RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 020295
(328 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 = 182 bits (464), Expect = 1e-55
Identities = 102/274 (37%), Positives = 149/274 (54%), Gaps = 25/274 (9%)
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 GYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTL 269
GYR A+YI T L + GG WL +R ++A +ALC L
Sbjct: 184 GYR-----------------ARYIRETARAL-LEEQGGRAWLQQIRGASYEDAREALCEL 225
Query: 270 PGVGPKVAACIALFSLDQHHAIPVDTHVWKIATR 303
PGVGPKVA CI L LD+ A+PVD HVW+IA R
Sbjct: 226 PGVGPKVADCICLMGLDKPQAVPVDVHVWRIANR 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 (272), Expect = 2e-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 = 99.4 bits (248), Expect = 3e-24
Identities = 57/231 (24%), Positives = 80/231 (34%), Gaps = 27/231 (11%)
Query: 96 SPSEPAAKSALLDFLNMGISLGELWEGFSASDCRFAELAKYLAGARVLRQDPVECLLQFL 155
S S + L L + L L DP E L++ +
Sbjct: 55 SASREPVAEDIEAALRRLFDLDPDLAPIIDALGPLPLLRAP-GLRLPLAPDPFEALVRAI 113
Query: 156 CSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRSAP 215
S ++A K+ L SL GN +H FP+ E+L+ E LR G
Sbjct: 114 LSQQVSVAAAAKIWARLVSL---YGNALE-IYHSFPTPEQLAAADEEALRRCGL------ 163
Query: 216 QSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPK 275
S R+ A+YI G L L+ L +EAI+ L L G+GP
Sbjct: 164 ------SGRK----AEYIISLARAAAE----GELDLSELKPLSDEEAIEELTALKGIGPW 209
Query: 276 VAACIALFSLDQHHAIPVDTHVWKIATRYLLPELAGVRLTPKLCSRVAEAF 326
A LF L + P D + A + L R T K +AE +
Sbjct: 210 TAEMFLLFGLGRPDVFPADDLGLRRAIKKLYR--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 = 93.1 bits (232), Expect = 4e-23
Identities = 46/182 (25%), Positives = 64/182 (35%), Gaps = 42/182 (23%)
Query: 149 ECLLQFLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAG 208
E L+ + S + K + L P+ E L+ E ELR
Sbjct: 2 EVLVSEILSQQTTDKAVNKAYERLFERY-------------GPTPEALAAADEEELRELI 48
Query: 209 F--GYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDAL 266
GYR R+ AKY+ + G LD +A + L
Sbjct: 49 RSLGYR-----------RK----AKYLKELARAIVEGFGG--------LVLDDPDAREEL 85
Query: 267 CTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPELAGVRLTPKLCSRVAEAF 326
LPGVG K A + LF+L A PVDTHV ++ R L + TP+ + E
Sbjct: 86 LALPGVGRKTANVVLLFALGP-DAFPVDTHVRRVLKRLGLIPK---KKTPEELEELLEEL 141
Query: 327 CE 328
Sbjct: 142 LP 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 = 78.8 bits (195), Expect = 6e-18
Identities = 41/158 (25%), Positives = 61/158 (38%), Gaps = 46/158 (29%)
Query: 156 CSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVEL----RNAGFGY 211
S R+ K + L F +FP+ E L+ E EL R GF
Sbjct: 1 LSQQTTDERVNKATERL--------------FEKFPTPEDLAAADEEELEELIRGLGFYR 46
Query: 212 RSAPQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPG 271
R +A+Y+ +L ++ G ++ + + L LPG
Sbjct: 47 R----------------KARYLIELARILVEEYGG-----------EVPDDREELLKLPG 79
Query: 272 VGPKVAACIALFSLDQHHAIPVDTHVWKIATRYLLPEL 309
VG K A + F+L + IPVDTHV +IA R L +
Sbjct: 80 VGRKTANAVLSFALGK-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 = 70.8 bits (174), Expect = 4e-15
Identities = 42/173 (24%), Positives = 62/173 (35%), Gaps = 34/173 (19%)
Query: 154 FLCSSNNNIARITKMVDFLASLGSHLGNVEGFEFHEFPSLERLSLVSEVELRNAGFGYRS 213
+ S + K+ L FE + FP+ E L+ E ELR G
Sbjct: 3 AILSQQTSDKAANKITKRL------------FERYGFPTPEDLAEADEEELRELIKGLG- 49
Query: 214 APQSSLLFSVRRSFKQAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVG 273
F R+ AKYI +L + G E ++AL LPGVG
Sbjct: 50 -------FYRRK----AKYIKELARILVEGYLG--------LVPLDLEELEALLALPGVG 90
Query: 274 PKVAACIALFSLDQH-HAIPVDTHVWKIATR-YLLPELAGVRLTPKLCSRVAE 324
A + LF+L + VDTHV ++A R L+ + + +
Sbjct: 91 RWTAEAVLLFALGRPDVFPAVDTHVRRVAKRLGLIDTKPPKKEVERELEELWP 143
>gnl|CDD|223255 COG0177, Nth, Predicted EndoIII-related endonuclease [DNA
replication, recombination, and repair].
Length = 211
Score = 61.4 bits (150), Expect = 4e-11
Identities = 33/121 (27%), Positives = 48/121 (39%), Gaps = 32/121 (26%)
Query: 187 FHEFPSLERLSLVSEVEL----RNAGFGYRSAPQSSLLFSVRRSFKQAKYITGTVDVLQS 242
F +P+ E L E EL ++ G YR+ +AK I +L
Sbjct: 55 FKRYPTPEDLLNADEEELEELIKSIGL-YRN---------------KAKNIKELARILLE 98
Query: 243 KHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIAT 302
K G + + L +LPGVG K A + F+ AI VDTHV +++
Sbjct: 99 KFGGEVP-----------DTREELLSLPGVGRKTANVVLSFAFG-IPAIAVDTHVHRVSN 146
Query: 303 R 303
R
Sbjct: 147 R 147
>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: 263 IDALCTLPGVGPKVAACIALF 283
+ L LPGVGPK A I +
Sbjct: 10 REELLALPGVGPKTAEAILSY 30
>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 = 35.8 bits (83), Expect = 0.013
Identities = 17/40 (42%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 264 DALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATR 303
+ L LPGVG K A + L AI VDTHV++++ R
Sbjct: 106 EELVKLPGVGRKTAN-VVLNVAFGIPAIAVDTHVFRVSNR 144
>gnl|CDD|234616 PRK00076, recR, recombination protein RecR; Reviewed.
Length = 196
Score = 35.5 bits (83), Expect = 0.018
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 258 DLQEAIDALCTLPGVGPKVAACIALFSLDQ 287
+++ I+AL LPG+GPK A +A L +
Sbjct: 5 PIEKLIEALRKLPGIGPKSAQRLAFHLLQR 34
>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 = 35.5 bits (82), Expect = 0.028
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 266 LCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYL 305
L LPGVG A I F+L++ + I +D +V ++ +R
Sbjct: 107 LAALPGVGRYTAGAILSFALNKPYPI-LDGNVKRVLSRLF 145
>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: 258 DLQEAIDALCTLPGVGPKVAACIALFSLDQ 287
+++ IDAL LPGVGPK A +A L +
Sbjct: 6 PIEKLIDALKKLPGVGPKSAQRLAFHLLQR 35
>gnl|CDD|224115 COG1194, MutY, A/G-specific DNA glycosylase [DNA replication,
recombination, and repair].
Length = 342
Score = 35.4 bits (82), Expect = 0.033
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 264 DALCTLPGVGPKVAACIALFSLDQHHAIPVDTHVWKIATRYL 305
+ L LPGVGP A I F+ +Q + +D +V ++ +R
Sbjct: 113 EELAALPGVGPYTAGAILSFAFNQPEPV-LDGNVKRVLSRLF 153
>gnl|CDD|223017 PHA03235, PHA03235, DNA packaging protein UL33; Provisional.
Length = 409
Score = 32.5 bits (74), Expect = 0.34
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 = 0.47
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 259 LQEAIDALCTLPGVGPKVAACIALFSL 285
+ + I++L LPG+GPK A +A L
Sbjct: 6 ISKLIESLKKLPGIGPKSAQRLAFHLL 32
>gnl|CDD|234645 PRK00116, ruvA, Holliday junction DNA helicase RuvA; Reviewed.
Length = 192
Score = 29.7 bits (68), Expect = 1.3
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 5/30 (16%)
Query: 258 DLQEAID-----ALCTLPGVGPKVAACIAL 282
+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 = 1.5
Identities = 9/32 (28%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 259 LQEA-IDALCTLPGVGPKVAACIALFSLDQHH 289
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 = 1.6
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 261 EAIDALCTLPGVGPKVAACIALFSLDQHHAI 291
E + + LPGVG A I SL +H I
Sbjct: 106 ETFEEVAALPGVGRSTAGAILSLSLGKHFPI 136
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 30.3 bits (69), Expect = 1.7
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 = 1.8
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 = 29.9 bits (68), Expect = 1.9
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 252 LSLRKLDLQEAIDALCTLPGVGPKVAACIA 281
L + + +L +LPG+GPK A IA
Sbjct: 37 LDAAERARRARAGSLTSLPGIGPKTAKVIA 66
>gnl|CDD|182661 PRK10702, PRK10702, endonuclease III; Provisional.
Length = 211
Score = 29.6 bits (66), Expect = 2.0
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 12/75 (16%)
Query: 229 QAKYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQH 288
+A+ + T +L +H+G ++ E AL LPGVG K A + L +
Sbjct: 85 KAENVIKTCRILLEQHNG-----------EVPEDRAALEALPGVGRKTAN-VVLNTAFGW 132
Query: 289 HAIPVDTHVWKIATR 303
I VDTH++++ R
Sbjct: 133 PTIAVDTHIFRVCNR 147
>gnl|CDD|215145 PLN02258, PLN02258, 9-cis-epoxycarotenoid dioxygenase NCED.
Length = 590
Score = 29.7 bits (67), Expect = 2.8
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 = 3.3
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 264 DALCTLPGVGPKVAACIA 281
+ L ++PG+GP AA +
Sbjct: 2 ELLLSIPGIGPITAAALL 19
>gnl|CDD|215382 PLN02712, PLN02712, arogenate dehydrogenase.
Length = 667
Score = 29.2 bits (65), Expect = 3.7
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 = 3.7
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 5/25 (20%)
Query: 258 DLQEAID-----ALCTLPGVGPKVA 277
+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 = 4.0
Identities = 13/56 (23%), Positives = 20/56 (35%)
Query: 231 KYITGTVDVLQSKHSGGAEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLD 286
+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 = 5.2
Identities = 12/42 (28%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 248 AEWLLSLRKLDLQEAIDALCTLPGVGPKVAACIALFSLDQHH 289
A SL L + + L + GVG VA I F + +
Sbjct: 528 ARHFGSLEALR-AASEEELAAVEGVGEVVAQSIVEFFAVEEN 568
>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 = 6.8
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 = 7.0
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 5/30 (16%)
Query: 258 DLQEAI-----DALCTLPGVGPKVAACIAL 282
L AI + L T+PG+G K A+ I L
Sbjct: 97 ALASAIISGNAELLSTIPGIGKKTASRIVL 126
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 28.2 bits (63), Expect = 7.2
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 = 7.4
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|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|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 = 8.7
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 = 8.8
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|235123 PRK03381, PRK03381, PII uridylyl-transferase; Provisional.
Length = 774
Score = 28.0 bits (63), Expect = 9.4
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 7/49 (14%)
Query: 270 PGVGPKVAACIALFSLDQHHAIPVDTH------VWKIATRYLLPELAGV 312
G+ K A +AL L A V +H + ++ R+ P A +
Sbjct: 610 RGLLSKAAGVLALHRLRVRSAS-VRSHDGVAVLEFVVSPRFGSPPDAAL 657
>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 = 9.5
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 0.135 0.415
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: 16,763,887
Number of extensions: 1562697
Number of successful extensions: 2037
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1982
Number of HSP's successfully gapped: 58
Length of query: 328
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 231
Effective length of database: 6,635,264
Effective search space: 1532745984
Effective search space used: 1532745984
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)