RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780347|ref|YP_003064760.1| riboflavin synthase subunit
alpha [Candidatus Liberibacter asiaticus str. psy62]
(204 letters)
>gnl|CDD|30655 COG0307, RibC, Riboflavin synthase alpha chain [Coenzyme
metabolism].
Length = 204
Score = 202 bits (515), Expect = 5e-53
Identities = 88/201 (43%), Positives = 125/201 (62%), Gaps = 10/201 (4%)
Query: 1 MFTGIVTDIGKIIAMTPIAKGMRLRVMT-SYNTSKMKLGCSIAHAGICLTVVRLSEEHSV 59
MFTGIV +IGK+ + G+ L + + +KLG SIA G+CLTV +E+
Sbjct: 1 MFTGIVEEIGKV---KKVENGITLTIESAKLILEDVKLGDSIAVNGVCLTVTEFNEDG-- 55
Query: 60 DNWYEVEVWAETNRITNIASWGIGTFINLERSVKLGDRLDGHLVSGHIDGTVEILFLDFI 119
+ V+V ET R TN+ +G +NLER++KLGDRL GHLVSGH+DGT EI+ ++
Sbjct: 56 ---FSVDVMPETLRRTNLGDLKVGDKVNLERALKLGDRLGGHLVSGHVDGTGEIVKIEKD 112
Query: 120 GDSMYCRLSL-PHNLEQFIAVKGSVCLNGVSLTVNLVGKNFFDVLLIRHTIEETTWKMHK 178
G+++ P L ++I KGS+ ++G+SLTVN V + F V LI HT+E TT K
Sbjct: 113 GNAVRFWFKAPPEELAKYIVEKGSIAVDGISLTVNEVEDDTFSVSLIPHTLERTTLGEKK 172
Query: 179 VGDLINIEVDSMMRYIARLYA 199
VGD +NIE+D + +Y+ RL A
Sbjct: 173 VGDRVNIEIDVLAKYVERLLA 193
>gnl|CDD|38520 KOG3310, KOG3310, KOG3310, Riboflavin synthase alpha chain
[Coenzyme transport and metabolism].
Length = 210
Score = 116 bits (291), Expect = 5e-27
Identities = 66/201 (32%), Positives = 109/201 (54%), Gaps = 9/201 (4%)
Query: 1 MFTGIVTDIGKIIAMTP-IAKGMRLRVMTSYNTSKMKLGCSIAHAGICLTVVRLSEEHSV 59
MFTGIV +G++ + G L++ LG SIA G CLTV + E
Sbjct: 1 MFTGIVECMGEVKDLGMADDGGFDLKIGARVILEDCHLGDSIAVNGTCLTVTEFNAEE-- 58
Query: 60 DNWYEVEVWAETNRITNIASWGIGTFINLERSVKLGDRLDGHLVSGHIDGTVEILFLDFI 119
+ V + ET R TN+ G+ +NLER+V+ R+ GH+V GH+D I+ ++
Sbjct: 59 ---FTVGIAPETLRKTNLEELKKGSPVNLERAVQPVSRMGGHVVQGHVDTVAVIVSMEVE 115
Query: 120 GDSMYCRLSL-PHNLEQFIAVKGSVCLNGVSLTVNLV--GKNFFDVLLIRHTIEETTWKM 176
GDS++ + L L ++I KG + ++G SLT+ V ++ F++++I +T +
Sbjct: 116 GDSIWFKFKLRDKGLLKYIVPKGFIAVDGTSLTIVDVDDEESCFNIMMIAYTQQNVIMPT 175
Query: 177 HKVGDLINIEVDSMMRYIARL 197
K+GD +N+EVD M +Y+ +L
Sbjct: 176 KKIGDKVNLEVDIMGKYVEKL 196
>gnl|CDD|144321 pfam00677, Lum_binding, Lumazine binding domain. This domain binds
to derivatives of lumazine in some proteins. Some
proteins have lost the residues involved in binding
lumazine.
Length = 86
Score = 62.2 bits (152), Expect = 1e-10
Identities = 30/86 (34%), Positives = 47/86 (54%), Gaps = 1/86 (1%)
Query: 104 SGHIDGTVEILFLDFIGDSMYCRLSLP-HNLEQFIAVKGSVCLNGVSLTVNLVGKNFFDV 162
+G ++G EI + G++ + LP L + + K S+ +NG+SLTV V N F
Sbjct: 1 TGIVEGVGEIAEIIENGNARSIWIKLPDKMLTKVLIGKDSIAVNGISLTVTEVTGNQFTF 60
Query: 163 LLIRHTIEETTWKMHKVGDLINIEVD 188
LI T++ T KVGD +N+E+D
Sbjct: 61 DLIPETLKRTNLGSLKVGDKVNLEID 86
Score = 44.9 bits (107), Expect = 2e-05
Identities = 26/94 (27%), Positives = 41/94 (43%), Gaps = 15/94 (15%)
Query: 3 TGIVTDIGKIIAMTPIAKGMRLRV------MTSYNTSKMKLGCSIAHAGICLTVVRLSEE 56
TGIV +G+I + + + +T K SIA GI LTV ++
Sbjct: 1 TGIVEGVGEIAEIIENGNARSIWIKLPDKMLTKVLIGK----DSIAVNGISLTVTEVT-- 54
Query: 57 HSVDNWYEVEVWAETNRITNIASWGIGTFINLER 90
N + ++ ET + TN+ S +G +NLE
Sbjct: 55 ---GNQFTFDLIPETLKRTNLGSLKVGDKVNLEI 85
>gnl|CDD|31266 COG1067, LonB, Predicted ATP-dependent protease [Posttranslational
modification, protein turnover, chaperones].
Length = 647
Score = 30.3 bits (68), Expect = 0.36
Identities = 28/133 (21%), Positives = 45/133 (33%), Gaps = 41/133 (30%)
Query: 48 LTVVRLSEEHSVDNWYEVEVWAETNRITNIASWGIGTFINLERSVKLGD----------- 96
L+V+ + H+ E RI+ G G +++ER +L
Sbjct: 434 LSVIEVPGHHAFG---------EPARISCAVHKGDGEIVDIERKAELAGNIHNKGMMIKQ 484
Query: 97 -------RLDGHL-VSGHIDGTVEILFLDFIGDS----MYCRL-----SLPHNLEQFIAV 139
D H+ S + +D GDS C L +P ++Q IA+
Sbjct: 485 AFLMSILNYDIHIPFSASLVFEQSYGEVD--GDSASLAEACALISALSKIP--VDQDIAI 540
Query: 140 KGSVCLNGVSLTV 152
GS+ G V
Sbjct: 541 TGSIDQFGEVQPV 553
>gnl|CDD|153084 cd01675, RNR_III, Class III ribonucleotide reductase.
Ribonucleotide reductase (RNR) catalyzes the reductive
synthesis of deoxyribonucleotides from their
corresponding ribonucleotides. It provides the
precursors necessary for DNA synthesis. RNRs are
separated into three classes based on their
metallocofactor usage. Class I RNRs, found in
eukaryotes, bacteria, and bacteriophage, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in strict or facultative anaerobic bacteria,
bacteriophage, and archaea, use an FeS cluster and
S-adenosylmethionine to generate a glycyl radical. Many
organisms have more than one class of RNR present in
their genomes. All three RNRs have a ten-stranded
alpha-beta barrel domain that is structurally similar to
the domain of PFL (pyruvate formate lyase). The class
III enzyme from phage T4 consists of two subunits, this
model covers the larger subunit which contains the
active and allosteric sites.
Length = 555
Score = 26.9 bits (60), Expect = 4.3
Identities = 9/41 (21%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 97 RLDGHLVSGHIDGTVEILFLDFIGDSMYCRLSLPHNLEQFI 137
L + H++G + I LD++ + YC +L +
Sbjct: 29 ILPKEIARAHLNGDIHIHDLDYLPLTPYCCG---WDLRPLL 66
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
0.324 0.138 0.416
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,418,808
Number of extensions: 122765
Number of successful extensions: 311
Number of sequences better than 10.0: 1
Number of HSP's gapped: 296
Number of HSP's successfully gapped: 8
Length of query: 204
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 115
Effective length of database: 4,340,536
Effective search space: 499161640
Effective search space used: 499161640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 55 (25.0 bits)