RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780628|ref|YP_003065041.1| coproporphyrinogen III oxidase
[Candidatus Liberibacter asiaticus str. psy62]
(395 letters)
>gnl|CDD|30980 COG0635, HemN, Coproporphyrinogen III oxidase and related Fe-S
oxidoreductases [Coenzyme metabolism].
Length = 416
Score = 356 bits (915), Expect = 5e-99
Identities = 149/383 (38%), Positives = 216/383 (56%), Gaps = 12/383 (3%)
Query: 17 NSLGVYVHWPFCVKKCPYCDFNSHVRRYKVGQENFIQSFLTEMQWMRQLTGP-RSISSIF 75
L +Y+H PFCV KCPYCDFNSHV + + ++ + L E++ + L G R + +I+
Sbjct: 33 KPLSLYIHIPFCVSKCPYCDFNSHVTKRGQPVDEYLDALLEEIELVAALLGGQREVKTIY 92
Query: 76 FGGGTPSLIEPQNIALILDGIAKNWT-VSSNVEITIEANPSSVEVNNFQGYRKAGVNRIS 134
FGGGTPSL+ P+ + +L + + + + + EITIEANP +VE F+ ++AGVNRIS
Sbjct: 93 FGGGTPSLLSPEQLERLLKALRELFNDLDPDAEITIEANPGTVEAEKFKALKEAGVNRIS 152
Query: 135 LGVQSLEEQSLRFLGRNHNASEAIAAIHLARN-IFPRMSFDLIYALPKQTMTQWEMELQR 193
LGVQS ++ L+ LGR H+ EA A+ LAR F ++ DLIY LP QT+ + +L++
Sbjct: 153 LGVQSFNDEVLKALGRIHDEEEAKEAVELARKAGFTSINIDLIYGLPGQTLESLKEDLEQ 212
Query: 194 ALSYAVDHLSLYQLTIEKGTLFYKMHKDGDLVLPSENVAVDLYNLTQSITSAHGLHAYEI 253
AL DHLSLY L IE GT F + G LP E+ D+Y L + + G YEI
Sbjct: 213 ALELGPDHLSLYSLAIEPGTKFAQRKIKGK-ALPDEDEKADMYELVEELLEKAGYRQYEI 271
Query: 254 SNHSFLGAESLHNLNYWRYGDYIGIGPGAHSRVKVGSHRVAISIEKHPESWLKMVRKNGH 313
SN + G E HNL YW DY+GIG GAH R+ +K+ +++L+ V + G
Sbjct: 272 SNFAKPGGECRHNLQYWETKDYLGIGAGAHGRI----GGTRYQNKKNLKTYLEAVDEGGL 327
Query: 314 AVVEKEFLSSEQQADEFLMMGLRLREGISVKDWEMLAGRN---LDIECERNLQRQGFIER 370
+VE E L+ + E L++GLRL G+ + + E G +E L G +E
Sbjct: 328 PLVEGEELTPDDLIREALILGLRLNFGVDLAELEERFGIFKFAEILELLAELIADGLLEL 387
Query: 371 VQFSRLRCTQRGMTMLDSVIANL 393
RLR T++G +L S+
Sbjct: 388 DG-DRLRLTEKGRLLLRSIAEAF 409
>gnl|CDD|146602 pfam04055, Radical_SAM, Radical SAM superfamily. Radical SAM
proteins catalyse diverse reactions, including unusual
methylations, isomerisation, sulphur insertion, ring
formation, anaerobic oxidation and protein radical
formation.
Length = 165
Score = 83.7 bits (207), Expect = 8e-17
Identities = 39/175 (22%), Positives = 75/175 (42%), Gaps = 12/175 (6%)
Query: 22 YVHWPFCVKKCPYCDFNSHVRRYKVGQENFIQSFLTEMQWMRQLT--GPRSISSIFFGGG 79
+ P C +C YC F S R K L+ + + + + + GG
Sbjct: 1 IIITPGCNLRCTYCAFPSIRARGKGR-------ELSPEEILEEAKELARLGVEVVILTGG 53
Query: 80 TPSLIEPQNIALILDGIAKNWTVSSNVEITIEANPSSVEVNNFQGYRKAGVNRISLGVQS 139
P L+ + +L+ + K + IT+E N + ++ + ++AG++R+S+ +QS
Sbjct: 54 EPLLLPD--LVELLERLLKL-EELEGIRITLETNGTLLDEELLEELKEAGLDRVSISLQS 110
Query: 140 LEEQSLRFLGRNHNASEAIAAIHLARNIFPRMSFDLIYALPKQTMTQWEMELQRA 194
+++ L+ + R H E + A+ L R + D I LP + E L+
Sbjct: 111 GDDEVLKIINRGHTFEEVLEALELLREAGIPVVVDNIVGLPGENDEDLEETLELL 165
>gnl|CDD|31436 COG1243, ELP3, Histone acetyltransferase [Transcription / Chromatin
structure and dynamics].
Length = 515
Score = 64.9 bits (158), Expect = 4e-11
Identities = 52/243 (21%), Positives = 88/243 (36%), Gaps = 44/243 (18%)
Query: 31 KCPYCDFN-------SHVRRYKV---GQENFIQSFLTEMQWMRQL-TGPRSISS---IFF 76
+C +C S+ +N + ++QL T + I
Sbjct: 81 RCVFCPGGPDKDSPQSYTGEEPAALRAIKNRYDPYEQVRARLKQLETIGHTSDKVELIIM 140
Query: 77 GGGTPSL-IEPQN-------------IALILDGIAKNWT-VSSNVEITIEANPSSV---E 118
GG +L +E Q + + KN T V ITIE P +
Sbjct: 141 GGTFTALSLEYQEWFLKVALKAMNDFGYDLEEAQRKNETAELRCVGITIETRPDYIDEEH 200
Query: 119 VNNFQGYRKAGVNRISLGVQSLEEQSLRFLGRNHNASEAIAAIHLARNIFPRMSFDLIYA 178
++ Y GV R+ LGVQS+ + L R H + + A L ++ ++ + ++
Sbjct: 201 LDQMLKY---GVTRVELGVQSIYDDVLERTKRGHTVEDVVEATRLLKDAGFKVGYHIMPG 257
Query: 179 LPKQTMTQWEMELQRAL------SYAVDHLSLYQLTIEKGTLFYKMHKDGDLVLPSENVA 232
LP E +L+ + D L +Y + +GT Y+M K G + A
Sbjct: 258 LPGSDF---ERDLESFREIFEDPRFRPDMLKIYPTLVIEGTELYEMWKRGLYKPYTTEEA 314
Query: 233 VDL 235
V+L
Sbjct: 315 VEL 317
>gnl|CDD|31435 COG1242, COG1242, Predicted Fe-S oxidoreductase [General function
prediction only].
Length = 312
Score = 49.8 bits (119), Expect = 1e-06
Identities = 27/103 (26%), Positives = 50/103 (48%)
Query: 133 ISLGVQSLEEQSLRFLGRNHNASEAIAAIHLARNIFPRMSFDLIYALPKQTMTQWEMELQ 192
+ LG+Q+ +++L+ + R H+ + + A+ R ++ LI LP +T + +
Sbjct: 146 VELGLQTAHDKTLKRINRGHDFACYVDAVKRLRKRGIKVCTHLINGLPGETRDEMLETAK 205
Query: 193 RALSYAVDHLSLYQLTIEKGTLFYKMHKDGDLVLPSENVAVDL 235
VD + L+ L + KGT KM++ G L S V+L
Sbjct: 206 IVAELGVDGIKLHPLHVVKGTPMEKMYEKGRLKFLSLEEYVEL 248
>gnl|CDD|100105 cd01335, Radical_SAM, Radical SAM superfamily. Enzymes of this
family generate radicals by combining a 4Fe-4S cluster
and S-adenosylmethionine (SAM) in close proximity. They
are characterized by a conserved CxxxCxxC motif, which
coordinates the conserved iron-sulfur cluster.
Mechanistically, they share the transfer of a single
electron from the iron-sulfur cluster to SAM, which
leads to its reductive cleavage to methionine and a
5'-deoxyadenosyl radical, which, in turn, abstracts a
hydrogen from the appropriately positioned carbon atom.
Depending on the enzyme, SAM is consumed during this
process or it is restored and reused. Radical SAM
enzymes catalyze steps in metabolism, DNA repair, the
biosynthesis of vitamins and coenzymes, and the
biosynthesis of many antibiotics. Examples are biotin
synthase (BioB), lipoyl synthase (LipA), pyruvate
formate-lyase (PFL), coproporphyrinogen oxidase (HemN),
lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide
reductase (ARR), and MoaA, an enzyme of the
biosynthesis of molybdopterin..
Length = 204
Score = 49.3 bits (117), Expect = 2e-06
Identities = 35/199 (17%), Positives = 73/199 (36%), Gaps = 14/199 (7%)
Query: 28 CVKKCPYCDFNSHVRRYKVGQENFIQSFLTEMQWMRQLTGPRSISSIFFGGGTPSLIEPQ 87
C C +C + R + + + + + GG P L
Sbjct: 7 CNLNCGFCSNPASKGRG----PESPPEIEEILDIVLEAKERG-VEVVILTGGEPLL--YP 59
Query: 88 NIALILDGIAKNWTVSSNVEITIEANPSSVEVNNFQGYRKAGVNRISLGVQSLEEQSLRF 147
+A +L + K EI+IE N + + + ++ G++ + + + S +E+
Sbjct: 60 ELAELLRRLKK---ELPGFEISIETNGTLLTEELLKELKELGLDGVGVSLDSGDEEVADK 116
Query: 148 L-GRNHNASEAIAAIHLARNIFPRMSFDLIYALPKQTMTQWEMELQRAL--SYAVDHLSL 204
+ G + E + A+ R +S L+ L + + ++E L + D +SL
Sbjct: 117 IRGSGESFKERLEALKELREAGLGLSTTLLVGLGDEDE-EDDLEELELLAEFRSPDRVSL 175
Query: 205 YQLTIEKGTLFYKMHKDGD 223
++L E+GT
Sbjct: 176 FRLLPEEGTPLELAAPVVP 194
>gnl|CDD|37746 KOG2535, KOG2535, KOG2535, RNA polymerase II elongator complex,
subunit ELP3/histone acetyltransferase [Chromatin
structure and dynamics, Transcription].
Length = 554
Score = 43.0 bits (101), Expect = 1e-04
Identities = 35/134 (26%), Positives = 57/134 (42%), Gaps = 5/134 (3%)
Query: 106 VEITIEANPSSVEVNNFQGYRKAGVNRISLGVQSLEEQSLRFLGRNHNASEAIAAIHLAR 165
+ ITIE P + G R+ +GVQS+ E R R H + HLA+
Sbjct: 223 IGITIETRPDYCLKRHLSDMLTYGCTRLEIGVQSVYEDVARDTNRGHTVKAVCESFHLAK 282
Query: 166 N----IFPRMSFDLIYALPKQTMTQWEMELQRALSYAVDHLSLYQLTIEKGTLFYKMHKD 221
+ + M DL ++ + Q++ E ++ D L +Y + +GT Y++ K
Sbjct: 283 DAGFKVVAHMMPDLPNVGMERDIEQFK-EYFENPAFRPDGLKIYPTLVIRGTGLYELWKT 341
Query: 222 GDLVLPSENVAVDL 235
G S + VDL
Sbjct: 342 GRYKSYSPSALVDL 355
>gnl|CDD|30966 COG0621, MiaB, 2-methylthioadenine synthetase [Translation,
ribosomal structure and biogenesis].
Length = 437
Score = 37.5 bits (87), Expect = 0.006
Identities = 21/89 (23%), Positives = 36/89 (40%), Gaps = 2/89 (2%)
Query: 135 LGVQSLEEQSLRFLGRNHNASEAIAAIHLARNIFPRMSF--DLIYALPKQTMTQWEMELQ 192
L VQS ++ L+ + R + E + I R P ++ D+I P +T +E L
Sbjct: 260 LPVQSGSDRILKRMKRGYTVEEYLEIIEKLRAARPDIAISTDIIVGFPGETEEDFEETLD 319
Query: 193 RALSYAVDHLSLYQLTIEKGTLFYKMHKD 221
D L +++ + GT M
Sbjct: 320 LVEEVRFDRLHVFKYSPRPGTPAALMPDQ 348
>gnl|CDD|133156 cd05489, xylanase_inhibitor_I_like, TAXI-I inhibits degradation of
xylan in the cell wall. Xylanase inhibitor-I (TAXI-I)
is a member of potent TAXI-type inhibitors of fungal and
bacterial family 11 xylanases. Plants developed a
diverse battery of defense mechanisms in response to
continual challenges by a broad spectrum of pathogenic
microorganisms. Their defense arsenal includes
inhibitors of cell wall-degrading enzymes, which hinder
a possible invasion and colonization by antagonists.
Xylanases of fungal and bacterial pathogens are the key
enzymes in the degradation of xylan in the cell wall.
Plants secrete proteins that inhibit these degradation
glycosidases, including xylanase. Surprisingly, TAXI-I
displays structural homology with the pepsin-like family
of aspartic proteases but is proteolytically
nonfunctional, because one or more residues of the
essential catalytic triad are absent. The structure of
the TAXI-inhibitor, Aspergillus niger xylanase I
complex, illustrates the ability of tight binding and
inhibition with subnanomolar affinity and indicates the
importance of the C-terminal end for the differences in
xylanase specificity among different TAXI-type
inhibitors. This family also contains pepsin-like
aspartic proteinases homologous to TAXI-I. Unlike
TAXI-I, they have active site aspartates and are
functionally active. This family of aspartate proteases
is classified by MEROPS as the peptidase family A1
(pepsin A, clan AA).
Length = 362
Score = 30.4 bits (69), Expect = 0.82
Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 4/57 (7%)
Query: 51 FIQSFLTEMQWMRQLTGPRSISSIFF--GGGTPSLIEPQ--NIALILDGIAKNWTVS 103
F Q+F + ++ + + + + I L+LDG NWT+
Sbjct: 251 FTQAFAKATARIPRVPAAAVFPELCYPASALGNTRLGYAVPAIDLVLDGGGVNWTIF 307
>gnl|CDD|38055 KOG2844, KOG2844, KOG2844, Dimethylglycine dehydrogenase precursor
[Amino acid transport and metabolism].
Length = 856
Score = 28.8 bits (64), Expect = 2.5
Identities = 15/57 (26%), Positives = 24/57 (42%)
Query: 198 AVDHLSLYQLTIEKGTLFYKMHKDGDLVLPSENVAVDLYNLTQSITSAHGLHAYEIS 254
A LY+ E+ L ++G + L S +D Y S AHG+ + +S
Sbjct: 100 AHTSRVLYRELEEETGLHTGWIQNGGIFLASNRQRLDEYKRLMSRGKAHGVESELLS 156
>gnl|CDD|35658 KOG0437, KOG0437, KOG0437, Leucyl-tRNA synthetase [Translation,
ribosomal structure and biogenesis].
Length = 1080
Score = 28.4 bits (63), Expect = 3.3
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 11/53 (20%)
Query: 293 VAISIEKHPESWLKMVRKNGHAVVEKE--------FLSSEQQADEFLMMGLRL 337
VA+ EK W K +R NGH ++ E F++ EQ ++F G RL
Sbjct: 686 VALFPEKK---WPKGIRANGHLMLNSEKMSKSTGNFMTLEQAIEKFGADGTRL 735
>gnl|CDD|112056 pfam03225, Viral_Hsp90, Viral heat shock protein Hsp90 homologue.
Length = 511
Score = 26.9 bits (60), Expect = 9.3
Identities = 13/38 (34%), Positives = 17/38 (44%)
Query: 166 NIFPRMSFDLIYALPKQTMTQWEMELQRALSYAVDHLS 203
I P M FD LP + +T+ E E R L + S
Sbjct: 459 GILPYMRFDFFKGLPLRLLTEEERESLRTLRLMTEDRS 496
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
0.320 0.134 0.401
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,747,982
Number of extensions: 248321
Number of successful extensions: 581
Number of sequences better than 10.0: 1
Number of HSP's gapped: 571
Number of HSP's successfully gapped: 16
Length of query: 395
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 299
Effective length of database: 4,189,273
Effective search space: 1252592627
Effective search space used: 1252592627
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 (21.8 bits)
S2: 58 (26.2 bits)