RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780128|ref|YP_003064541.1| VRR-NUC domain-containing
protein [Candidatus Liberibacter asiaticus str. psy62]
(103 letters)
>gnl|CDD|149740 pfam08774, VRR_NUC, VRR-NUC domain.
Length = 96
Score = 50.5 bits (121), Expect = 1e-07
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 17 RLVTGAKKLDCWVRKASFVGRRGCPDRLIITPNGGL-WWIEVKKPTGRLSHQQMSEIEEL 75
R G K + + + R+G PD ++ P G +EVK P +LS +Q + ++ L
Sbjct: 23 RKNWGKKGAEALGKYFRYGLRKGVPDLILFLPPGKRFLLVEVKGPGDKLSPEQRAWLDRL 82
Query: 76 RRRGQRVKVLVSME 89
R G +V V S+E
Sbjct: 83 ARSGFKVAVCDSVE 96
>gnl|CDD|180076 PRK05429, PRK05429, gamma-glutamyl kinase; Provisional.
Length = 372
Score = 31.6 bits (73), Expect = 0.052
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 5/32 (15%)
Query: 60 PTGRLSHQQMSE----IEELRRRGQRVKVLVS 87
G L +++E I LR G V VLVS
Sbjct: 23 GGGGLDRARIAELARQIAALRAAGHEV-VLVS 53
>gnl|CDD|181960 PRK09567, nirA, ferredoxin-nitrite reductase; Reviewed.
Length = 593
Score = 30.4 bits (69), Expect = 0.11
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 51 GLWWIEVKKPTGRLSHQQMSEIEELRRR 78
GL WI V P GRL+ QM + ++ R
Sbjct: 373 GLNWIGVVLPVGRLTTDQMRGLAKIAAR 400
>gnl|CDD|173190 PRK14727, PRK14727, putative mercuric reductase; Provisional.
Length = 479
Score = 28.8 bits (64), Expect = 0.31
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 12/50 (24%)
Query: 39 GC-PDRLII-----------TPNGGLWWIEVKKPTGRLSHQQMSEIEELR 76
GC P +++I P G+ + G L HQQ + +EELR
Sbjct: 59 GCVPSKILIRAAQLAHQQRSNPFDGVEAVAPSIDRGLLLHQQQARVEELR 108
>gnl|CDD|152399 pfam11964, DUF3478, Protein of unknown function (DUF3478). This
family of proteins is functionally uncharacterized.
This protein is found in bacteria and archaea. Proteins
in this family are typically between 120 to 132 amino
acids in length. This protein has a single completely
conserved residue A that may be functionally important.
Length = 118
Score = 28.3 bits (64), Expect = 0.40
Identities = 7/40 (17%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 59 KPTGRLSHQQMSE----IEELRRRGQRVKVLVSMEEVDNF 94
K +G+L+H+ +E +V++L+ +++ + +
Sbjct: 16 KVSGKLTHEDYEVLIPALEAKLEEHGKVRLLIDLDDFEGW 55
>gnl|CDD|162287 TIGR01290, nifB, nitrogenase cofactor biosynthesis protein NifB.
This model describes NifB, a protein required for the
biosynthesis of the iron-molybdenum (or iron-vanadium)
cofactor used by the nitrogen-fixing enzyme nitrogenase.
Archaeal homologs lack the most C-terminal region and
score between the trusted and noise cutoffs of this
model.
Length = 442
Score = 26.7 bits (59), Expect = 1.3
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 52 LWWIEVKKPTGR-----LSHQQMSEIEELRRRGQRVKV 84
+W+ E ++ TGR L +Q+ +E+L RG VKV
Sbjct: 156 VWY-EGERYTGREAADLLIERQLEGLEKLTERGILVKV 192
>gnl|CDD|183048 PRK11239, PRK11239, hypothetical protein; Provisional.
Length = 215
Score = 26.6 bits (59), Expect = 1.5
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 74 ELRRRGQRVKVLVSMEEVDNFLEELA 99
ELR R R+ M EV++ LE+LA
Sbjct: 116 ELRSRAARMYEFSDMAEVESTLEQLA 141
>gnl|CDD|171551 PRK12512, PRK12512, RNA polymerase sigma factor; Provisional.
Length = 184
Score = 26.6 bits (59), Expect = 1.6
Identities = 13/28 (46%), Positives = 18/28 (64%), Gaps = 5/28 (17%)
Query: 72 IEELRRRGQRVKVLVSMEEVDNFLEELA 99
I+ LRRRG+RV V ++D+F E L
Sbjct: 90 IDALRRRGRRVFV-----DIDDFAETLP 112
>gnl|CDD|133958 PHA01753, PHA01753, Holliday junction resolvase.
Length = 121
Score = 26.4 bits (58), Expect = 1.8
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 32 ASFVGRRGCPDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRR 77
S G++ PD +I T N ++ IEVK + + +IE+L R
Sbjct: 30 VSGTGKQALPD-IIATKNNTIYPIEVKSTSKDVVTVDKFQIEKLFR 74
>gnl|CDD|132172 TIGR03128, RuMP_HxlA, 3-hexulose-6-phosphate synthase. at the
cost of also yielding formaldehyde. These latter
species tend usually have a formaldehyde-activating
enzyme to attach formaldehyde to the C1 carrier
tetrahydromethanopterin. In these species, the enzyme
is viewed as a lyase rather than a synthase and is
called D-arabino 3-hexulose 6-phosphate formaldehyde
lyase. Note that there is some overlap in specificity
with the Escherichia coli enzyme 3-keto-L-gulonate
6-phosphate decarboxylase.
Length = 206
Score = 26.2 bits (58), Expect = 2.2
Identities = 8/39 (20%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 54 WIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEEVD 92
IE+ T + ++ + ++E++ KVL ++ +D
Sbjct: 27 IIEIG--TPLIKNEGIEAVKEMKEAFPDRKVLADLKTMD 63
>gnl|CDD|178779 PLN03241, PLN03241, magnesium chelatase subunit H; Provisional.
Length = 1353
Score = 26.0 bits (57), Expect = 2.3
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 57 VKKPTGRLSHQQMSEIEELRRRGQRVKVLVSM 88
VK+ TGR+ ++ + EL R RV VL +M
Sbjct: 1018 VKEGTGRVVRYELIPLSELGR--PRVDVLCNM 1047
>gnl|CDD|130875 TIGR01816, sdhA_forward, succinate dehydrogenase, flavoprotein
subunit, E. coli/mitochondrial subgroup. Succinate
dehydrogenase and fumarate reductase are homologous
enzymes reversible in principle but favored under
different circumstances. This model represents a
narrowly defined clade of the succinate dehydrogenase
flavoprotein subunit as found in mitochondria, in
Rickettsia, in E. coli and other Proteobacteria, and in
a few other lineages. However, this model excludes all
known fumarate reductases. It also excludes putative
succinate dehydrogenases that appear to diverged before
the split between E. coli succinate dehydrogenase and
fumarate reductase.
Length = 565
Score = 25.9 bits (57), Expect = 2.4
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 10/53 (18%)
Query: 61 TGRLSHQQMSEIEELRRRGQRVKV----------LVSMEEVDNFLEELACTLY 103
TG + + + +I L+ R + VK+ LV E+ N LE T
Sbjct: 449 TGEVLQKGVEKISALKERYKNVKINDKSKVWNTDLVEALELQNLLECAEATAV 501
>gnl|CDD|173501 PTZ00265, PTZ00265, multidrug resistance protein (mdr1);
Provisional.
Length = 1466
Score = 25.8 bits (56), Expect = 2.5
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 8/44 (18%)
Query: 6 FHYQTEKDVEKRLVTGAKKLDCWVRKA---SFVGRRGCPDRLII 46
FHY T KDVE K L+ + + +FVG GC I+
Sbjct: 390 FHYDTRKDVEIY-----KDLNFTLTEGKTYAFVGESGCGKSTIL 428
>gnl|CDD|148371 pfam06728, PIG-U, GPI transamidase subunit PIG-U. Many
eukaryotic proteins are anchored to the cell surface
via glycosylphosphatidylinositol (GPI), which is
posttranslationally attached to the carboxyl-terminus
by GPI transamidase. The mammalian GPI transamidase is
a complex of at least four subunits, GPI8, GAA1, PIG-S,
and PIG-T. PIG-U is thought to represent a fifth
subunit in this complex and may be involved in the
recognition of either the GPI attachment signal or the
lipid portion of GPI.
Length = 174
Score = 25.6 bits (57), Expect = 2.9
Identities = 7/9 (77%), Positives = 8/9 (88%)
Query: 46 ITPNGGLWW 54
+TPN GLWW
Sbjct: 17 LTPNIGLWW 25
>gnl|CDD|161984 TIGR00663, dnan, DNA polymerase III, beta subunit. University).
Length = 367
Score = 25.8 bits (57), Expect = 3.0
Identities = 10/50 (20%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 54 WIEVKKPTGR---LSHQQMSEIEELRRRGQRVKVLVSMEEVDNFLEELAC 100
E+K+ R L+ ++ + + L G+++K +E+ EE+
Sbjct: 260 REELKEAIKRVSLLADEKRNLVLTLSENGKKLKESSDTQEIGEAEEEIEV 309
>gnl|CDD|151032 pfam10459, Peptidase_S46, Peptidase S46. Dipeptidyl-peptidase 7
(DPP-7) is the best characterized member of this family.
It is a serine peptidase that is located on the cell
surface and is predicted to have two N-terminal
transmembrane domains.
Length = 696
Score = 25.6 bits (57), Expect = 3.1
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 69 MSEIEELRRRGQRVKVLVSMEEV 91
S EEL G RV VLV + +V
Sbjct: 88 KSRAEELPAPGLRVYVLVRITDV 110
>gnl|CDD|152934 pfam12500, DUF3706, Protein of unknown function (DUF3706). This
domain family is found in bacteria, and is typically
between 174 and 217 amino acids in length. There is a
conserved TRSP sequence motif.
Length = 199
Score = 25.3 bits (56), Expect = 3.9
Identities = 13/52 (25%), Positives = 17/52 (32%), Gaps = 12/52 (23%)
Query: 46 ITPNGGLWWIEVKKPTGRL------SHQQMSEIEELR------RRGQRVKVL 85
GGL W TGR + + R+G+RV VL
Sbjct: 55 DVTRGGLPWPSYLPDTGRFGILPEDRAGLEAALAAAAARLAEVRKGERVLVL 106
>gnl|CDD|149699 pfam08722, TnsA_N, TnsA endonuclease N terminal. The Tn7
transposase is composed of proteins TnsA and TnsB. DNA
breakage at the 5' end of the transposon is carried out
by TnsA, and breakage and joining at the 3' end is
carried out by TnsB. The N terminal domain of TnsA is
catalytic.
Length = 81
Score = 25.2 bits (56), Expect = 3.9
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 41 PDRLIITPNGGLWWIEVKKPTGRLSHQQMSEIEELRRR 78
PD L+ +G +EV K + L ++ E E+ RR
Sbjct: 31 PDFLVTYKDGKPEAVEV-KYSEDLEDERTLEKFEIERR 67
>gnl|CDD|162024 TIGR00757, RNaseEG, ribonuclease, Rne/Rng family. The C-terminal
half of RNase E (excluded from the seed alignment for
this model) lacks ribonuclease activity but participates
in mRNA degradation by organizing the degradosome.
Length = 414
Score = 24.6 bits (54), Expect = 6.4
Identities = 11/22 (50%), Positives = 11/22 (50%)
Query: 72 IEELRRRGQRVKVLVSMEEVDN 93
I EL R GQ V V V E N
Sbjct: 80 ISELLRPGQSVLVQVVKEPRGN 101
>gnl|CDD|149435 pfam08371, PLD_envelope, Phospholipase D/viral envelope. This
domain is found in phospholipases and viral envelope
proteins between Phospholipase D (PLD) active site
motifs (pfam00641). PLD is associated with Golgi
membranes and alters their lipid content by the
conversion of phospholipids into phosphatidic acid,
which is thought to be involved in the regulation of
lipid movement. This might explain the prevalence of
this domain in viral envelope proteins.
Length = 163
Score = 24.5 bits (54), Expect = 6.8
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 9/35 (25%)
Query: 74 ELRR----RGQRVKVLVS-----MEEVDNFLEELA 99
LRR RG +V++L+S + FL+ L
Sbjct: 121 ALRRAAIERGVKVRLLISCWKHSDPSMFAFLKSLQ 155
>gnl|CDD|185641 PTZ00462, PTZ00462, Serine-repeat antigen protein; Provisional.
Length = 1004
Score = 24.3 bits (52), Expect = 8.0
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 83 KVLVSMEEVDNFLEE 97
K L+ +EE+D+FL+E
Sbjct: 374 KELIKLEELDDFLKE 388
>gnl|CDD|183520 PRK12421, PRK12421, ATP phosphoribosyltransferase regulatory
subunit; Provisional.
Length = 392
Score = 24.2 bits (53), Expect = 8.7
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 70 SEIEELRRRGQRVKVLVSMEEVDNFLEELACT 101
+ I ELR++G+RV L+ ++ + E C
Sbjct: 348 AAIAELRQQGERVVQLLPGDDGSS---EPGCD 376
>gnl|CDD|184712 PRK14501, PRK14501, putative bifunctional trehalose-6-phosphate
synthase/HAD hydrolase subfamily IIB; Provisional.
Length = 726
Score = 24.1 bits (53), Expect = 8.9
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 50 GGLW--WIEVKKPTGRLSHQQMSEIEELRRRGQRVKVLVSMEEVDNFLE 96
GGLW W + S +Q + IE V V +S EEVD + E
Sbjct: 42 GGLWVGWPGLD--LEEESEEQRARIEPRLEELGLVPVFLSAEEVDRYYE 88
>gnl|CDD|129833 TIGR00750, lao, LAO/AO transport system ATPase. Mutations have
also been found that do not phosphorylate the
periplasmic binding proteins, yet still allow
transport. The ATPase activity of this protein seems to
be necessary, however.
Length = 300
Score = 24.0 bits (52), Expect = 9.8
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 72 IEELRRRGQRVKVL 85
ELRRRG +V V+
Sbjct: 55 GMELRRRGLKVAVI 68
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 0.137 0.428
Gapped
Lambda K H
0.267 0.0880 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,748,270
Number of extensions: 102724
Number of successful extensions: 295
Number of sequences better than 10.0: 1
Number of HSP's gapped: 294
Number of HSP's successfully gapped: 50
Length of query: 103
Length of database: 5,994,473
Length adjustment: 70
Effective length of query: 33
Effective length of database: 4,481,913
Effective search space: 147903129
Effective search space used: 147903129
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: 50 (22.8 bits)