderophores.
Phytosiderophores are iron chelators whose secretion by
the roots is greatly increased in instances of iron
deficiency.
Length = 277
Score = 30.4 bits (69), Expect = 0.35
Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 14/80 (17%)
Query: 87 VVEDVADLWA-------LERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKI 139
+VE + DL+A L S VNAL+ L + P P I + L I+ +I
Sbjct: 9 LVEKILDLYAAISKLESLSPSPDVNALFTQLVTTCIP-----PSPIDVTKLGPEIQ--EI 61
Query: 140 RELIFAISATIEGQTTAHYI 159
R L+ + + EG +HY
Sbjct: 62 RSLLIRLCSEAEGLLESHYS 81
>gnl|CDD|33999 COG4277, COG4277, Predicted DNA-binding protein with the
Helix-hairpin-helix motif [General function prediction
only].
Length = 404
Score = 28.0 bits (62), Expect = 1.8
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 15 KILARIPGFGPRSARR 30
K L R+PG G +SARR
Sbjct: 330 KELLRVPGIGVKSARR 345
>gnl|CDD|146710 pfam04216, FdhE, Protein involved in formate dehydrogenase
formation. The function of these proteins is unknown.
They may possibly be involved in the formation of
formate dehydrogenase.
Length = 287
Score = 27.7 bits (62), Expect = 2.0
Identities = 16/64 (25%), Positives = 28/64 (43%), Gaps = 24/64 (37%)
Query: 60 CSICGN--------VDTTDP------CAIC------IDQQRDASVIIVVEDVA----DLW 95
C+ CG+ ++ +P C C +DQ++D + V +D+A DL
Sbjct: 212 CTNCGSTKGLAYWSLEEGEPGVRAETCDTCHSYLKILDQEKDPDLEPVADDLASLALDLL 271
Query: 96 ALER 99
A E+
Sbjct: 272 AREK 275
>gnl|CDD|30977 COG0632, RuvA, Holliday junction resolvasome, DNA-binding subunit
[DNA replication, recombination, and repair].
Length = 201
Score = 27.5 bits (61), Expect = 2.4
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 14 IKILARIPGFGPRSARRATLHLVKKKEQLLG 44
+K L++IPG G ++A R L L K L
Sbjct: 107 VKALSKIPGIGKKTAERIVLELKGKLAAFLK 137
>gnl|CDD|36325 KOG1109, KOG1109, KOG1109, Vacuole membrane protein VMP1 [General
function prediction only].
Length = 440
Score = 27.7 bits (61), Expect = 2.4
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 10 IENLIKILARIPGFGPRSARRATLHLVKKKEQLL 43
E + IL +PG G R R L++K++QLL
Sbjct: 339 FEERVSILDTVPGLGHR-LREPFRWLLEKQKQLL 371
>gnl|CDD|31216 COG1012, PutA, NAD-dependent aldehyde dehydrogenases [Energy
production and conversion].
Length = 472
Score = 27.6 bits (61), Expect = 2.6
Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 9/62 (14%)
Query: 82 ASVIIVVEDVADLWALERSKAVNALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRE 141
AS +IV E V D + +L +G L P +GP LI ++ ++
Sbjct: 279 ASRLIVHESVYDEFVERLVARAASL--KVGDPLDPSTDLGP-------LISEEQLDRVEG 329
Query: 142 LI 143
I
Sbjct: 330 YI 331
>gnl|CDD|133359 cd04159, Arl10_like, Arl10-like subfamily. Arl9/Arl10 was
identified from a human cancer-derived EST dataset. No
functional information about the subfamily is available
at the current time, but crystal structures of human
Arl10b and Arl10c have been solved.
Length = 159
Score = 26.5 bits (59), Expect = 5.1
Identities = 28/80 (35%), Positives = 41/80 (51%), Gaps = 13/80 (16%)
Query: 80 RDASVIIVVEDVADLWALERSKAVNALYHVLGG-SLS--PLDRIG-----PEDIGIQSLI 131
R + I+ V D AD ALE +K N L+ +L SL PL +G P + + LI
Sbjct: 66 RGVNAIVYVVDAADRTALEAAK--NELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELI 123
Query: 132 ERIEVKKI--RE-LIFAISA 148
E++ +K I RE ++IS
Sbjct: 124 EQMNLKSITDREVSCYSISC 143
>gnl|CDD|112424 pfam03606, DcuC, C4-dicarboxylate anaerobic carrier.
Length = 456
Score = 26.5 bits (59), Expect = 5.8
Identities = 11/48 (22%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 109 VLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTA 156
V+GG ++R G D G+++L++ ++ + I ++A T
Sbjct: 82 VVGGFAGVMNRTGAIDAGVKALVKPLKGIES-PYILLLAAYFSLGGTV 128
>gnl|CDD|133068 cd03856, M14_Nna1_like, Peptidase M14-like domain of Nna-1 (Nervous
system Nuclear protein induced by Axotomy), also known
as ATP/GTP binding protein (AGTPBP-1) and cytosolic
carboxypeptidase (CCP), and related proteins. The
Peptidase M14 family of metallocarboxypeptidases are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. This subfamily includes the human AGTPBP-1
and AGBL -2, -3, -4, and -5, and the mouse Nna1/CCP-1
and CCP -2 through -6. Nna1-like proteins are active
metallopeptidases that are thought to act on cytosolic
proteins such as alpha-tubulin, to remove a C-terminal
tyrosine. Nna1 is widely expressed in the developing and
adult nervous systems, including cerebellar Purkinje and
granule neurons, miral cells of the olfactory bulb and
retinal photoreceptors. Nna1 is also induced in
axotomized motor neurons. Mutations in Nna1 cause
Purkinje cell degeneration (pcd). The Nna1 CP domain is
required to prevent the retinal photoreceptor loss and
cerebellar ataxia phenotypes of pcd mice, and a
functional zinc-binding domain is needed for Nna-1 to
support neuron survival in these mice. Nna1-like
proteins from the different phyla are highly diverse,
but they all contain a characteristic N-terminal
conserved domain right before the CP domain. It has been
suggested that this N-terminal domain might act as a
folding domain.
Length = 269
Score = 25.9 bits (57), Expect = 7.4
Identities = 15/56 (26%), Positives = 23/56 (41%)
Query: 105 ALYHVLGGSLSPLDRIGPEDIGIQSLIERIEVKKIRELIFAISATIEGQTTAHYIM 160
AL L G+ L I G E + ++ IF I+ G+T A ++M
Sbjct: 18 ALCESLQGNSCDLLTITSPPEGNDIKYEHLCSFANKKYIFLIARVHPGETNASWVM 73
>gnl|CDD|143443 cd07125, ALDH_PutA-P5CDH, Delta(1)-pyrroline-5-carboxylate
dehydrogenase, PutA. The proline catabolic enzymes of
the aldehyde dehydrogenase (ALDH) protein superfamily,
proline dehydrogenase and
Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH,
(EC=1.5.1.12 )), catalyze the two-step oxidation of
proline to glutamate; P5CDH catalyzes the oxidation of
glutamate semialdehyde, utilizing NAD+ as the electron
acceptor. In some bacteria, the two enzymes are fused
into the bifunctional flavoenzyme, proline utilization A
(PutA) These enzymes play important roles in cellular
redox control, superoxide generation, and apoptosis. In
certain prokaryotes such as Escherichia coli, PutA is
also a transcriptional repressor of the proline
utilization genes.
Length = 518
Score = 25.6 bits (57), Expect = 8.8
Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 126 GIQSLIERIEVKKIRELIFA 145
GI S ER E++ RE + A
Sbjct: 440 GIHSRDER-EIEYWRERVEA 458
>gnl|CDD|35317 KOG0094, KOG0094, KOG0094, GTPase Rab6/YPT6/Ryh1, small G protein
superfamily [Intracellular trafficking, secretion, and
vesicular transport].
Length = 221
Score = 25.6 bits (56), Expect = 8.8
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 80 RDASVIIVVEDVADLWALERSK 101
RD+SV ++V D+ D + E +
Sbjct: 93 RDSSVAVIVYDITDRNSFENTS 114
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 0.139 0.398
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,379,398
Number of extensions: 120659
Number of successful extensions: 285
Number of sequences better than 10.0: 1
Number of HSP's gapped: 284
Number of HSP's successfully gapped: 26
Length of query: 201
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 112
Effective length of database: 4,340,536
Effective search space: 486140032
Effective search space used: 486140032
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 (25.0 bits)