RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780383|ref|YP_003064796.1| endonuclease III [Candidatus
Liberibacter asiaticus str. psy62]
(227 letters)
>gnl|CDD|130155 TIGR01083, nth, endonuclease III. This equivalog model identifes
nth members of the pfam00730 superfamily (HhH-GPD:
Helix-hairpin-helix and Gly/Pro rich loop followed by a
conserved aspartate). The major members of the
superfamily are nth and mutY.
Length = 191
Score = 265 bits (680), Expect = 6e-72
Identities = 100/191 (52%), Positives = 140/191 (73%)
Query: 23 KELEEIFYLFSLKWPSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQK 82
++ +EI +P P EL Y N F L+VA +LSAQ+TD +VNKATK LFE+ TPQ
Sbjct: 1 QKAQEILERLRKNYPHPTTELDYNNPFELLVATILSAQATDKSVNKATKKLFEVYPTPQA 60
Query: 83 MLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGAN 142
+ G ++L+ YI++IG+YR K++NII+L IL+ + ++P+ E L +LPG+GRK AN
Sbjct: 61 LAQAGLEELEEYIKSIGLYRNKAKNIIALCRILVERYGGEVPEDREELVKLPGVGRKTAN 120
Query: 143 VILSMAFGIPTIGVDTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHG 202
V+L++AFGIP I VDTH+FR+SNR+GL+ GK P+KVE+ LL++IP + H+WL+LHG
Sbjct: 121 VVLNVAFGIPAIAVDTHVFRVSNRLGLSKGKDPDKVEEELLKLIPREFWTKLHHWLILHG 180
Query: 203 RYVCKARKPQC 213
RY CKARKP C
Sbjct: 181 RYTCKARKPLC 191
>gnl|CDD|182661 PRK10702, PRK10702, endonuclease III; Provisional.
Length = 211
Score = 227 bits (580), Expect = 2e-60
Identities = 96/187 (51%), Positives = 136/187 (72%)
Query: 37 PSPKGELYYVNHFTLIVAVLLSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIR 96
P P EL + + F L++AVLLSAQ+TDV+VNKAT L+ +A+TP ML +G + ++ YI+
Sbjct: 18 PHPTTELNFSSPFELLIAVLLSAQATDVSVNKATAKLYPVANTPAAMLELGVEGVKTYIK 77
Query: 97 TIGIYRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGV 156
TIG+Y K+EN+I IL+ + + ++P+ L LPG+GRK ANV+L+ AFG PTI V
Sbjct: 78 TIGLYNSKAENVIKTCRILLEQHNGEVPEDRAALEALPGVGRKTANVVLNTAFGWPTIAV 137
Query: 157 DTHIFRISNRIGLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSC 216
DTHIFR+ NR APGK +VE+ LL+++P + + + H+WL+LHGRY C ARKP+C SC
Sbjct: 138 DTHIFRVCNRTQFAPGKNVEQVEEKLLKVVPAEFKVDCHHWLILHGRYTCIARKPRCGSC 197
Query: 217 IISNLCK 223
II +LC+
Sbjct: 198 IIEDLCE 204
>gnl|CDD|128754 smart00478, ENDO3c, endonuclease III. includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 149
Score = 161 bits (409), Expect = 2e-40
Identities = 64/149 (42%), Positives = 96/149 (64%), Gaps = 1/149 (0%)
Query: 57 LSAQSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILI 116
LS Q++D VNKAT+ LFE TP+ + A E++L+ IR +G YR+K++ +I L+ IL+
Sbjct: 1 LSQQTSDEAVNKATERLFEKFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARILV 60
Query: 117 NEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNRIGLAPGK-TP 175
E+ ++P E L +LPG+GRK AN +LS A G P I VDTH+ RI+ R+GL K TP
Sbjct: 61 EEYGGEVPDDREELLKLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKSTP 120
Query: 176 NKVEQSLLRIIPPKHQYNAHYWLVLHGRY 204
+VE+ L +++P + + L+ GR
Sbjct: 121 EEVEKLLEKLLPKEDWRELNLLLIDFGRT 149
>gnl|CDD|130156 TIGR01084, mutY, A/G-specific adenine glycosylase. This equivalog
model identifies mutY members of the pfam00730
superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro
rich loop followed by a conserved aspartate). The major
members of the superfamily are nth and mutY.
Length = 275
Score = 61.7 bits (150), Expect = 2e-10
Identities = 37/133 (27%), Positives = 63/133 (47%), Gaps = 7/133 (5%)
Query: 101 YRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHI 160
Y ++ N+ + ++ EF + PQ E L LPG+GR A ILS A P +D ++
Sbjct: 78 YYARARNLHKAAQEVVEEFGGEFPQDFEDLAALPGVGRYTAGAILSFALNKPYPILDGNV 137
Query: 161 FRISNRIGLA----PGK--TPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQ 214
R+ +R+ A PGK N++ ++P + L+ G +C +KP+C
Sbjct: 138 KRVLSRL-FAVEGWPGKKKVENRLWTLAESLLPKADPEAFNQALMDLGAMICTRKKPKCD 196
Query: 215 SCIISNLCKRIKQ 227
C + + C +Q
Sbjct: 197 LCPLQDFCLAYQQ 209
>gnl|CDD|172427 PRK13910, PRK13910, DNA glycosylase MutY; Provisional.
Length = 289
Score = 52.3 bits (125), Expect = 1e-07
Identities = 33/123 (26%), Positives = 59/123 (47%), Gaps = 2/123 (1%)
Query: 101 YRKKSENIISLSHILINEFDNKIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHI 160
Y +++N+ + I + E +++P + L +LPGIG AN IL F + VD +I
Sbjct: 45 YYSRAKNLKKSAEICVKEHHSQLPNDYQSLLKLPGIGAYTANAILCFGFREKSACVDANI 104
Query: 161 FRISNRI-GLAPGKTPNKVEQSLLRIIPPKHQYNAHYWLVLHGRYVCKARKPQCQSCIIS 219
R+ R+ GL P ++ + +N + L+ G +C + KP+C C ++
Sbjct: 105 KRVLLRLFGLDPNIHAKDLQIKANDFLNLNESFNHNQALIDLGALIC-SPKPKCAICPLN 163
Query: 220 NLC 222
C
Sbjct: 164 PYC 166
>gnl|CDD|182805 PRK10880, PRK10880, adenine DNA glycosylase; Provisional.
Length = 350
Score = 46.6 bits (111), Expect = 5e-06
Identities = 35/111 (31%), Positives = 55/111 (49%), Gaps = 15/111 (13%)
Query: 122 KIPQTLEGLTRLPGIGRKGANVILSMAFGIPTIGVDTHIFRISNR---IGLAPGKTPNKV 178
+ P+T E + LPG+GR A ILS++ G +D ++ R+ R + PGK +V
Sbjct: 103 EFPETFEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGWPGK--KEV 160
Query: 179 EQSLLRI---IPPKH---QYN-AHYWLVLHGRYVCKARKPQCQSCIISNLC 222
E L ++ + P ++N A L G VC KP+C+ C + N C
Sbjct: 161 ENRLWQLSEQVTPAVGVERFNQAMMDL---GAMVCTRSKPKCELCPLQNGC 208
>gnl|CDD|184390 PRK13913, PRK13913, 3-methyladenine DNA glycosylase; Provisional.
Length = 218
Score = 41.0 bits (96), Expect = 2e-04
Identities = 25/92 (27%), Positives = 44/92 (47%), Gaps = 4/92 (4%)
Query: 81 QKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEFDN----KIPQTLEGLTRLPGI 136
+K+ I KL +R G Y +K++ +I LS ++ +F + K T E L GI
Sbjct: 70 KKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSENILKDFGSFENFKQEVTREWLLDQKGI 129
Query: 137 GRKGANVILSMAFGIPTIGVDTHIFRISNRIG 168
G++ A+ IL + VD + + ++G
Sbjct: 130 GKESADAILCYVCAKEVMVVDKYSYLFLKKLG 161
>gnl|CDD|129676 TIGR00588, ogg, 8-oxoguanine DNA-glycosylase (ogg). All proteins
in this family for which functions are known are
8-oxo-guanaine DNA glycosylases that function in base
excision repair. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University). This family is distantly realted
to the Nth-MutY superfamily.
Length = 310
Score = 38.7 bits (90), Expect = 0.001
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 14/88 (15%)
Query: 92 QNYIRTIGI-YRKKSENIISLSHILINEFDNKI-PQTLEG---------LTRLPGIGRKG 140
+ ++R +G+ YR + I + L+ E + Q + G L LPG+G K
Sbjct: 175 EAHLRKLGLGYRARY--IRETARALLEEQGGRAWLQQIRGASYEDAREALCELPGVGPKV 232
Query: 141 ANVILSMAFGIPTI-GVDTHIFRISNRI 167
A+ I M P VD H++RI+NR
Sbjct: 233 ADCICLMGLDKPQAVPVDVHVWRIANRD 260
>gnl|CDD|151111 pfam10576, EndIII_4Fe-2S, Iron-sulfur binding domain of
endonuclease III. Escherichia coli endonuclease III (EC
4.2.99.18) is a DNA repair enzyme that acts both as a
DNA N-glycosylase, removing oxidized pyrimidines from
DNA, and as an apurinic/apyrimidinic (AP) endonuclease,
introducing a single-strand nick at the site from which
the damaged base was removed. Endonuclease III is an
iron-sulfur protein that binds a single 4Fe-4S cluster.
The 4Fe-4S cluster does not seem to be important for
catalytic activity, but is probably involved in the
proper positioning of the enzyme along the DNA strand.
The 4Fe-4S cluster is bound by four cysteines which are
all located in a 17 amino acid region at the C-terminal
end of endonuclease III. A similar region is also
present in the central section of mutY and in the
C-terminus of ORF-10 and of the Micro-coccus UV
endonuclease.
Length = 17
Score = 36.2 bits (85), Expect = 0.007
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 206 CKARKPQCQSCIISNLC 222
C ARKP+C+ C +++LC
Sbjct: 1 CTARKPKCEECPLADLC 17
>gnl|CDD|128798 smart00525, FES, FES domain. iron-sulpphur binding domain in
DNA-(apurinic or apyrimidinic site) lyase (subfamily of
ENDO3).
Length = 21
Score = 34.5 bits (80), Expect = 0.023
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 205 VCKARKPQCQSCIISNLC 222
+C ARKP+C C + +LC
Sbjct: 1 ICTARKPRCDECPLKDLC 18
>gnl|CDD|182370 PRK10308, PRK10308, 3-methyl-adenine DNA glycosylase II;
Provisional.
Length = 283
Score = 33.2 bits (76), Expect = 0.064
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 9/69 (13%)
Query: 79 TPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSH-ILINEFDNKIP----QTLEGLTRL 133
TP+++ A + L + +G+ K++E +I L++ L IP Q ++ L
Sbjct: 157 TPERLAAADPQAL----KALGMPLKRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTF 212
Query: 134 PGIGRKGAN 142
PGIGR AN
Sbjct: 213 PGIGRWTAN 221
>gnl|CDD|129193 TIGR00084, ruvA, Holliday junction DNA helicase, RuvA subunit.
RuvA specifically binds Holliday junctions as a sandwich
of two tetramers and maintains the configuration of the
junction. It forms a complex with two hexameric rings of
RuvB, the subunit that contains helicase activity. The
complex drives ATP-dependent branch migration of the
Holliday junction recombination intermediate. The
endonuclease RuvC resolves junctions.
Length = 191
Score = 29.3 bits (66), Expect = 0.88
Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 95 IRTIGIYRKKSENIISLSHILINEFDNKI-PQTLEGLTRLPGIGRKGANVIL 145
I+ G+ K + I LS++ EF I + ++ L ++PG+G+K A +L
Sbjct: 75 IKVNGVGPKLALAI--LSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124
>gnl|CDD|178801 PRK00024, PRK00024, hypothetical protein; Reviewed.
Length = 224
Score = 28.9 bits (66), Expect = 1.0
Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 23/79 (29%)
Query: 76 IADTPQ------KMLAIGEKKLQNY------IRTIGIYRKKSENIISLSHILINEFDN-- 121
I D P+ ++L G L + +RT G K ++++ L+ L+ F +
Sbjct: 3 IKDWPEEERPRERLLKYGAAALSDAELLAILLRT-GT---KGKSVLDLARELLQRFGSLR 58
Query: 122 ---KIPQTLEGLTRLPGIG 137
+LE L + GIG
Sbjct: 59 GLLDA--SLEELQSIKGIG 75
>gnl|CDD|183792 PRK12850, groEL, chaperonin GroEL; Reviewed.
Length = 544
Score = 28.9 bits (65), Expect = 1.1
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 136 IGRKGANVILSMAFGIPTIGVD 157
+G KG NV+L +FG P I D
Sbjct: 31 LGPKGRNVVLEKSFGAPRITKD 52
>gnl|CDD|178794 PRK00013, groEL, chaperonin GroEL; Reviewed.
Length = 542
Score = 28.5 bits (65), Expect = 1.3
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 3/24 (12%)
Query: 136 IGRKGANVILSMAFGIPTI---GV 156
+G KG NV+L +FG PTI GV
Sbjct: 30 LGPKGRNVVLEKSFGAPTITKDGV 53
>gnl|CDD|177864 PLN02217, PLN02217, probable pectinesterase/pectinesterase
inhibitor.
Length = 670
Score = 28.5 bits (63), Expect = 1.4
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 64 VNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENII 109
V VN++ HL I D P K + G K +Y I Y+ + I+
Sbjct: 293 VQVNRSMTHLVFIGDGPDKTVISGSK---SYKDGITTYKTATVAIV 335
>gnl|CDD|183791 PRK12849, groEL, chaperonin GroEL; Reviewed.
Length = 542
Score = 28.2 bits (64), Expect = 1.6
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 3/24 (12%)
Query: 136 IGRKGANVILSMAFGIPTI---GV 156
+G KG NV++ +FG PTI GV
Sbjct: 30 LGPKGRNVVIDKSFGAPTITKDGV 53
>gnl|CDD|162814 TIGR02348, GroEL, chaperonin GroL. This family consists of GroEL,
the larger subunit of the GroEL/GroES cytosolic
chaperonin. It is found in bacteria, organelles derived
from bacteria, and occasionally in the Archaea. The
bacterial GroEL/GroES group I chaperonin is replaced a
group II chaperonin, usually called the thermosome in
the Archaeota and CCT (chaperone-containing TCP) in the
Eukaryota. GroEL, thermosome subunits, and CCT subunits
all fall under the scope of Pfam model pfam00118.
Length = 524
Score = 28.4 bits (64), Expect = 1.7
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 136 IGRKGANVILSMAFGIPTIGVD 157
+G KG NV+L +FG PTI D
Sbjct: 29 LGPKGRNVVLEKSFGAPTITKD 50
>gnl|CDD|184762 PRK14606, ruvA, Holliday junction DNA helicase RuvA; Provisional.
Length = 188
Score = 28.1 bits (62), Expect = 1.9
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 125 QTLEGLTRLPGIGRKGANVIL 145
Q +EGL++LPGI +K A I+
Sbjct: 105 QDVEGLSKLPGISKKTAERIV 125
>gnl|CDD|151424 pfam10977, DUF2797, Protein of unknown function (DUF2797). This
family of proteins has no known function.
Length = 233
Score = 27.7 bits (62), Expect = 2.5
Identities = 6/16 (37%), Positives = 9/16 (56%)
Query: 204 YVCKARKPQCQSCIIS 219
Y C ++ QC CI+
Sbjct: 31 YPCFSKLAQCDLCIMK 46
>gnl|CDD|161960 TIGR00615, recR, recombination protein RecR. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University).
Length = 195
Score = 27.7 bits (62), Expect = 2.7
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 119 FDNKIPQTLEGLTRLPGIGRKGA 141
+ I + +E L +LPGIG K A
Sbjct: 2 YPPPISKLIESLKKLPGIGPKSA 24
>gnl|CDD|181177 PRK07945, PRK07945, hypothetical protein; Provisional.
Length = 335
Score = 27.6 bits (62), Expect = 2.7
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 130 LTRLPGIGRKGANVI 144
LT LPGIG K A VI
Sbjct: 51 LTSLPGIGPKTAKVI 65
>gnl|CDD|171771 PRK12852, groEL, chaperonin GroEL; Reviewed.
Length = 545
Score = 27.5 bits (61), Expect = 3.2
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 136 IGRKGANVILSMAFGIPTIGVD 157
+G KG NV++ +FG P I D
Sbjct: 31 LGPKGRNVVIEKSFGAPRITKD 52
>gnl|CDD|173066 PRK14602, ruvA, Holliday junction DNA helicase RuvA; Provisional.
Length = 203
Score = 27.0 bits (60), Expect = 4.2
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 130 LTRLPGIGRKGANVIL 145
LTR+ GIG+K A I
Sbjct: 111 LTRVSGIGKKTAQHIF 126
>gnl|CDD|185455 PTZ00114, PTZ00114, Heat shock protein 60; Provisional.
Length = 555
Score = 26.8 bits (60), Expect = 5.1
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 3/23 (13%)
Query: 137 GRKGANVILSMAFGIPTI---GV 156
G KG NVI+ +G P I GV
Sbjct: 43 GPKGRNVIIEQEYGSPKITKDGV 65
>gnl|CDD|172594 PRK14104, PRK14104, chaperonin GroEL; Provisional.
Length = 546
Score = 26.5 bits (58), Expect = 5.5
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 136 IGRKGANVILSMAFGIPTIGVD 157
+G KG NV+L +FG P I D
Sbjct: 31 LGPKGRNVVLDKSFGAPRITKD 52
>gnl|CDD|172944 PRK14469, PRK14469, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 343
Score = 26.6 bits (59), Expect = 5.6
Identities = 11/33 (33%), Positives = 23/33 (69%)
Query: 91 LQNYIRTIGIYRKKSENIISLSHILINEFDNKI 123
++ I + IY+KK+ N +++ +ILI F+++I
Sbjct: 234 IEEIINAVKIYQKKTGNRVTIEYILIKGFNDEI 266
>gnl|CDD|178876 PRK00116, ruvA, Holliday junction DNA helicase RuvA; Reviewed.
Length = 192
Score = 26.6 bits (60), Expect = 5.8
Identities = 8/12 (66%), Positives = 11/12 (91%)
Query: 130 LTRLPGIGRKGA 141
LT++PGIG+K A
Sbjct: 110 LTKVPGIGKKTA 121
>gnl|CDD|131842 TIGR02795, tol_pal_ybgF, tol-pal system protein YbgF. Members of
this protein family are the product of one of seven
genes regularly clustered in operons to encode the
proteins of the tol-pal system, which is critical for
maintaining the integrity of the bacterial outer
membrane. The gene for this periplasmic protein has been
designated orf2 and ybgF. All members of the seed
alignment were from unique tol-pal gene regions from
completed bacterial genomes. The architecture of this
protein is a signal sequence, a low-complexity region
usually rich in Asn and Gln, a well-conserved region
with tandem repeats that resemble the tetratricopeptide
(TPR) repeat, involved in protein-protein interaction.
Length = 119
Score = 26.5 bits (59), Expect = 6.2
Identities = 9/13 (69%), Positives = 9/13 (69%), Gaps = 2/13 (15%)
Query: 188 PKHQY--NAHYWL 198
PK Y NAHYWL
Sbjct: 33 PKSTYAPNAHYWL 45
>gnl|CDD|128574 smart00278, HhH1, Helix-hairpin-helix DNA-binding motif class 1.
Length = 20
Score = 26.1 bits (59), Expect = 6.9
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 130 LTRLPGIGRKGANVILSM 147
L ++PGIG K A IL
Sbjct: 3 LLKVPGIGPKTAEKILEA 20
>gnl|CDD|171770 PRK12851, groEL, chaperonin GroEL; Reviewed.
Length = 541
Score = 26.2 bits (58), Expect = 6.9
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 127 LEGLTRLPG-----IGRKGANVILSMAFGIPTIGVD 157
L G+ L +G KG NV++ +FG PTI D
Sbjct: 17 LRGVNILADAVKVTLGPKGRNVVIDKSFGAPTITND 52
>gnl|CDD|114830 pfam06134, RhaA, L-rhamnose isomerase (RhaA). This family consists
of several bacterial L-rhamnose isomerase proteins
(EC:5.3.1.14).
Length = 416
Score = 26.3 bits (58), Expect = 7.2
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 5/30 (16%)
Query: 171 PGK--TPNKVEQSL---LRIIPPKHQYNAH 195
PGK TP ++ L L +IP KH+ N H
Sbjct: 64 PGKATTPEELRADLEKALSLIPGKHRLNLH 93
>gnl|CDD|178844 PRK00076, recR, recombination protein RecR; Reviewed.
Length = 196
Score = 25.8 bits (58), Expect = 8.4
Identities = 11/22 (50%), Positives = 13/22 (59%), Gaps = 3/22 (13%)
Query: 128 EGLTRLPGIGRKGANVILSMAF 149
E L +LPGIG K A +AF
Sbjct: 11 EALRKLPGIGPKSA---QRLAF 29
>gnl|CDD|130809 TIGR01748, rhaA, L-rhamnose isomerase. This enzyme interconverts
L-rhamnose and L-rhamnulose. In some species, including
E. coli, this is the first step in rhamnose catabolism.
Sequential steps are catalyzed by rhamnulose kinase
(rhaB), then rhamnulose-1-phosphate aldolase (rhaD) to
yield glycerone phosphate and (S)-lactaldehyde.
Characterization of this family is based on members in
E. coli and Salmonella.
Length = 414
Score = 26.0 bits (57), Expect = 8.6
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 5/30 (16%)
Query: 171 PGK--TPNKVEQSL---LRIIPPKHQYNAH 195
PGK TP+++ L + +IP KH+ N H
Sbjct: 62 PGKARTPSELRADLEKAMSLIPGKHRLNLH 91
>gnl|CDD|129520 TIGR00426, TIGR00426, competence protein ComEA helix-hairpin-helix
repeat region. Members of the subfamily recognized by
this model include competence protein ComEA and closely
related proteins from a number of species that exhibit
competence for transformation by exongenous DNA,
including Streptococcus pneumoniae, Bacillus subtilis,
Neisseria meningitidis, and Haemophilus influenzae. This
model represents a region of two tandem copies of a
helix-hairpin-helix domain (pfam00633), each about 30
residues in length. Limited sequence similarity can be
found among some members of this family N-terminal to
the region covered by this model.
Length = 69
Score = 26.0 bits (57), Expect = 8.8
Identities = 20/80 (25%), Positives = 33/80 (41%), Gaps = 25/80 (31%)
Query: 60 QSTDVNVNKATKHLFEIADTPQKMLAIGEKKLQNYIRTIGIYRKKSENIISLSHILINEF 119
+ T VN+N AT E+ + M +G KK + + YR++
Sbjct: 4 EGTRVNINTAT--AEELQ---RAMNGVGLKKAEAIVS----YREEYGPF----------- 43
Query: 120 DNKIPQTLEGLTRLPGIGRK 139
+T+E L ++PGIG
Sbjct: 44 -----KTVEDLKQVPGIGNS 58
>gnl|CDD|148130 pfam06330, TRI5, Trichodiene synthase (TRI5). This family
consists of several fungal trichodiene synthase
proteins (EC:4.2.3.6). TRI5 encodes the enzyme
trichodiene synthase, which has been shown to catalyse
the first step in the trichothecene pathways of
Fusarium and Trichothecium species.
Length = 376
Score = 25.6 bits (56), Expect = 9.6
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 67 NKATKHLFEIADTPQKMLAIGEKKLQNYIRTI 98
NKA H + Q++L + K+LQ +RTI
Sbjct: 41 NKAAHHFAQ--PRQQQILKVDPKRLQASLRTI 70
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
0.321 0.138 0.411
Gapped
Lambda K H
0.267 0.0744 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,601,542
Number of extensions: 221812
Number of successful extensions: 478
Number of sequences better than 10.0: 1
Number of HSP's gapped: 473
Number of HSP's successfully gapped: 45
Length of query: 227
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 137
Effective length of database: 4,049,753
Effective search space: 554816161
Effective search space used: 554816161
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: 55 (24.9 bits)