RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780215|ref|YP_003064628.1| hypothetical protein
CLIBASIA_00500 [Candidatus Liberibacter asiaticus str. psy62]
(262 letters)
>gnl|CDD|161662 TIGR00010, TIGR00010, hydrolase, TatD family. Several genomes have
multiple paralogs related to this family. However, a set
of 17 proteins can be found, one each from 17 of the
first 20 genomes, such that each member forms a
bidirectional best hit across genomes with all other
members of the set. This core set (and one other
near-perfect member), but not the other paralogs, form
the seed for this model. Additionally, members of the
seed alignment and all trusted hits, but not all
paralogs, have a conserved motif DxHxH near the amino
end. The member from E. coli was recently shown to have
DNase activity.
Length = 252
Score = 251 bits (644), Expect = 1e-67
Identities = 110/254 (43%), Positives = 165/254 (64%), Gaps = 3/254 (1%)
Query: 2 LIDTHCHLLLPDFDEDRHDVIMRAHQANVLKMIAIAIKVKDFVPLIKLCQDYPSSIFCSV 61
LID HCHL DF+ED +VI RA A V ++A+ ++DF+ ++L + YP+ ++ +V
Sbjct: 1 LIDAHCHLDFLDFEEDVEEVIERAKAAGVTAVVAVGTDLEDFLRALELAEKYPN-VYAAV 59
Query: 62 GTHPCHAHEENEVLVDELVCLASHPRVVAIGETGLDRYHNAHTIEEQKVVFLRHIEASRI 121
G HP ++ + + EL LA+HP+VVAIGETGLD Y Q+ VF ++ +
Sbjct: 60 GVHPLDVDDDTKEDIKELERLAAHPKVVAIGETGLDYYKADEYKRRQEEVFRAQLQLAEE 119
Query: 122 TGIPLVIHSRSADDDMAAILQEEMKKGPFPFVIHCFSSSQKLADICLELGGYISFTGMIT 181
+P++IH+R A++D+ IL+EE K V+HCF+ +LA L+LG YIS +G++T
Sbjct: 120 LNLPVIIHARDAEEDVLDILREE--KPKVGGVLHCFTGDAELAKKLLDLGFYISISGIVT 177
Query: 182 FPKYDALRAIARGIPMDRVLVETDSPYIVPVSCQGKRNEPAYVVNTAKALAKEKDVSYED 241
F +LR + R IP++R+LVETDSPY+ PV +GKRNEPA+V T +A+A+ K + E+
Sbjct: 178 FKNAKSLREVVRKIPLERLLVETDSPYLAPVPYRGKRNEPAFVRYTVEAIAEIKGMDVEE 237
Query: 242 LMEETTKNALKLFS 255
L + TTKNA +LF
Sbjct: 238 LAQITTKNAKRLFG 251
>gnl|CDD|182752 PRK10812, PRK10812, putative DNAse; Provisional.
Length = 265
Score = 197 bits (503), Expect = 2e-51
Identities = 103/257 (40%), Positives = 152/257 (59%), Gaps = 7/257 (2%)
Query: 1 MLIDTHCHLLLPDFD---EDRHDVIMRAHQANVLKMIAIAIKVKDFVPLIKLCQDYPSSI 57
L+D+HCHL D+ +D DV+ +A +V +A+A + + + L + + +
Sbjct: 2 FLVDSHCHLDGLDYQSLHKDVDDVLAKAAARDVKFCLAVATTLPGYRHMRDLVGERDNVV 61
Query: 58 FCSVGTHPCHAHEENEVLVDELVCLASHPRVVAIGETGLDRYHNAHTIEEQKVVFLRHIE 117
F S G HP + E +V +EL LA+ VVA+GETGLD Y+ T Q+ F HI+
Sbjct: 62 F-SCGVHPLNQDEPYDV--EELRRLAAEEGVVAMGETGLDYYYTPETKVRQQESFRHHIQ 118
Query: 118 ASRITGIPLVIHSRSADDDMAAILQEEMKKGPFPFVIHCFSSSQKLADICLELGGYISFT 177
R P+++H+R A D AIL+EE K V+HCF+ ++ A L+LG YISF+
Sbjct: 119 IGRELNKPVIVHTRDARADTLAILREE-KVTDCGGVLHCFTEDRETAGKLLDLGFYISFS 177
Query: 178 GMITFPKYDALRAIARGIPMDRVLVETDSPYIVPVSCQGKRNEPAYVVNTAKALAKEKDV 237
G++TF + LR AR +P+DR+LVETDSPY+ PV +GK N+PA V + A+ +A K V
Sbjct: 178 GIVTFRNAEQLRDAARYVPLDRLLVETDSPYLAPVPHRGKENQPAMVRDVAEYMAVLKGV 237
Query: 238 SYEDLMEETTKNALKLF 254
S E+L + TT N +LF
Sbjct: 238 SVEELAQVTTDNFARLF 254
>gnl|CDD|182449 PRK10425, PRK10425, DNase TatD; Provisional.
Length = 258
Score = 138 bits (349), Expect = 2e-33
Identities = 81/252 (32%), Positives = 126/252 (50%), Gaps = 15/252 (5%)
Query: 12 PDFDEDRHDVIMRAHQANVLKMIAIAIKVKDFVPLIKLCQDYPSSIFCSVGTHPCHAHEE 71
F +DR DV+ RA A V M+ +++ KL + YPS + + G HP + +
Sbjct: 11 SQFAKDRDDVVARAFAAGVNGMLITGTNLRESQQAQKLARQYPSC-WSTAGVHPHDSSQW 69
Query: 72 NEVLVDELVCLASHPRVVAIGETGLDRYHNAHTIEEQKVVFLRHIEASRITGIPLVIHSR 131
+ ++ LA+ P VVAIGE GLD N T EEQ+ F+ + + +P+ +H R
Sbjct: 70 QAATEEAIIELAAQPEVVAIGECGLDFNRNFSTPEEQERAFVAQLAIAAELNMPVFMHCR 129
Query: 132 SADDDMAAILQEEMKKGPFPFVIHCFSSSQKLADICLELGGYISFTGMITFPKYD----- 186
A + A+L+ + K P V+HCF+ +++ CL G YI TG + D
Sbjct: 130 DAHERFMALLEPWLDKLPGA-VLHCFTGTREEMQACLARGLYIGITGWVC----DERRGL 184
Query: 187 ALRAIARGIPMDRVLVETDSPYIVPVSCQGK----RNEPAYVVNTAKALAKEKDVSYEDL 242
LR + IP +R+L+ETD+PY++P K RNEPA++ + + +A + L
Sbjct: 185 ELRELLPLIPAERLLLETDAPYLLPRDLTPKPASRRNEPAFLPHILQRIAHWRGEDAAWL 244
Query: 243 MEETTKNALKLF 254
T NA LF
Sbjct: 245 AATTDANARTLF 256
>gnl|CDD|171118 PRK11449, PRK11449, putative deoxyribonuclease YjjV; Provisional.
Length = 258
Score = 123 bits (309), Expect = 6e-29
Identities = 75/255 (29%), Positives = 128/255 (50%), Gaps = 5/255 (1%)
Query: 2 LIDTHCHLLLPDFDEDRHDVIMRAHQANVLKMIAIAIKVKDFVPLIKLCQDYPSSIFCSV 61
IDTHCH P F D + RA QA V K+I A + ++F ++ L + Y ++ ++
Sbjct: 5 FIDTHCHFDFPPFSGDEEASLQRAAQAGVGKIIVPATEAENFARVLALAERYQP-LYAAL 63
Query: 62 GTHPCHAHEENEVLVDELV-CLASHP-RVVAIGETGLDRYHNAHTIEEQKVVFLRHIEAS 119
G HP + ++V +D+L L P +VVA+GE GLD + + E Q+ + ++ +
Sbjct: 64 GLHPGMLEKHSDVSLDQLQQALERRPAKVVAVGEIGLDLFGDDPQFERQQWLLDEQLKLA 123
Query: 120 RITGIPLVIHSRSADDDMAAILQEEMKKGPFPFVIHCFSSSQKLADICLELGGYISFTGM 179
+ +P+++HSR D +A L+ P V+H FS S + A+ ++LG I G
Sbjct: 124 KRYDLPVILHSRRTHDKLAMHLKRH--DLPRTGVVHGFSGSLQQAERFVQLGYKIGVGGT 181
Query: 180 ITFPKYDALRAIARGIPMDRVLVETDSPYIVPVSCQGKRNEPAYVVNTAKALAKEKDVSY 239
IT+P+ R + +P+ +L+ETD+P + QG+ N P L + +
Sbjct: 182 ITYPRASKTRDVIAKLPLASLLLETDAPDMPLNGFQGQPNRPEQAARVFDVLCELRPEPA 241
Query: 240 EDLMEETTKNALKLF 254
+++ E N LF
Sbjct: 242 DEIAEVLLNNTYTLF 256
>gnl|CDD|180280 PRK05835, PRK05835, fructose-bisphosphate aldolase; Provisional.
Length = 307
Score = 30.3 bits (68), Expect = 0.48
Identities = 23/54 (42%), Positives = 30/54 (55%), Gaps = 7/54 (12%)
Query: 107 EQKVVFLRHIEASRITGIPLVIHSRSA--DDDMAAILQE--EMK--KG-PFPFV 153
E K+ F R E R+T IPLV+H SA DD + L ++K KG PF F+
Sbjct: 188 EPKLDFERLQEVKRLTNIPLVLHGASAIPDDVRKSYLDAGGDLKGSKGVPFEFL 241
>gnl|CDD|180713 PRK06826, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1151
Score = 29.9 bits (68), Expect = 0.76
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 103 HTIEEQKVVFLRHIEASRITGIPLV 127
H I EQ+ V I+ S+ GIPLV
Sbjct: 179 HGIPEQRKVNEELIKLSKELGIPLV 203
>gnl|CDD|132639 TIGR03600, phage_DnaB, phage replicative helicase, DnaB family,
HK022 subfamily. Members of this family are phage (or
prophage-region) homologs of the bacterial homohexameric
replicative helicase DnaB. Some phage may rely on host
DnaB, while others encode their own verions. This model
describes the largest phage-specific clade among the
close homologs of DnaB, but there are, or course, other
DnaB homologs from phage that fall outside the scope of
this model.
Length = 421
Score = 28.5 bits (64), Expect = 1.8
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 186 DALRAIARGI-----PMDRVLVETDSPYIVPVSCQGKRNEP-AYVVNTAKALAKEKDV 237
+R+IAR I +D ++V D ++ + RNE + KALAKE DV
Sbjct: 290 AQIRSIARRIKRKKGGLDLIVV--DYIQLMAPTRGRDRNEELGGISRGLKALAKELDV 345
>gnl|CDD|182210 PRK10050, PRK10050, curli assembly protein CsgF; Provisional.
Length = 138
Score = 28.0 bits (62), Expect = 2.3
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 216 GKRNEPAYVVNTAKALAKEKDVSYEDLMEETTKNALKLFSK 256
G N A+++N+A+A KD SY D T +AL F++
Sbjct: 33 GNPNNGAFLLNSAQAQNSYKDPSYNDDFGIETPSALDNFTQ 73
>gnl|CDD|179185 PRK00962, PRK00962, hypothetical protein; Provisional.
Length = 165
Score = 28.1 bits (63), Expect = 2.4
Identities = 13/33 (39%), Positives = 15/33 (45%)
Query: 220 EPAYVVNTAKALAKEKDVSYEDLMEETTKNALK 252
EP YV KA +E D+ LM E KN
Sbjct: 66 EPDYVYKYIKAYNEENDLLVAKLMAEALKNKTN 98
>gnl|CDD|182623 PRK10657, PRK10657, isoaspartyl dipeptidase; Provisional.
Length = 388
Score = 27.5 bits (62), Expect = 3.7
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 11/57 (19%)
Query: 160 SQKLADICLEL---GGYISFTGMITF-------PKYDAL-RAIARGIPMDRVLVETD 205
++ L + LE GG I T +AL RA+ G+P+ RV + +D
Sbjct: 229 NEPLFEQALEFAKKGGVIDLTTSDPDFLGEGEVAPAEALKRALEAGVPLSRVTLSSD 285
>gnl|CDD|180822 PRK07069, PRK07069, short chain dehydrogenase; Validated.
Length = 251
Score = 27.0 bits (60), Expect = 4.7
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 181 TFPKYDALRAIARGIPMDRV 200
+ +A R +ARG+P+ R+
Sbjct: 197 RLGEEEATRKLARGVPLGRL 216
>gnl|CDD|180765 PRK06939, PRK06939, 2-amino-3-ketobutyrate coenzyme A ligase;
Provisional.
Length = 397
Score = 27.1 bits (61), Expect = 4.7
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 82 LASHPRVVAIGETGLDRY 99
LA+HP ++A + LD +
Sbjct: 55 LANHPELIAAAKAALDSH 72
>gnl|CDD|115893 pfam07268, EppA_BapA, Exported protein precursor (EppA/BapA). This
family consists of a number of exported protein
precursor (EppA and BapA) sequences which seem to be
specific to Borrelia burgdorferi (Lyme disease
spirochete). bapA gene sequences are quite stable but
the encoded proteins do not provoke a strong immune
response in most individuals. Conversely, EppA proteins
are much more antigenic but are more variable in
sequence. It is thought that BapA and EppA play
important roles during the Borrelia burgdorferi
infectious cycle.
Length = 163
Score = 26.6 bits (59), Expect = 5.7
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 32 KMIAIAIKVKDFVPLIKLCQDYPSSIF 58
K+I +I + D + L + YP SIF
Sbjct: 99 KIITDSIFLSDIDNINNLIEGYPDSIF 125
>gnl|CDD|161739 TIGR00167, cbbA, ketose-bisphosphate aldolases.
fructose-bisphosphate and tagatose-bisphosphate
aldolase.
Length = 288
Score = 26.9 bits (60), Expect = 5.9
Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 11/60 (18%)
Query: 89 VAIGETGLDRYHNAHTIEEQKVVFLRHIEASRITGIPLVIHSRSADDDMAAILQEEMKKG 148
AIG H + E + + F R E + +PLV+H S I EE+KK
Sbjct: 177 AAIGNV-----HGVYKGEPKGLDFERLEEIQKYVNLPLVLHGGS------GIPDEEIKKA 225
>gnl|CDD|183417 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 26.6 bits (60), Expect = 6.0
Identities = 11/40 (27%), Positives = 21/40 (52%), Gaps = 9/40 (22%)
Query: 112 FLRHIEASRITGIPLVIH--SRSADDDMAA--ILQEEMKK 147
FL+HIE +R+ ++H A D + ++ E++K
Sbjct: 230 FLKHIERTRL-----LLHLVDIEAVDPVEDYKTIRNELEK 264
>gnl|CDD|162608 TIGR01928, menC_lowGC/arch, o-succinylbenzoic acid (OSB)
synthetase. This model describes the enzyme
o-succinylbenzoic acid synthetase (menC) that is
involved in one of the steps of the menaquinone
biosynthesis pathway. It takes SHCHC and makes it into
2-succinylbenzoate. Included in this model are low GC
gram positive bacteria and archaea. Also included in the
seed and in the model are enzymes with the com-name of
N-acylamino acid racemase (or the more general term,
racemase / racemase family), which refers to the
enzyme's industrial application as racemases, and not to
its biological function as o-succinylbenzoic acid
synthetase.
Length = 324
Score = 26.7 bits (59), Expect = 6.1
Identities = 25/90 (27%), Positives = 33/90 (36%), Gaps = 6/90 (6%)
Query: 96 LDRYHNAHTIEE----QKVVFLRHIEASRITGIPLVIHSRSADDDMAAI-LQEEMKKGPF 150
LDRY + IEE + L + IT I L S DD I L
Sbjct: 195 LDRYQLLY-IEEPFKIDDLSMLDELAKGTITPICLDESITSLDDARNLIELGNVKVINIK 253
Query: 151 PFVIHCFSSSQKLADICLELGGYISFTGMI 180
P + + QK + C E G + GM+
Sbjct: 254 PGRLGGLTEVQKAIETCREHGAKVWIGGML 283
>gnl|CDD|148409 pfam06787, UPF0254, Uncharacterized protein family (UPF0254).
Length = 160
Score = 26.6 bits (59), Expect = 6.4
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 220 EPAYVVNTAKALAKEKDVSYEDLMEETTKNALK 252
EP YV+ KA +E D+ +M E K
Sbjct: 66 EPDYVIKYIKAYNEENDLKVAKMMAEAVKEKTN 98
>gnl|CDD|162204 TIGR01107, Na_K_ATPase_bet, Sodium Potassium ATPase beta subunit.
This model describes the Na+/K+ ATPase beta subunit in
eukaryotes. Na+/K+ ATPase(also called Sodium-Potassium
pump) is intimately associated with the plasma membrane.
It couples the energy released by the hydrolysis of ATP
to extrude 3 Na+ ions, with the concomitant uptake of
2K+ ions, against their ionic gradients.
Length = 289
Score = 26.2 bits (58), Expect = 8.3
Identities = 11/29 (37%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 195 IPMDRVL-VETDSPYIVPVSCQGKRNEPA 222
I M+R++ + +P + PV C GKR+E
Sbjct: 180 IKMNRIIGFKPKNPGVPPVDCTGKRDEDD 208
>gnl|CDD|182483 PRK10468, PRK10468, hydrogenase 2 small subunit; Provisional.
Length = 371
Score = 26.3 bits (58), Expect = 9.2
Identities = 26/90 (28%), Positives = 39/90 (43%), Gaps = 18/90 (20%)
Query: 63 THPCHAHEENEVLVDELVCLASHPRV-VAIGETGLDRYHNAHTIEEQKVVFLRHIEAS-- 119
THP E LV E + L H + A G + HNA +E+ K ++ ++ S
Sbjct: 70 THP-----TVENLVLETISLEYHEVLSAAFGHQVEENKHNA--LEKYKGQYVLVVDGSIP 122
Query: 120 --------RITGIPLVIHSRSADDDMAAIL 141
+ G P+V H R A + AAI+
Sbjct: 123 LKDNGIYCMVAGEPIVDHIRKAAEGAAAII 152
>gnl|CDD|179353 PRK01917, PRK01917, cation-binding hemerythrin HHE family protein;
Provisional.
Length = 139
Score = 26.3 bits (58), Expect = 9.2
Identities = 11/33 (33%), Positives = 14/33 (42%), Gaps = 3/33 (9%)
Query: 66 CHAHEENEVLVDELVCLASHPRVVAIGETGLDR 98
CH E +EVL V +V G+ L R
Sbjct: 71 CHRAEHDEVLA---VAADVREKVARDGDFELGR 100
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
0.323 0.137 0.409
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 4,319,627
Number of extensions: 278471
Number of successful extensions: 672
Number of sequences better than 10.0: 1
Number of HSP's gapped: 663
Number of HSP's successfully gapped: 32
Length of query: 262
Length of database: 5,994,473
Length adjustment: 92
Effective length of query: 170
Effective length of database: 4,006,537
Effective search space: 681111290
Effective search space used: 681111290
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (25.3 bits)