RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781207|ref|YP_003065620.1| hypothetical protein
CLIBASIA_05570 [Candidatus Liberibacter asiaticus str. psy62]
(80 letters)
>gnl|CDD|163264 TIGR03437, Soli_cterm, Solibacter uncharacterized C-terminal
domain. This model describes a protein domain found in
90 proteins of Solibacter usitatus Ellin6076, nearly
always as the C-terminal domain of a much larger
protein. No homologs to this domain are detected outside
of S. usitatus, a member of the Acidobacteria.
Length = 215
Score = 29.2 bits (66), Expect = 0.23
Identities = 11/41 (26%), Positives = 18/41 (43%)
Query: 11 AATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGAS 51
+ G A ++ LA + V + GV A V+ AG +
Sbjct: 134 PTSPAVADGAPAPSSPLAPALAPVTVTIGGVPATVLYAGLA 174
>gnl|CDD|151927 pfam11490, DNA_pol3_alph_N, DNA polymerase III polC-type
N-terminus. This is an N-terminal domain of DNA
polymerase III polC subunit A that is found only in
Firmicutes. DNA polymerase polC-type III enzyme
functions as the 'replicase' in low G + C Gram-positive
bacteria. Purine asymmetry is a characteristic of
organisms with a heterodimeric DNA polymerase III
alpha-subunit constituted by polC which probably plays a
direct role in the maintenance of strand-biased gene
distribution; since, among prokaryotic genomes, the
distribution of genes on the leading and lagging strands
of the replication fork is known to be biased. The
domain is associated with DNA_pol3_alpha pfam07733.
Length = 180
Score = 28.1 bits (63), Expect = 0.59
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 50 ASDLAMHKMREQ-EEEEKKLLKKGLKKRQKN 79
+S+ + + EQ EEEE KL ++ L+ +K
Sbjct: 140 SSEEEIEEFEEQKEEEEAKLAEEALEALKKK 170
>gnl|CDD|184359 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 27.2 bits (61), Expect = 0.94
Identities = 15/38 (39%), Positives = 17/38 (44%), Gaps = 1/38 (2%)
Query: 15 GAVVGT-VATAAALATPIGWVGAAVAGVGAAVVGAGAS 51
GA VGT +A A G A G AA GA A+
Sbjct: 272 GAAVGTGLAAGGAAVAAAAGAGLAAGGGAAAAGGAAAA 309
Score = 26.0 bits (58), Expect = 2.2
Identities = 16/41 (39%), Positives = 17/41 (41%)
Query: 11 AATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGAS 51
T A G AAA A GAA AG AA GA+
Sbjct: 275 VGTGLAAGGAAVAAAAGAGLAAGGGAAAAGGAAAAARGGAA 315
>gnl|CDD|181451 PRK08506, PRK08506, replicative DNA helicase; Provisional.
Length = 472
Score = 26.5 bits (59), Expect = 1.5
Identities = 10/25 (40%), Positives = 20/25 (80%)
Query: 56 HKMREQEEEEKKLLKKGLKKRQKNY 80
+K RE++E+EKK K+G ++R+ ++
Sbjct: 390 YKEREEKEKEKKAKKEGKEERRIHF 414
>gnl|CDD|173559 PTZ00366, PTZ00366, Surface antigen (SAG) superfamily;
Provisional.
Length = 392
Score = 26.5 bits (59), Expect = 1.6
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 11 AATVGAVVGTV--ATAAALATPIGWVGAAVAGVGAAVVG 47
A + V+ TV A++A+ A+ V A +G AA+ G
Sbjct: 349 ATSSCNVIVTVKAASSASSASSSLQVVATASGA-AALTG 386
>gnl|CDD|152276 pfam11840, DUF3360, Protein of unknown function (DUF3360). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 489 to 517 amino acids in
length.
Length = 491
Score = 26.2 bits (58), Expect = 2.1
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 7 ITSIAATVGAVVGTVATAAALATPIG 32
+ ++AAT+G VV A AA A P+G
Sbjct: 62 VPAMAATIGKVVMVSAVVAAFAAPLG 87
>gnl|CDD|185582 PTZ00373, PTZ00373, 60S Acidic ribosomal protein P2; Provisional.
Length = 112
Score = 26.0 bits (57), Expect = 2.3
Identities = 16/37 (43%), Positives = 17/37 (45%)
Query: 32 GWVGAAVAGVGAAVVGAGASDLAMHKMREQEEEEKKL 68
G AA GAA GA A K E+EEEE L
Sbjct: 70 GVAAAAAPAAGAATAGAKAEAKKEEKKEEEEEEEDDL 106
>gnl|CDD|152736 pfam12301, CD99L2, CD99 antigen like protein 2. This family of
proteins is found in eukaryotes. Proteins in this family
are typically between 165 and 237 amino acids in length.
CD99L2 and CD99 are involved in trans-endothelial
migration of neutrophils in vitro and in the recruitment
of neutrophils into inflamed peritoneum.
Length = 154
Score = 25.9 bits (57), Expect = 2.5
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 28 ATPIGWVGAAVAGVGAAVVGAGASDLAMHKMR 59
G + V+ V A++GA +S +A K +
Sbjct: 107 GAETGTIAGIVSAVAVALLGAVSSYIAYQKKK 138
>gnl|CDD|149583 pfam08581, Tup_N, Tup N-terminal. The N-terminal domain of the
Tup protein has been shown to interact with the Ssn6
transcriptional co-repressor.
Length = 79
Score = 25.7 bits (57), Expect = 2.6
Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 52 DLAMH--KMREQEEEEKKLLKKGLKKR 76
+L KM+++ EEE LK+ L+ R
Sbjct: 50 ELEQAHRKMKQKYEEEIARLKRELEAR 76
>gnl|CDD|148271 pfam06566, Chon_Sulph_att, Chondroitin sulphate attachment
domain. This family represents the chondroitin
sulphate attachment domain of vertebrate neural
transmembrane proteoglycans that contain EGF modules.
Evidence has been accumulated to support the idea that
neural proteoglycans are involved in various cellular
events including mitogenesis, differentiation, axonal
outgrowth and synaptogenesis. This domain contains
several potential sites of chondroitin sulphate
attachment, as well as potential sites of N-linked
glycosylation.
Length = 253
Score = 25.7 bits (56), Expect = 2.7
Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 4 WNSITSIAATVGAVVGTVA--TAAALATPIGWVGAAVAGVGAAVVGAGASD 52
+ S A VG VG A+A TP W+ A+ G+G AG+ D
Sbjct: 45 PEEVGSEEAPVGPGVGPEEGLEASAAVTPTAWLEASSPGLGGVTAEAGSGD 95
>gnl|CDD|177560 PHA03231, PHA03231, glycoprotein BALF4; Provisional.
Length = 829
Score = 25.3 bits (56), Expect = 3.2
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 9/39 (23%)
Query: 3 FWNSITSIAATVGAVVGTVATAAALATPIGWVGAAVAGV 41
F + ++ VG VV VA A VG+ V+GV
Sbjct: 667 FMQGLGAVGKAVGNVVSGVAGA---------VGSIVSGV 696
>gnl|CDD|129854 TIGR00771, DcuC, c4-dicarboxylate anaerobic carrier family protein.
catalyzing fumarate-succinate exchange and fumarate
uptake.
Length = 388
Score = 25.2 bits (55), Expect = 3.8
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 1/58 (1%)
Query: 1 MGFWNSITSIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVG-AGASDLAMHK 57
+ F +I A +G + A+A +G + +AGV G A S + K
Sbjct: 320 IAFNTAIPPHAVELGYTHVNLGMPMAIAGALGRTASPIAGVVVVCAGLAMVSPFEVVK 377
>gnl|CDD|173571 PTZ00378, PTZ00378, hypothetical protein; Provisional.
Length = 518
Score = 25.2 bits (55), Expect = 3.9
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 3/61 (4%)
Query: 9 SIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGASDLAMHKMREQEEEEKKL 68
++ V + G ATAA LA +G G+ +A S LA R+ E ++
Sbjct: 427 AVTVLVQTLAGNAATAAHLAVAMGARFLCSGGLFSAHQCEVVSQLA---SRQDELTHSRM 483
Query: 69 L 69
L
Sbjct: 484 L 484
>gnl|CDD|130706 TIGR01645, half-pint, poly-U binding splicing factor, half-pint
family. In the case of PUF60 (GP|6176532), in complex
with p54, and in the presence of U2AF, facilitates
association of U2 snRNP with pre-mRNA.
Length = 612
Score = 25.0 bits (54), Expect = 4.0
Identities = 20/44 (45%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 12 ATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGASDLAM 55
ATV A+ A AAA AT + AA A GAAV+G A A
Sbjct: 292 ATVSAIPAAAAVAAAAAT--AKIMAAEAVAGAAVLGPRAQSPAT 333
>gnl|CDD|115462 pfam06805, Lambda_tail_I, Bacteriophage lambda tail assembly
protein I. This family consists of several
Bacteriophage lambda tail assembly protein I and related
phage and bacterial sequences. Members of this family
are typically around 200 residues in length. The
function of this family is unknown.
Length = 194
Score = 25.1 bits (55), Expect = 4.1
Identities = 13/36 (36%), Positives = 16/36 (44%)
Query: 16 AVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGAS 51
++G V A T GA AG GA + GAS
Sbjct: 93 TILGAVLIVAGFFTAGASAGAGAAGAGAFLFSLGAS 128
>gnl|CDD|131845 TIGR02798, ligK_PcmE, 4-carboxy-4-hydroxy-2-oxoadipate
aldolase/oxaloacetate decarboxylase. Members of this
protein family 4-carboxy-4-hydroxy-2-oxoadipate
aldolase, also called 4-oxalocitramalate aldolase. This
enzyme of the protocatechuate 4,5-cleavage pathway
converts its substrate to pyruvate plus oxaloacetate.
Protocatechuate is an intermediate in many pathways for
degrading aromatic compounds, including lignin,
fluorene, etc. Hara, et al. showed the LigK gene was not
only a 4-carboxy-4-hydroxy-2-oxoadipate aldolase but
also the enzyme of the following step, oxaloacetate
decarboxylase.
Length = 222
Score = 24.8 bits (54), Expect = 5.0
Identities = 19/59 (32%), Positives = 26/59 (44%)
Query: 9 SIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGASDLAMHKMREQEEEEKK 67
++ AT+G+V V A AL P V A GV + L + RE EE K+
Sbjct: 137 TVKATLGSVNIPVVCANALVNPGDVVVADDDGVVVVPRANAGAVLDAAQAREANEEAKR 195
>gnl|CDD|149170 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 24.9 bits (55), Expect = 5.3
Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 57 KMREQE------EEEKKLLKKGLKKRQK 78
+ RE + EE++K +K KK +
Sbjct: 294 EEREAKLAKLSPEEQRKYEEKERKKEAR 321
Score = 23.7 bits (52), Expect = 9.5
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 54 AMHKMREQEEEEKKLLKKGLKKRQKN 79
A + R++E +EKK KK ++ K
Sbjct: 275 AAEEERQEEAQEKKEEKKKEEREAKL 300
>gnl|CDD|151650 pfam11208, DUF2992, Protein of unknown function (DUF2992). This
bacterial family of proteins has no known function.
Length = 132
Score = 24.5 bits (54), Expect = 5.4
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 57 KMREQEEEEKKLLKKGLKKRQK 78
K +++EE+E+K K KK+ K
Sbjct: 107 KEKKEEEKERKRQLKQQKKKAK 128
>gnl|CDD|149683 pfam08703, PLC-beta_C, PLC-beta C terminal. This domain
corresponds to the alpha helical C terminal domain of
phospholipase C beta.
Length = 185
Score = 24.4 bits (53), Expect = 6.5
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 55 MHKMREQEEEEKKLLKKGLKKRQKN 79
+ K++E E+EKK LKK L +++
Sbjct: 58 LKKLKEICEKEKKELKKKLDRKRLE 82
>gnl|CDD|163530 TIGR03818, MotA1, flagellar motor stator protein MotA. This model
represents one family of MotA proteins which are often
not identified by the "transporter, MotA/TolQ/ExbB
proton channel family" model, pfam01618.
Length = 282
Score = 24.4 bits (54), Expect = 6.6
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 14 VGAVVGTVATAAALATPIGWVGAAVAGVGAAVVG 47
V AV+G V T ++ P +G +A AA+VG
Sbjct: 178 VAAVLGVVITMGSIDGPPEVLGVLIA---AALVG 208
>gnl|CDD|177761 PLN00162, PLN00162, transport protein sec23; Provisional.
Length = 761
Score = 24.1 bits (53), Expect = 7.4
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 22 ATAAALATPIGWVGAAVAGVGAAVV 46
T AAL+ G +GA V G GA ++
Sbjct: 263 CTGAALSVAAGLLGACVPGTGARIM 287
>gnl|CDD|150600 pfam09946, DUF2178, Predicted membrane protein (DUF2178). This
domain, found in various hypothetical archaeal
proteins, has no known function.
Length = 111
Score = 24.2 bits (53), Expect = 7.6
Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 10/58 (17%)
Query: 9 SIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGASDLAMHKMREQEEEEK 66
I +GA+VG A G + V A + G A ++ E+E+
Sbjct: 9 LIVIIMGAIVG-------WAVSSGN---PLVAVLAVIAGILAIYFLKSRVDGVVEDER 56
>gnl|CDD|184041 PRK13413, mpi, multiple promoter invertase; Provisional.
Length = 200
Score = 24.3 bits (53), Expect = 8.0
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 56 HKMREQEEEEKKLLKKGLKKR 76
+K+ +EE+ KKLL KG K
Sbjct: 156 YKLTGKEEKIKKLLDKGTSKS 176
>gnl|CDD|163311 TIGR03534, RF_mod_PrmC, protein-(glutamine-N5) methyltransferase,
release factor-specific. Members of this protein
family are HemK (PrmC), a protein once thought to be
involved in heme biosynthesis but now recognized to be
a protein-glutamine methyltransferase that modifies the
peptide chain release factors. All members of the seed
alignment are encoded next to the release factor 1 gene
(prfA) and confirmed by phylogenetic analysis. SIMBAL
analysis (manuscript in prep.) shows the motif
[LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers
specificity for the release factors rather than for
ribosomal protein L3.
Length = 251
Score = 24.0 bits (53), Expect = 8.1
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 51 SDLAMHKMREQEEEEKKLLKKGLKKRQKNY 80
+DL +H +E EE + L +R K
Sbjct: 15 TDLLLHPEKELTPEELARFEALLARRAKGE 44
>gnl|CDD|151929 pfam11492, Dicistro_VP4, Cricket paralysis virus, VP4. This is a
family of minor capsid proteins, known as VP4, from the
dicistroviridae. The dicistroviridae is a group of
small, RNA-containing viruses that are closely
structurally related to the picornaviridae. VP4 is a
short, extended polypeptide chain found within the
viral capsid, at the interface between the external
protein shell and packaged RNA genome.
Length = 56
Score = 24.2 bits (53), Expect = 8.2
Identities = 10/40 (25%), Positives = 17/40 (42%), Gaps = 3/40 (7%)
Query: 5 NSITSIAATVGAVVGTVATA---AALATPIGWVGAAVAGV 41
I+ A+TV V +++ +A WV AV +
Sbjct: 11 GVISKPASTVSEVASALSSIPVIGNIAKATSWVSDAVGDI 50
>gnl|CDD|147912 pfam06011, TRP, Transient receptor potential (TRP) ion channel.
This family of proteins are transient receptor potential
(TRP) ion channels. They are essential for cellular
viability and are involved in cell growth and cell wall
synthesis. The genes for these proteins are homologous
to polycystic kidney disease related ion channel genes.
Length = 532
Score = 24.1 bits (53), Expect = 8.5
Identities = 16/69 (23%), Positives = 25/69 (36%), Gaps = 18/69 (26%)
Query: 6 SITSIAATVGAVVGTVATAAALA------TP--------IGWVGAAVAGVGAAVVGA--- 48
++ + ATV V + T LA + + W A +AG+G
Sbjct: 106 TVPDLDATVRVGVYSTDTGTVLACVQATLSNGKTVSQKAVKWATAVIAGLGLLASAFASI 165
Query: 49 -GASDLAMH 56
G S+ A H
Sbjct: 166 YGPSNTAAH 174
>gnl|CDD|162094 TIGR00893, 2A0114, d-galactonate transporter.
Length = 399
Score = 23.8 bits (52), Expect = 8.8
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 10 IAATVGAVVGTVATAAALATPIGWVGAAVAGVG 42
IA G ++ ++ + PI +GA A G
Sbjct: 344 IAGLTGGLINSLGNLGGIVGPIV-IGAIAATTG 375
>gnl|CDD|178188 PLN02576, PLN02576, protoporphyrinogen oxidase.
Length = 496
Score = 23.8 bits (52), Expect = 8.9
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 29 TPIGWVGAAVAGVGAAVVGAGASDLA 54
+ I AA + AVVGAG S LA
Sbjct: 1 SAIAEGSAAASSKDVAVVGAGVSGLA 26
>gnl|CDD|165416 PHA03145, PHA03145, helicase-primase primase subunit; Provisional.
Length = 1058
Score = 23.8 bits (51), Expect = 8.9
Identities = 12/35 (34%), Positives = 15/35 (42%)
Query: 17 VVGTVATAAALATPIGWVGAAVAGVGAAVVGAGAS 51
++G +A A L P GW A G GA A
Sbjct: 454 MLGRLAEAERLLVPHGWPAFAPPKPGEGDGGATAP 488
>gnl|CDD|173158 PRK14695, PRK14695, serine/threonine transporter SstT; Provisional.
Length = 319
Score = 23.9 bits (51), Expect = 9.6
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 6 SITSIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGASDLA 54
++ +A T+ + T+ T L P+ + A V V AA+ GAS +A
Sbjct: 211 NMAGVAITINLL--TLVTVNTLGIPVDFATAFVLSVVAAISACGASGIA 257
>gnl|CDD|177542 PHA03144, PHA03144, helicase-primase primase subunit; Provisional.
Length = 746
Score = 23.9 bits (52), Expect = 9.8
Identities = 14/42 (33%), Positives = 17/42 (40%)
Query: 3 FWNSITSIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAA 44
WN T VG + + A AA A + AAVA A
Sbjct: 572 LWNRRTDTEDFVGFPLRSAAARAAKAALRALLRAAVADSADA 613
>gnl|CDD|151469 pfam11022, DUF2611, Protein of unknown function (DUF2611). This
family is conserved in the Dikarya of Fungi. The
function is not known.
Length = 70
Score = 23.9 bits (52), Expect = 9.8
Identities = 16/50 (32%), Positives = 24/50 (48%)
Query: 31 IGWVGAAVAGVGAAVVGAGASDLAMHKMREQEEEEKKLLKKGLKKRQKNY 80
IG +G+ GV A G A A + ++E+K +K+ LKK K
Sbjct: 19 IGTLGSLFGGVALATGGKKAPKPATPPINASSKDEEKFIKEFLKKHSKEE 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
0.313 0.126 0.355
Gapped
Lambda K H
0.267 0.0827 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,278,754
Number of extensions: 75067
Number of successful extensions: 619
Number of sequences better than 10.0: 1
Number of HSP's gapped: 590
Number of HSP's successfully gapped: 189
Length of query: 80
Length of database: 5,994,473
Length adjustment: 50
Effective length of query: 30
Effective length of database: 4,914,073
Effective search space: 147422190
Effective search space used: 147422190
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (22.9 bits)