RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781211|ref|YP_003065624.1| hypothetical protein
CLIBASIA_05590 [Candidatus Liberibacter asiaticus str. psy62]
(234 letters)
>gnl|CDD|147324 pfam05088, Bac_GDH, Bacterial NAD-glutamate dehydrogenase. This
family consists of several bacterial proteins which are
closely related to NAD-glutamate dehydrogenase found in
Streptomyces clavuligerus. Glutamate dehydrogenases
(GDHs) are a broadly distributed group of enzymes that
catalyse the reversible oxidative deamination of
glutamate to ketoglutarate and ammonia.
Length = 1526
Score = 32.1 bits (74), Expect = 0.14
Identities = 12/60 (20%), Positives = 21/60 (35%), Gaps = 3/60 (5%)
Query: 43 RNPSSSSSSTEEAGEPKPPIEDYTLSCPDYVSE---AEVTAHIEAFKEAGVDARVAQKVV 99
RN E +P + P+ + + +A EAGV +A++V
Sbjct: 1336 RNRRQPLDIAAEIERFRPGVAALRPQLPELLPGEEREALEERAQALVEAGVPEALARRVA 1395
>gnl|CDD|34937 COG5373, COG5373, Predicted membrane protein [Function unknown].
Length = 931
Score = 32.3 bits (73), Expect = 0.14
Identities = 11/52 (21%), Positives = 16/52 (30%)
Query: 12 PSTPPVVECERSQRSNPPPSKEEAVQSDPQGRNPSSSSSSTEEAGEPKPPIE 63
P E S PP A + + S+ + A P P+E
Sbjct: 63 APLPAAAESIASPEVPPPVPPAPAQEGEAPAAEQPSAVPAPSAAPAPAEPVE 114
>gnl|CDD|38826 KOG3620, KOG3620, KOG3620, Uncharacterized conserved protein
[Function unknown].
Length = 1626
Score = 30.1 bits (67), Expect = 0.62
Identities = 10/62 (16%), Positives = 18/62 (29%), Gaps = 8/62 (12%)
Query: 10 PLPSTPPVVECERSQRSNPPPSK--------EEAVQSDPQGRNPSSSSSSTEEAGEPKPP 61
+P P + Q+ P E+ V + G S +S E +
Sbjct: 1202 VVPEPPSKNKGSPPQQEVKSPKPKKKGNKKPEQRVLKEQNGSADKMSKTSIPPGREEERE 1261
Query: 62 IE 63
+
Sbjct: 1262 RK 1263
>gnl|CDD|34842 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 30.0 bits (67), Expect = 0.64
Identities = 28/114 (24%), Positives = 42/114 (36%), Gaps = 15/114 (13%)
Query: 101 KLVDHGRKIGEQF-GASLE---EERKLLQTKLGSDYETREKDIARYFR-----KEKIPDN 151
D ++ E+ AS+E + + L +Y + +++ R R E D
Sbjct: 1663 LCFDEFNRLSEETMSASVELYLSSKDKTKFFLQMNYGYKPRELTRSLRAIFGYAETRIDT 1722
Query: 152 DVQSLISAWGFEKTFNFFDRYAQQNKESSTG-----DTFVRSEGSQEADRDFDK 200
SLI W E DR QQ KESST D +R+ A +
Sbjct: 1723 PDVSLIIDWYCEAIREKIDRLVQQ-KESSTSRQDLYDFGLRAIREMIAGHIGEA 1775
>gnl|CDD|111727 pfam02873, MurB_C, UDP-N-acetylenolpyruvoylglucosamine reductase,
C-terminal domain. Members of this family are
UDP-N-acetylenolpyruvoylglucosamine reductase enzymes
EC:1.1.1.158. This enzyme is involved in the
biosynthesis of peptidoglycan.
Length = 103
Score = 27.6 bits (62), Expect = 2.7
Identities = 14/31 (45%), Positives = 20/31 (64%), Gaps = 2/31 (6%)
Query: 95 AQKVVDKLVDHGR-KIGEQFGASLEEERKLL 124
A+ VVD L+ H R + E+FG LE E K++
Sbjct: 73 AEDVVD-LIRHVRQTVFEKFGIWLEPEVKII 102
>gnl|CDD|143456 cd07138, ALDH_CddD_SSP0762, Rhodococcus ruber 6-oxolauric acid
dehydrogenase-like. The 6-oxolauric acid dehydrogenase
(CddD) from Rhodococcus ruber SC1 which converts
6-oxolauric acid to dodecanedioic acid, and the aldehyde
dehydrogenase (locus SSP0762) from Staphylococcus
saprophyticus subsp. saprophyticus ATCC 15305 and other
similar sequences, are included in this CD.
Length = 466
Score = 27.5 bits (62), Expect = 3.3
Identities = 14/48 (29%), Positives = 23/48 (47%)
Query: 99 VDKLVDHGRKIGEQFGASLEEERKLLQTKLGSDYETREKDIARYFRKE 146
VD+ V R+ + A+ EER L ++ YE R ++A+ E
Sbjct: 38 VDRAVAAARRAFPAWSATSVEERAALLERIAEAYEARADELAQAITLE 85
>gnl|CDD|147126 pfam04812, HNF-1B_C, Hepatocyte nuclear factor 1 (HNF-1), beta
isoform C terminus. This family consists of a region
found within the alpha isoform and at the C terminus of
the beta isoform of the homeobox-containing
transcription factor of HNF-1. Different isoforms of
HNF-1 are generated by the differential use of
polyadenylation sites and by alternative splicing. The
C-terminal region of HNF-1 is responsible for the
activation of transcription. Mutations and
polymorphisms in HNF-1 cause the type 3 form of
maturity-onset diabetes of the young (MODY3).
Length = 233
Score = 27.6 bits (61), Expect = 3.5
Identities = 14/42 (33%), Positives = 18/42 (42%)
Query: 10 PLPSTPPVVECERSQRSNPPPSKEEAVQSDPQGRNPSSSSSS 51
ST P + S PPSK V+ QG +SSS+
Sbjct: 10 SAASTNPTLSHHSHSPSPGPPSKLHGVRYSQQGSCEVTSSST 51
>gnl|CDD|39814 KOG4614, KOG4614, KOG4614, Inner membrane protein required for
assembly of the F0 sector of ATP synthase
[Posttranslational modification, protein turnover,
chaperones].
Length = 287
Score = 27.4 bits (60), Expect = 3.9
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 118 EEERKLLQTKLGSDYETREKDIARYFRKEKIPD 150
E+ER L ++ Y R K++ K +IPD
Sbjct: 61 EDERARLNDEMTRGYFARMKELKEEGGKSQIPD 93
>gnl|CDD|144035 pfam00296, Bac_luciferase, Luciferase-like monooxygenase.
Length = 250
Score = 27.3 bits (61), Expect = 4.2
Identities = 12/42 (28%), Positives = 17/42 (40%), Gaps = 4/42 (9%)
Query: 53 EEAGEPKPPIEDYTLSCPDYV---SEAEVTAHIEAFKEAGVD 91
AG + S P V + +V + A+ EAGVD
Sbjct: 209 AAAGRDPADV-RVVASLPVIVAVGTPEQVAERLRAYAEAGVD 249
>gnl|CDD|114305 pfam05575, V_cholerae_RfbT, Vibrio cholerae RfbT protein. This
family consists of several RfbT proteins from Vibrio
cholerae. It has been found that genetic alteration of
the rfbT gene is responsible for serotype conversion of
Vibrio cholerae O1 and determines the difference between
the Ogawa and Inaba serotypes, in that the presence of
rfbT is sufficient for Inaba-to-Ogawa serotype
conversion.
Length = 286
Score = 26.6 bits (58), Expect = 5.6
Identities = 37/157 (23%), Positives = 68/157 (43%), Gaps = 20/157 (12%)
Query: 72 YVSEAEVTAHIEAFKEAGVDARVAQKVVDKLVDH---GRKIGEQFGASLEEERKLLQTKL 128
++++ ++ A IE E R+ ++ + LV+ G IGE G ++ E + ++
Sbjct: 100 HITQGKIIA-IEPLTEMENSIRMNVQLNNPLVEFHHFGCAIGENEGENIFEVYEF-DNRV 157
Query: 129 GSDYETREKDIARYFRKEKI-----------PDNDVQSLISAWGFE-KTFNFFDRYAQQN 176
S Y + DIA + ++ P N V I A G E + N + +++
Sbjct: 158 SSLYFKKNTDIADKVKNSQVLVRKLSSLDISPTNSVVIKIDAEGAEIEILNQIYEFTEKH 217
Query: 177 KESSTGDTFVRSEGS-QEADRDFDKVFN--TPDFGSR 210
F + G Q ++R FD++FN FGS+
Sbjct: 218 NGIEYYICFEFAMGHIQRSNRTFDEIFNIINSKFGSK 254
>gnl|CDD|145079 pfam01735, PLA2_B, Lysophospholipase catalytic domain. This family
consists of Lysophospholipase / phospholipase B
EC:3.1.1.5 and cytosolic phospholipase A2 EC:3.1.4 which
also has a C2 domain pfam00168. Phospholipase B enzymes
catalyse the release of fatty acids from
lysophsopholipids and are capable in vitro of
hydrolysing all phospholipids extractable form yeast
cells. Cytosolic phospholipase A2 associates with
natural membranes in response to physiological increases
in Ca2+ and selectively hydrolyses arachidonyl
phospholipids, the aligned region corresponds the the
carboxy-terminal Ca2+-independent catalytic domain of
the protein as discussed in.
Length = 490
Score = 26.5 bits (59), Expect = 5.9
Identities = 18/88 (20%), Positives = 30/88 (34%), Gaps = 8/88 (9%)
Query: 123 LLQTKLGSDYETREKDIARYFRKEKIPDNDVQSLISAWGFEKTFNFFDRYAQQNKESSTG 182
LL S + + ++F K+ D+D S F+ + Q +S T
Sbjct: 239 LLVINSTSSLPSFLNILIKHFLKDLSEDSDDISQYPPNPFQDANDINQNATQSIVDSDTL 298
Query: 183 DTFVRSEGSQ--------EADRDFDKVF 202
E Q + +RD D +F
Sbjct: 299 FLVDGGEDGQNIPLWPLLQPERDVDVIF 326
>gnl|CDD|37018 KOG1807, KOG1807, KOG1807, Helicases [Replication, recombination
and repair].
Length = 1025
Score = 26.1 bits (57), Expect = 7.5
Identities = 25/125 (20%), Positives = 45/125 (36%), Gaps = 6/125 (4%)
Query: 18 VECERSQRSNPPPSKEEAVQSDPQGRNPSSSSSSTEEAGEPKPPIEDYTLSCPDYVSEAE 77
+E E S+R PP + E + + +++ E EP +E Y P + E
Sbjct: 84 IENESSERKCPPSTVGEHSMQEKRFSLTELTNALFEVEKEPAIDMESYRTL-PSRPTLEE 142
Query: 78 VTAHIEAFKEAGVDARVAQKVVDKLVD-HGRKIGEQFGASLEEERKLLQTKLGSDYETRE 136
+ + + + +D H R + E F + L E LL K +
Sbjct: 143 QVLATDPVLSNRIGGKY--DSLWSYLDLHFRLLREDFVSPLREGILLL--KKNKNLLGAR 198
Query: 137 KDIAR 141
+A+
Sbjct: 199 AAVAK 203
>gnl|CDD|39437 KOG4236, KOG4236, KOG4236, Serine/threonine protein kinase PKC
mu/PKD and related proteins [Signal transduction
mechanisms].
Length = 888
Score = 26.2 bits (57), Expect = 7.6
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 4/44 (9%)
Query: 99 VDKLVDHGRKIGEQFGASLEEERKLLQTKLGSDYETREKDIARY 142
VDK + H Q L E L+ ++G Y T E D AR+
Sbjct: 813 VDKSLSHPWLQDYQTWLDLRE----LEVRIGERYITHESDDARW 852
>gnl|CDD|38806 KOG3600, KOG3600, KOG3600, Thyroid hormone receptor-associated
protein complex, subunit TRAP240 [Transcription].
Length = 2238
Score = 26.2 bits (57), Expect = 7.7
Identities = 8/29 (27%), Positives = 12/29 (41%)
Query: 28 PPPSKEEAVQSDPQGRNPSSSSSSTEEAG 56
PP S E + D R + + E+ G
Sbjct: 324 PPTSPEYGCRGDVSCRQCAEAEYQGEDGG 352
>gnl|CDD|37788 KOG2577, KOG2577, KOG2577, Transcription factor E2F/dimerization
partner (TDP) [Transcription].
Length = 354
Score = 26.2 bits (57), Expect = 7.8
Identities = 12/52 (23%), Positives = 21/52 (40%)
Query: 2 SDETDQLTPLPSTPPVVECERSQRSNPPPSKEEAVQSDPQGRNPSSSSSSTE 53
+ + +P + E S NP S+E S+ PS+S+S +
Sbjct: 258 GSSSSSEDTISPSPYLPEQPASLALNPQQSEELLDSSNLLSFFPSTSASGSS 309
>gnl|CDD|173951 cd08192, Fe-ADH7, Iron-containing alcohol dehydrogenases-like,
involved in the linear alkylbenzenesulfonate (LAS)
degradation pathway. NAD-dependent iron-containing
alcohol dehydrogenase-like. Proteins in this family are
NAD-dependent alcohol dehydrogenases which are involved
in the linear alkylbenzenesulfonate (LAS) degradation
pathway. They catalyze the oxidation of beta-hydroxy
CoA ester to beta-oxo CoA ester, which then be subject
to CoA-dependent thiolysis to yield acetyl-CoA and
6-C8-SPC-CoA. The major laundry surfactant in worldwide
use is commercial linear alkylbenzenesulfonate (LAS)
which contains 20 congeners of linear alkanes (C10 to
C13). LAS is fully biodegradable in oxic environments.
Degradation involves microbial communities.
Parvibaculum lavamentivorans DS-1T is a representative
member of many heterotrophic, LAS-degrading
communities, in which it catalyzes the first steps of
LAS degradation. Strain DS-1T is a small heterotrophic
bacterium able to omega-oxygenate the commercial
surfactant linear alkylbenzenesulfonate (LAS) and
shorten the side chain by beta-oxidation to yield
sulfophenylcarboxylates (SPC). Parvibaculum
lavamentivorans utilizes 3-C12-LAS as the sole carbon
and energy source, and excretes largely 4-C6-SPC.
Length = 370
Score = 26.4 bits (59), Expect = 7.9
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 74 SEAEVTAHIEAFKEAGVDARVA 95
+EA V A + A++ G D +A
Sbjct: 66 TEAAVEAGLAAYRAGGCDGVIA 87
>gnl|CDD|143482 cd00622, PLPDE_III_ODC, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Ornithine Decarboxylase. This
subfamily is composed mainly of eukaryotic ornithine
decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes
from prokaryotes represented by Vibrio vulnificus
LysineOrnithine decarboxylase. These are fold type III
PLP-dependent enzymes that differ from most bacterial
ODCs which are fold type I PLP-dependent enzymes. ODC
participates in the formation of putrescine by
catalyzing the decarboxylation of ornithine, the first
step in polyamine biosynthesis. Members of this
subfamily contain an N-terminal PLP-binding TIM-barrel
domain and a C-terminal beta-sandwich domain, similar to
bacterial alanine racemases. They exist as homodimers
with active sites that lie at the interface between the
TIM barrel domain of one subunit and the beta-sandwich
domain of the other subunit. Homodimer formation and the
presence of the PLP cofactor are required for catalytic
activity. Also members of this subfamily are proteins
with homology to ODC but do not possess any catalytic
activity, the Antizyme inhibitor (AZI) and ODC-paralogue
(ODC-p). AZI binds to the regulatory protein Antizyme
with a higher affinity than ODC and prevents ODC
degradation. ODC-p is a novel ODC-like protein, present
only in mammals, that is specifically exressed in the
brain and testes. ODC-p may function as a
tissue-specific antizyme inhibitory protein.
Length = 362
Score = 25.9 bits (58), Expect = 8.8
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 74 SEAEVTAHIEAFKEAGVDARVAQKVVDKLVDHGRKIGEQFGASLEEERKLLQT 126
SE E+ + A + R+A L RK FGA EE R+LL+
Sbjct: 99 SEDELEKIAKHAPGAKLLLRIATDDSGALCPLSRK----FGADPEEARELLRR 147
>gnl|CDD|35786 KOG0566, KOG0566, KOG0566, Inositol-1,4,5-triphosphate 5-phosphatase
(synaptojanin), INP51/INP52/INP53 family [Intracellular
trafficking, secretion, and vesicular transport].
Length = 1080
Score = 26.1 bits (57), Expect = 9.6
Identities = 17/72 (23%), Positives = 26/72 (36%), Gaps = 10/72 (13%)
Query: 8 LTPLPSTPPVVECERSQRSNPPPSKEEAVQSDPQGRNPSSSSSSTEEAGEPKPPIEDYTL 67
L P P PP S RS P +K + ++ + +S S A P Y +
Sbjct: 982 LIPRPIRPP------SARSPSPSAKSPS-PTEAPNSSSTSMPSPASAATLSGPW---YVI 1031
Query: 68 SCPDYVSEAEVT 79
S P ++
Sbjct: 1032 SKPLAPPQSNNG 1043
>gnl|CDD|30613 COG0264, Tsf, Translation elongation factor Ts [Translation,
ribosomal structure and biogenesis].
Length = 296
Score = 26.0 bits (57), Expect = 9.7
Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 5/69 (7%)
Query: 74 SEAEVTAHIEAFKEAGVDARVAQKVVDKL---VDHGRKIGEQFGASLEEERKLLQTKLGS 130
E + A F+E ++A+ ++K V+ + E G ++EEE L K+G
Sbjct: 80 CETDFVAKNAEFQELA--NKIAKAALEKKPADVEELKAAFEPGGKTVEEEIAALIAKIGE 137
Query: 131 DYETREKDI 139
+ R +
Sbjct: 138 NISLRRFAV 146
>gnl|CDD|107203 cd01560, Thr-synth_2, Threonine synthase catalyzes the final step
of threonine biosynthesis. The conversion of
O-phosphohomoserine into threonine and inorganic
phosphate is pyridoxal 5'-phosphate dependent. The
Thr-synth_1 CD includes members from higher plants,
cyanobacteria, archaebacteria and eubacterial groups.
This CD, Thr-synth_2, includes enzymes from fungi and
eubacterial groups, as well as, metazoan threonine
synthase-like proteins..
Length = 460
Score = 26.0 bits (58), Expect = 10.0
Identities = 11/50 (22%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 124 LQTKLGSDYETREKDIARYFRKEKIPDNDVQSLISAWGFEKTFNFFDRYA 173
+ + G Y+ ++ F ++IP++D++SLI ++ ++FF
Sbjct: 42 IASWSGLSYQELAFEVLSLFIGDEIPEDDLKSLI-----DRAYSFFRHPD 86
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
0.308 0.126 0.355
Gapped
Lambda K H
0.267 0.0535 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,769,470
Number of extensions: 138225
Number of successful extensions: 577
Number of sequences better than 10.0: 1
Number of HSP's gapped: 575
Number of HSP's successfully gapped: 58
Length of query: 234
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 143
Effective length of database: 4,297,318
Effective search space: 614516474
Effective search space used: 614516474
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 56 (25.8 bits)