RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 021493
(311 letters)
>gnl|CDD|211589 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 [DNA metabolism, DNA
replication, recombination, and repair].
Length = 310
Score = 194 bits (494), Expect = 3e-60
Identities = 102/257 (39%), Positives = 149/257 (57%), Gaps = 8/257 (3%)
Query: 37 KWTPLNLTQSELSLPLTFPTGQTFRWK-KTGPLQYTGPI---GPHLISLKHLQNGDVCY- 91
+W + + +SEL L L +GQ+FRW+ + P ++G + + +L + +C
Sbjct: 4 RWASIPIPRSELRLDLVLRSGQSFRWRWEESPAHWSGLLVIADQPVWTLTQTEEQLLCTV 63
Query: 92 HIHTSPSEPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECL 151
+ P++ ++ L + + +SL +L+ + + D F +A+ G R+LRQDP ECL
Sbjct: 64 YRGDKPTQDELETKLEKYFQLDVSLAQLYTHWGSVDKHFQYVAQKFQGVRLLRQDPFECL 123
Query: 152 LQFLCSSNNNIARITKMVDFLASL-GSHLGNVEGFEFHEFPSLERL-SLVSEVELRNAGF 209
+ F+CSSNNNIARIT+MV+ L G L ++G +H FPSL L +E LR G
Sbjct: 124 ISFICSSNNNIARITRMVERLCQAFGPRLITLDGVTYHGFPSLHALTGPEAEAHLRKLGL 183
Query: 210 GYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLD 269
GYRA+YI T L + GG WL +R ++A +ALC LPGVGPKVA CI L LD
Sbjct: 184 GYRARYIRETARAL-LEEQGGRAWLQQIRGASYEDAREALCELPGVGPKVADCICLMGLD 242
Query: 270 QHHAIPVDTHVWKIATR 286
+ A+PVD HVW+IA R
Sbjct: 243 KPQAVPVDVHVWRIANR 259
>gnl|CDD|219650 pfam07934, OGG_N, 8-oxoguanine DNA glycosylase, N-terminal domain.
The presence of 8-oxoguanine residues in DNA can give
rise to G-C to T-A transversion mutations. This enzyme
is found in archaeal, bacterial and eukaryotic species,
and is specifically responsible for the process which
leads to the removal of 8-oxoguanine residues. It has
DNA glycosylase activity (EC:3.2.2.23) and DNA lyase
activity (EC:4.2.99.18). The region featured in this
family is the N-terminal domain, which is organised into
a single copy of a TBP-like fold. The domain contributes
residues to the 8-oxoguanine binding pocket.
Length = 113
Score = 108 bits (273), Expect = 1e-29
Identities = 44/114 (38%), Positives = 61/114 (53%), Gaps = 3/114 (2%)
Query: 40 PLNLTQSELSLPLTFPTGQTFRWKKTGPLQYTGPIGPHLISLKHLQNGDVCYHIHTSP-- 97
L L++ EL L LT +GQ+FRWKKT YTG IG ++ LK D+ Y
Sbjct: 1 SLPLSKEELDLKLTLLSGQSFRWKKTEDTSYTGVIGGRVVELKQ-DEDDLEYRFLGKEDL 59
Query: 98 SEPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECL 151
A+ L D+ ++ + L +L+E +S D F + A G R+LRQDP ECL
Sbjct: 60 KGKDAEEFLRDYFDLDVDLNDLYEQWSKKDPLFKKAADKFRGLRILRQDPFECL 113
>gnl|CDD|223200 COG0122, AlkA, 3-methyladenine DNA glycosylase/8-oxoguanine DNA
glycosylase [DNA replication, recombination, and
repair].
Length = 285
Score = 110 bits (276), Expect = 3e-28
Identities = 56/215 (26%), Positives = 79/215 (36%), Gaps = 12/215 (5%)
Query: 96 SPSEPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECLLQFL 155
S S + L L + L L DP E L++ +
Sbjct: 55 SASREPVAEDIEAALRRLFDLDPDLAPIIDALGPLPLLRAP-GLRLPLAPDPFEALVRAI 113
Query: 156 CSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGF-GYRAK 214
S ++A K+ L SL GN +H FP+ E+L+ E LR G G +A+
Sbjct: 114 LSQQVSVAAAAKIWARLVSL---YGNALE-IYHSFPTPEQLAAADEEALRRCGLSGRKAE 169
Query: 215 YITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAI 274
YI G L L+ L +EAI+ L L G+GP A LF L +
Sbjct: 170 YIISLARAAAE----GELDLSELKPLSDEEAIEELTALKGIGPWTAEMFLLFGLGRPDVF 225
Query: 275 PVDTHVWKIATRYLLPELAGVRLTPKLCSRVAEAF 309
P D + A + L R T K +AE +
Sbjct: 226 PADDLGLRRAIKKLYR--LPTRPTEKEVRELAERW 258
>gnl|CDD|238013 cd00056, ENDO3c, endonuclease III; includes endonuclease III
(DNA-(apurinic or apyrimidinic site) lyase), alkylbase
DNA glycosidases (Alka-family) and other DNA
glycosidases.
Length = 158
Score = 100 bits (251), Expect = 7e-26
Identities = 42/167 (25%), Positives = 60/167 (35%), Gaps = 29/167 (17%)
Query: 149 ECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAG 208
E L+ + S + K + L P+ E L+ E ELR
Sbjct: 2 EVLVSEILSQQTTDKAVNKAYERLFERY-------------GPTPEALAAADEEELRELI 48
Query: 209 FG----YRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIA 264
+AKY+ + G LD +A + L LPGVG K A +
Sbjct: 49 RSLGYRRKAKYLKELARAIVEGFGG--------LVLDDPDAREELLALPGVGRKTANVVL 100
Query: 265 LFSLDQHHAIPVDTHVWKIATRYLLPELAGVRLTPKLCSRVAEAFCE 311
LF+L A PVDTHV ++ R L + TP+ + E
Sbjct: 101 LFALGP-DAFPVDTHVRRVLKRLGLIPK---KKTPEELEELLEELLP 143
>gnl|CDD|214684 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 = 85.8 bits (213), Expect = 1e-20
Identities = 40/142 (28%), Positives = 60/142 (42%), Gaps = 31/142 (21%)
Query: 156 CSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVEL----RNAGFGY 211
S R+ K + L F +FP+ E L+ E EL R GF
Sbjct: 1 LSQQTTDERVNKATERL--------------FEKFPTPEDLAAADEEELEELIRGLGFYR 46
Query: 212 -RAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQ 270
+A+Y+ +L ++ G ++ + + L LPGVG K A + F+L +
Sbjct: 47 RKARYLIELARILVEEYGG-----------EVPDDREELLKLPGVGRKTANAVLSFALGK 95
Query: 271 HHAIPVDTHVWKIATRYLLPEL 292
IPVDTHV +IA R L +
Sbjct: 96 -PFIPVDTHVLRIAKRLGLVDK 116
>gnl|CDD|216088 pfam00730, HhH-GPD, HhH-GPD superfamily base excision DNA repair
protein. This family contains a diverse range of
structurally related DNA repair proteins. The
superfamily is called the HhH-GPD family after its
hallmark Helix-hairpin-helix and Gly/Pro rich loop
followed by a conserved aspartate. This includes
endonuclease III, EC:4.2.99.18 and MutY an A/G-specific
adenine glycosylase, both have a C terminal 4Fe-4S
cluster. The family also includes 8-oxoguanine DNA
glycosylases. The methyl-CPG binding protein MBD4 also
contains a related domain that is a thymine DNA
glycosylase. The family also includes
DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other
members of the AlkA family.
Length = 144
Score = 75.1 bits (185), Expect = 1e-16
Identities = 41/161 (25%), Positives = 61/161 (37%), Gaps = 27/161 (16%)
Query: 154 FLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNA----GF 209
+ S + K+ L FE + FP+ E L+ E ELR GF
Sbjct: 3 AILSQQTSDKAANKITKRL------------FERYGFPTPEDLAEADEEELRELIKGLGF 50
Query: 210 -GYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSL 268
+AKYI +L + G E ++AL LPGVG A + LF+L
Sbjct: 51 YRRKAKYIKELARILVEGYLG--------LVPLDLEELEALLALPGVGRWTAEAVLLFAL 102
Query: 269 DQH-HAIPVDTHVWKIATR-YLLPELAGVRLTPKLCSRVAE 307
+ VDTHV ++A R L+ + + +
Sbjct: 103 GRPDVFPAVDTHVRRVAKRLGLIDTKPPKKEVERELEELWP 143
>gnl|CDD|223255 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA
replication, recombination, and repair].
Length = 211
Score = 66.1 bits (162), Expect = 7e-13
Identities = 33/106 (31%), Positives = 46/106 (43%), Gaps = 19/106 (17%)
Query: 187 FHEFPSLERLSLVSEVEL----RNAGFGYR--AKYITGTVDVLQSKHSGGAEWLLSLRKL 240
F +P+ E L E EL ++ G YR AK I +L K G
Sbjct: 55 FKRYPTPEDLLNADEEELEELIKSIGL-YRNKAKNIKELARILLEKFGGEVP-------- 105
Query: 241 DLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATR 286
+ + L +LPGVG K A + F+ AI VDTHV +++ R
Sbjct: 106 ---DTREELLSLPGVGRKTANVVLSFAFG-IPAIAVDTHVHRVSNR 147
>gnl|CDD|224115 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication,
recombination, and repair].
Length = 342
Score = 39.2 bits (92), Expect = 0.002
Identities = 27/103 (26%), Positives = 47/103 (45%), Gaps = 16/103 (15%)
Query: 190 FPSLERLSLVSEVELRNA--GFGY--RAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEA 245
FP+++ L+ E E+ A G GY RA+ + + +H G + +
Sbjct: 63 FPTIKALAAAPEDEVLKAWEGLGYYSRARNLHKAAQEVVERHGG-----------EFPDD 111
Query: 246 IDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYL 288
+ L LPGVGP A I F+ +Q + +D +V ++ +R
Sbjct: 112 EEELAALPGVGPYTAGAILSFAFNQPEPV-LDGNVKRVLSRLF 153
>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 [DNA
metabolism, DNA replication, recombination, and repair].
Length = 275
Score = 38.2 bits (89), Expect = 0.003
Identities = 24/103 (23%), Positives = 46/103 (44%), Gaps = 16/103 (15%)
Query: 190 FPSLERLSLVSEVELRNA--GFGY--RAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEA 245
FP+++ L+ + E+ G GY RA+ + + + G + +
Sbjct: 55 FPTVQALANAPQDEVLKLWEGLGYYARARNLHKAAQEVVEEFGG-----------EFPQD 103
Query: 246 IDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYL 288
+ L LPGVG A I F+L++ + I +D +V ++ +R
Sbjct: 104 FEDLAALPGVGRYTAGAILSFALNKPYPI-LDGNVKRVLSRLF 145
>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 [DNA metabolism, DNA
replication, recombination, and repair].
Length = 191
Score = 37.3 bits (87), Expect = 0.004
Identities = 31/106 (29%), Positives = 48/106 (45%), Gaps = 19/106 (17%)
Query: 187 FHEFPSLERLSLVSEVEL----RNAGFGYR--AKYITGTVDVLQSKHSGGAEWLLSLRKL 240
F +P+ + L+ EL ++ G YR AK I +L ++ G
Sbjct: 52 FEVYPTPQALAQAGLEELEEYIKSIGL-YRNKAKNIIALCRILVERYGG----------- 99
Query: 241 DLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATR 286
++ E + L LPGVG K A + L AI VDTHV++++ R
Sbjct: 100 EVPEDREELVKLPGVGRKTAN-VVLNVAFGIPAIAVDTHVFRVSNR 144
>gnl|CDD|109681 pfam00633, HHH, Helix-hairpin-helix motif. The helix-hairpin-helix
DNA-binding motif is found to be duplicated in the
central domain of RuvA. The HhH domain of DisA, a
bacterial checkpoint control protein, is a DNA-binding
domain.
Length = 30
Score = 33.1 bits (77), Expect = 0.008
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 246 IDALCTLPGVGPKVAACIALF 266
+ L LPGVGPK A I +
Sbjct: 10 REELLALPGVGPKTAEAILSY 30
>gnl|CDD|234616 PRK00076, recR, recombination protein RecR; Reviewed.
Length = 196
Score = 35.5 bits (83), Expect = 0.017
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 241 DLQEAIDALCTLPGVGPKVAACIALFSLDQ 270
+++ I+AL LPG+GPK A +A L +
Sbjct: 5 PIEKLIEALRKLPGIGPKSAQRLAFHLLQR 34
>gnl|CDD|223430 COG0353, RecR, Recombinational DNA repair protein (RecF pathway)
[DNA replication, recombination, and repair].
Length = 198
Score = 34.9 bits (81), Expect = 0.031
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 241 DLQEAIDALCTLPGVGPKVAACIALFSLDQ 270
+++ IDAL LPGVGPK A +A L +
Sbjct: 6 PIEKLIDALKKLPGVGPKSAQRLAFHLLQR 35
>gnl|CDD|223017 PHA03235, PHA03235, DNA packaging protein UL33; Provisional.
Length = 409
Score = 32.5 bits (74), Expect = 0.30
Identities = 11/48 (22%), Positives = 16/48 (33%)
Query: 3 SLKNSPSPLKRPRLTPQPPPTPPNPQTLTTNKPSKWTPLNLTQSELSL 50
S +KR + P TP N + L+QS +L
Sbjct: 359 SSGTRQQKIKRSQSLNLPNATPKNKPKTRCAQNDTDNATRLSQSHHNL 406
>gnl|CDD|233054 TIGR00615, recR, recombination protein RecR. All proteins in this
family for which functions are known are involved in the
initiation of recombination and recombinational repair.
RecF is also required. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 195
Score = 31.2 bits (71), Expect = 0.44
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 242 LQEAIDALCTLPGVGPKVAACIALFSL 268
+ + I++L LPG+GPK A +A L
Sbjct: 6 ISKLIESLKKLPGIGPKSAQRLAFHLL 32
>gnl|CDD|182661 PRK10702, PRK10702, endonuclease III; Provisional.
Length = 211
Score = 31.1 bits (70), Expect = 0.51
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 12/78 (15%)
Query: 209 FGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSL 268
+ +A+ + T +L +H+G ++ E AL LPGVG K A + L +
Sbjct: 82 YNSKAENVIKTCRILLEQHNG-----------EVPEDRAALEALPGVGRKTAN-VVLNTA 129
Query: 269 DQHHAIPVDTHVWKIATR 286
I VDTH++++ R
Sbjct: 130 FGWPTIAVDTHIFRVCNR 147
>gnl|CDD|234645 PRK00116, ruvA, Holliday junction DNA helicase RuvA; Reviewed.
Length = 192
Score = 29.7 bits (68), Expect = 1.2
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 5/30 (16%)
Query: 241 DLQEAID-----ALCTLPGVGPKVAACIAL 265
+L +AI AL +PG+G K A I L
Sbjct: 97 ELVQAIANGDVKALTKVPGIGKKTAERIVL 126
>gnl|CDD|205093 pfam12826, HHH_2, Helix-hairpin-helix motif. The HhH domain of
DisA, a bacterial checkpoint control protein, is a
DNA-binding domain.
Length = 64
Score = 27.8 bits (63), Expect = 1.4
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 242 LQEA-IDALCTLPGVGPKVAACIALFSLDQHH 272
L A ++ L + +GP VA I F + +
Sbjct: 29 LANASVEELLEIDDIGPIVAQSIVEFFANPAN 60
>gnl|CDD|182805 PRK10880, PRK10880, adenine DNA glycosylase; Provisional.
Length = 350
Score = 30.1 bits (68), Expect = 1.4
Identities = 22/82 (26%), Positives = 34/82 (41%), Gaps = 14/82 (17%)
Query: 208 GFGY--RAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIAL 265
G GY RA+ + + + H G + E + + LPGVG A I
Sbjct: 79 GLGYYARARNLHKAAQQVATLHGG-----------EFPETFEEVAALPGVGRSTAGAILS 127
Query: 266 FSLDQHHAIPVDTHVWKIATRY 287
SL +H I +D +V ++ R
Sbjct: 128 LSLGKHFPI-LDGNVKRVLARC 148
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 30.3 bits (69), Expect = 1.5
Identities = 15/53 (28%), Positives = 19/53 (35%), Gaps = 6/53 (11%)
Query: 7 SPSPLKRPRLTPQPPPTPPNPQTLTTNKPSKWTPLNLTQ------SELSLPLT 53
SP P K P P T N + LNL + ++L LP T
Sbjct: 405 SPPPAKASPPIPVPAEPTEPSPTPPANAANAPPSLNLEELWQQILAKLELPST 457
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 30.3 bits (68), Expect = 1.7
Identities = 8/39 (20%), Positives = 11/39 (28%)
Query: 3 SLKNSPSPLKRPRLTPQPPPTPPNPQTLTTNKPSKWTPL 41
++ S P P+ PP P P P
Sbjct: 2890 AVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQ 2928
>gnl|CDD|236135 PRK07945, PRK07945, hypothetical protein; Provisional.
Length = 335
Score = 29.6 bits (67), Expect = 1.8
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 235 LSLRKLDLQEAIDALCTLPGVGPKVAACIA 264
L + + +L +LPG+GPK A IA
Sbjct: 37 LDAAERARRARAGSLTSLPGIGPKTAKVIA 66
>gnl|CDD|188255 TIGR02852, spore_dpaB, dipicolinic acid synthetase, B subunit.
Members of this family represent the B subunit of
dipicolinic acid synthetase, an enzyme that synthesizes
a small molecule that appears to confer heat stability
to bacterial endospores such as those of Bacillus
subtilis. The A and B subunits are together in what was
originally designated the spoVF locus for stage V of
endospore formation [Cellular processes, Sporulation and
germination].
Length = 187
Score = 29.3 bits (66), Expect = 1.9
Identities = 17/72 (23%), Positives = 30/72 (41%), Gaps = 9/72 (12%)
Query: 188 HEFPSLERLSLVSEVELRNAGFGYRAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAID 247
P LE +L G R ++ TV ++ GAEW+ + ++ +AI+
Sbjct: 16 AVMPQLE--------KLIAEGAEVRP-IVSYTVQSTNTRFGEGAEWIKKIEEITGFKAIN 66
Query: 248 ALCTLPGVGPKV 259
+ GPK+
Sbjct: 67 TIVEAEPFGPKI 78
>gnl|CDD|215145 PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygenase NCED.
Length = 590
Score = 29.7 bits (67), Expect = 2.6
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 2 QSLKNSPSPLKRPRLTPQPPPTPPNPQTLTTNKPSKWTPL 41
SL ++PS L P+L+ P P T + + PL
Sbjct: 42 SSLLHTPSILPLPKLSS-PSPPSVTLPPAATTQTPQLNPL 80
>gnl|CDD|217002 pfam02371, Transposase_20, Transposase IS116/IS110/IS902 family.
Transposases are needed for efficient transposition of
the insertion sequence or transposon DNA. This family
includes transposases for IS116, IS110 and IS902. This
region is often found with pfam01548. The exact function
of this region is uncertain. This family contains a HHH
motif suggesting a DNA-binding function.
Length = 87
Score = 27.5 bits (62), Expect = 2.7
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 247 DALCTLPGVGPKVAACIA 264
+ L ++PG+GP AA +
Sbjct: 2 ELLLSIPGIGPITAAALL 19
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 29.2 bits (65), Expect = 2.9
Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 10/60 (16%)
Query: 17 TPQPPPTPPNPQTLTTNKPSKWTPLNLTQSELSLPLTFPTGQTFRWKKTGPLQYTGPIGP 76
+P PPP PP P T+KP+ +P LSL Q+ PL + P
Sbjct: 1 SPPPPPQPP-PSLFPTSKPTTMSP------RLSL---SIKSQSATATDKQPLPNSNPDNT 50
>gnl|CDD|223705 COG0632, RuvA, Holliday junction resolvasome, DNA-binding subunit
[DNA replication, recombination, and repair].
Length = 201
Score = 28.4 bits (64), Expect = 3.6
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 5/25 (20%)
Query: 241 DLQEAID-----ALCTLPGVGPKVA 260
+L +AI AL +PG+G K A
Sbjct: 97 ELAQAIANEDVKALSKIPGIGKKTA 121
>gnl|CDD|214830 smart00813, Alpha-L-AF_C, Alpha-L-arabinofuranosidase C-terminus.
This entry represents the C terminus (approximately 200
residues) of bacterial and eukaryotic
alpha-L-arabinofuranosidase. This catalyses the
hydrolysis of non-reducing terminal
alpha-L-arabinofuranosidic linkages in
L-arabinose-containing polysaccharides.
Length = 189
Score = 28.4 bits (64), Expect = 3.8
Identities = 13/56 (23%), Positives = 20/56 (35%)
Query: 214 KYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLD 269
+D SK G + + +EA+ +L G+ K A L S D
Sbjct: 98 DSDVPALDASASKDEDGGSLTVKVVNRSPEEAVTVTISLRGLKAKSAEGTVLTSPD 153
>gnl|CDD|236137 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated.
Length = 665
Score = 28.6 bits (65), Expect = 5.0
Identities = 12/42 (28%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 231 AEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHH 272
A SL L + + L + GVG VA I F + +
Sbjct: 528 ARHFGSLEALR-AASEEELAAVEGVGEVVAQSIVEFFAVEEN 568
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 28.2 bits (63), Expect = 5.9
Identities = 11/67 (16%), Positives = 20/67 (29%), Gaps = 3/67 (4%)
Query: 2 QSLKNSPSPLKRPRLTPQPPPTPPNPQTLTTNKPS-KWTPLNLTQSELSLPLTFPTGQTF 60
+K+ + RL PP + T + P + S L+ +T
Sbjct: 360 SQIKSPA--FTQLRLESCPPQIKSSNSQQTVSSPQPQPVAKLEQGSLLTAASPQTKKETI 417
Query: 61 RWKKTGP 67
+ P
Sbjct: 418 HQEVPSP 424
>gnl|CDD|219448 pfam07522, DRMBL, DNA repair metallo-beta-lactamase. The
metallo-beta-lactamase fold contains five sequence
motifs. The first four motifs are found in pfam00753 and
are common to all metallo-beta-lactamases. The fifth
motif appears to be specific to function. This entry
represents the fifth motif from metallo-beta-lactamases
involved in DNA repair.
Length = 107
Score = 26.9 bits (60), Expect = 5.9
Identities = 19/56 (33%), Positives = 22/56 (39%), Gaps = 12/56 (21%)
Query: 55 PTGQTFRWKKTGPLQYTGPIGPHLISLKHLQNGDVCYHIHTSPSEPAAKSALLDFL 110
PTG TFR KT L P + V Y H+S SE L DF+
Sbjct: 48 PTGWTFRPPKTNVLDRIKPSRGKITIY------GVPYSEHSSFSE------LKDFV 91
>gnl|CDD|218658 pfam05616, Neisseria_TspB, Neisseria meningitidis TspB protein.
This family consists of several Neisseria meningitidis
TspB virulence factor proteins.
Length = 502
Score = 28.4 bits (63), Expect = 6.2
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 3/34 (8%)
Query: 5 KNSPSPLKRPRLTPQPPPTP---PNPQTLTTNKP 35
N+P+P + P P P P P P+ T +P
Sbjct: 342 ANNPNPRENPGTRPNPEPDPDLNPDANPDTDGQP 375
>gnl|CDD|184761 PRK14605, ruvA, Holliday junction DNA helicase RuvA; Provisional.
Length = 194
Score = 27.6 bits (61), Expect = 6.6
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 5/30 (16%)
Query: 241 DLQEAI-----DALCTLPGVGPKVAACIAL 265
L AI + L T+PG+G K A+ I L
Sbjct: 97 ALASAIISGNAELLSTIPGIGKKTASRIVL 126
>gnl|CDD|240521 cd13394, Syo1_like, Fungal symportin 1 (syo1) and similar proteins.
This family of eukaryotic proteins includes
Saccharomyces cerevisiae Ydl063c and Chaetomium
thermophilum Syo1, which mediate the co-import of two
ribosomal proteins, Rpl5 and Rpl11 (which both interact
with 5S rRNA) into the nucleus. Import precedes their
association with rRNA and subsequent ribosome assembly
in the nucleolus. The primary structure of syo1 is a
mixture of Armadillo- (ARM, N-terminal part of syo1) and
HEAT-repeats (C-terminal part of syo1).
Length = 597
Score = 28.0 bits (63), Expect = 7.7
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 133 LAKYLAGARVLRQDP---VECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVE 183
L K L G +L+Q+ ++ L++ ++ ++ + V L SL GN+E
Sbjct: 446 LLKSLGGEILLQQNTHDFIQSLIEA-SKTDADLELRVRCVGVLGSLAQVPGNIE 498
>gnl|CDD|114270 pfam05539, Pneumo_att_G, Pneumovirinae attachment membrane
glycoprotein G.
Length = 408
Score = 27.7 bits (61), Expect = 7.9
Identities = 16/56 (28%), Positives = 21/56 (37%), Gaps = 2/56 (3%)
Query: 2 QSLKNSPSPLKRPRLTPQPPPTPPNPQTLTTNKPSKWTPLNLTQSELSLPLTFPTG 57
Q K P+ R PP + T +P+ P TQS S P + P G
Sbjct: 269 QRRKTPPAT-SNRRSPHSTATPPPTTKRQETGRPTP-RPTATTQSGSSPPHSSPPG 322
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 27.7 bits (62), Expect = 8.2
Identities = 13/54 (24%), Positives = 18/54 (33%), Gaps = 1/54 (1%)
Query: 91 YHIHTSPSEPAAKSALLDFLNMGISLGELWEGFSASDC-RFAELAKYLAGARVL 143
HIH + L+ + + G + R LAGARVL
Sbjct: 284 VHIHVGLRSVTGRIVPLEKNAELNLVKPIALGDNDRLVLRDNSAVIKLAGARVL 337
>gnl|CDD|216421 pfam01299, Lamp, Lysosome-associated membrane glycoprotein (Lamp).
Length = 305
Score = 27.8 bits (62), Expect = 8.4
Identities = 14/58 (24%), Positives = 22/58 (37%), Gaps = 12/58 (20%)
Query: 5 KNSPSPLKRPRLTPQPPPTPPNPQTLTTNKPSKWTPLN------LTQSELSLPLTFPT 56
++PSP +P P P P +P ++ N L L L +T+ T
Sbjct: 83 ADTPSPTTVATPSPSPTPVPSSP------AVGNYSVTNGNGTCLLASMGLQLNITYET 134
>gnl|CDD|235123 PRK03381, PRK03381, PII uridylyl-transferase; Provisional.
Length = 774
Score = 27.6 bits (62), Expect = 9.2
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 7/49 (14%)
Query: 253 PGVGPKVAACIALFSLDQHHAIPVDTH------VWKIATRYLLPELAGV 295
G+ K A +AL L A V +H + ++ R+ P A +
Sbjct: 610 RGLLSKAAGVLALHRLRVRSAS-VRSHDGVAVLEFVVSPRFGSPPDAAL 657
>gnl|CDD|216648 pfam01690, PLRV_ORF5, Potato leaf roll virus readthrough protein.
This family consists mainly of the potato leaf roll
virus readthrough protein. This is generated via a
readthrough of open reading frame 3 a coat protein
allowing transcription of open reading frame 5 to give
an extended coat protein with a large c-terminal
addition or read through domain. The readthrough
protein is thought to play a role in the circulative
aphid transmission of potato leaf roll virus. Also in
the family is open reading frame 6 from beet western
yellows virus and potato leaf roll virus both
luteovirus and an unknown protein from cucurbit
aphid-borne yellows virus a closterovirus.
Length = 460
Score = 27.8 bits (62), Expect = 9.2
Identities = 9/22 (40%), Positives = 9/22 (40%)
Query: 7 SPSPLKRPRLTPQPPPTPPNPQ 28
P P P TP PP P P
Sbjct: 4 EPGPKPGPTPTPPPPAPTPEPT 25
>gnl|CDD|217835 pfam03999, MAP65_ASE1, Microtubule associated protein (MAP65/ASE1
family).
Length = 619
Score = 27.5 bits (61), Expect = 9.9
Identities = 16/54 (29%), Positives = 22/54 (40%)
Query: 6 NSPSPLKRPRLTPQPPPTPPNPQTLTTNKPSKWTPLNLTQSELSLPLTFPTGQT 59
P P P T N + +T+N PS NLT+S LS + + T
Sbjct: 457 MEPPYGSTESSVPSTPSTRRNDRNITSNTPSLKRTPNLTKSSLSQEASLISKST 510
>gnl|CDD|237540 PRK13880, PRK13880, conjugal transfer coupling protein TraG;
Provisional.
Length = 636
Score = 27.8 bits (62), Expect = 9.9
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 189 EFPSLERLSLVSEVELRNAGFGYRAKYITGTVDVLQSKHSG 229
EFPSL +L ++ E AG+G + I ++ L+S+ +G
Sbjct: 451 EFPSLGKLEILQESLAFVAGYGIKCYLICQDINQLKSRETG 491
>gnl|CDD|199842 cd03858, M14_CP_N-E_like, Peptidase M14 carboxypeptidase subfamily
N/E-like. Carboxypeptidase (CP) N/E-like subfamily of
the M14 family of metallocarboxypeptidases (MCPs). The
M14 family are zinc-binding CPs which hydrolyze single,
C-terminal amino acids from polypeptide chains, and have
a recognition site for the free C-terminal carboxyl
group, which is a key determinant of specificity. The
N/E subfamily includes eight members, of which five
(CPN, CPE, CPM, CPD, CPZ) are considered enzymatically
active, while the other three are non-active (CPX1,
PCX2, ACLP/AEBP1) and lack the critical active site and
substrate-binding residues considered necessary for CP
activity. These non-active members may function as
binding proteins or display catalytic activity towards
other substrates. Unlike the A/B CP subfamily, enzymes
belonging to the N/E subfamily are not produced as
inactive precursors that require proteolysis to produce
the active form; rather, they rely on their substrate
specificity and subcellular compartmentalization to
prevent inappropriate cleavages that would otherwise
damage the cell. In addition, all members of the N/E
subfamily contain an extra C-terminal domain that is not
present in the A/B subfamily. This domain has structural
homology to transthyretin and other proteins and has
been proposed to function as a folding domain. The
active N/E enzymes fulfill a variety of cellular
functions, including prohormone processing, regulation
of peptide hormone activity, alteration of
protein-protein or protein-cell interactions and
transcriptional regulation.
Length = 293
Score = 27.6 bits (62), Expect = 10.0
Identities = 12/41 (29%), Positives = 20/41 (48%), Gaps = 10/41 (24%)
Query: 151 LLQFLCSSNNNIARITKMVD-----FLASLGSHLGNVEGFE 186
L Q+LC + RIT +V+ + S+ N +G+E
Sbjct: 75 LAQYLCENYGGDPRITNLVNSTRIHIMPSM-----NPDGYE 110
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.136 0.420
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,995,644
Number of extensions: 1494181
Number of successful extensions: 1999
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1940
Number of HSP's successfully gapped: 61
Length of query: 311
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 214
Effective length of database: 6,635,264
Effective search space: 1419946496
Effective search space used: 1419946496
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: 59 (26.5 bits)