RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5133
(313 letters)
>gnl|CDD|233042 TIGR00598, rad14, DNA repair protein. All proteins in this family
for which functions are known are used for the
recognition of DNA damage as part of nucleotide excision
repair. 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 = 172
Score = 215 bits (549), Expect = 3e-70
Identities = 99/173 (57%), Positives = 125/173 (72%), Gaps = 1/173 (0%)
Query: 135 CVECKKKFPQSFLYDKFGHSVCDSCRDGESKHCLVTRTDAKNEYLLKDCDLDKREPVLRF 194
C EC K F S+L+D F +VCD+CRD + K+ L+T+T+AK EYLLKDCDLDKREP+LR
Sbjct: 1 CEECGKIFMDSYLFDHFDCAVCDNCRDKDDKYKLLTKTEAKEEYLLKDCDLDKREPLLRR 60
Query: 195 LRAKNPHNKHWGDMKLYLSLQVEQRAIEVWGSEEELEQERERRAEKASNSKLKQYNKKIK 254
+ KNPHN WGDMKLYL LQVE+RA+EVWGSEE L++E+ERR E K K++ KK+K
Sbjct: 61 IVKKNPHNPRWGDMKLYLKLQVEKRALEVWGSEEALDEEKERREESKEEMKEKKFEKKLK 120
Query: 255 ALRMAVRSSLFNKISTSPSSHSHQFGMEVHNEEDDTYTRKCSTCDFEETFEKI 307
LR AVRSS + H H+FG E + E+DTY R C+TC EET+EK+
Sbjct: 121 ELRRAVRSSEYTNKKEG-RVHEHEFGPETNGVEEDTYRRTCTTCGLEETYEKM 172
>gnl|CDD|227474 COG5145, RAD14, DNA excision repair protein [DNA replication,
recombination, and repair].
Length = 292
Score = 112 bits (280), Expect = 7e-29
Identities = 71/199 (35%), Positives = 103/199 (51%), Gaps = 4/199 (2%)
Query: 105 GGFLLDYDDKYEEKYIKQPAPLLLESEQPTCVECKKKFPQSFLYDKFGHSVCDSCRDG-E 163
G F + D+ +E P L + P C EC + L D FG SVC SCR
Sbjct: 90 GEFFAEEQDERKEVREDAPILLPIAL-APKCKECLQIELDDELEDTFGISVCRSCRHSMP 148
Query: 164 SKHCLVTRTDAKNEYLLKDCDLDKREPVLRFLRAKNPHNKHWGDMKLYLSLQVEQRAIEV 223
K+ L+T+T+ K++YLL D +L K + + R L+ NPH W M LYL +VEQ AI+
Sbjct: 149 DKYKLLTKTECKSDYLLTDPEL-KDQELFRRLQKPNPHKGTWSKMHLYLREEVEQFAIKK 207
Query: 224 WGSEEELEQERERRAEKASNSKLKQYNKKIKALRMAVRSSLFNKIST-SPSSHSHQFGME 282
WGS EEL++E++RR + + K K+ KKIK LR R+S ++++ H H F
Sbjct: 208 WGSLEELDREKQRREKMKDDRKEKKLEKKIKELRRKTRTSNYSRMDVREKEKHVHVFDEF 267
Query: 283 VHNEEDDTYTRKCSTCDFE 301
V + + +C E
Sbjct: 268 VDGPNEPGVIIQRCSCGLE 286
>gnl|CDD|147390 pfam05181, XPA_C, XPA protein C-terminus.
Length = 52
Score = 78.5 bits (194), Expect = 6e-19
Identities = 26/53 (49%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 164 SKHCLVTRTDAKNEYLLKDCDLDKREPVLRFLRAKNPHNKHWGDMKLYLSLQV 216
K+ L+T+T+ K +YLL D +L RE +L L NPH WGDM LYL QV
Sbjct: 1 EKYSLLTKTECKEDYLLTDPELKDRE-LLPHLLKPNPHKSTWGDMMLYLRCQV 52
>gnl|CDD|189926 pfam01286, XPA_N, XPA protein N-terminal.
Length = 34
Score = 43.5 bits (103), Expect = 2e-06
Identities = 16/33 (48%), Positives = 22/33 (66%)
Query: 131 EQPTCVECKKKFPQSFLYDKFGHSVCDSCRDGE 163
+ P C EC K F S+L++ F +VCD+CRD E
Sbjct: 2 DYPICEECGKPFMDSYLFNHFDCAVCDACRDAE 34
>gnl|CDD|220185 pfam09334, tRNA-synt_1g, tRNA synthetases class I (M). This family
includes methionyl tRNA synthetases.
Length = 388
Score = 31.8 bits (73), Expect = 0.42
Identities = 20/131 (15%), Positives = 41/131 (31%), Gaps = 24/131 (18%)
Query: 115 YEEKYIKQPAPLLLESEQPTCVECKKKFPQSFLYDKFGHSVCDSCRDGESKHC--LVTRT 172
YE+ I + E E CV ++ P ++ + + R + + C + T
Sbjct: 108 YEKGDIYEG-----EYEGWYCVSDERFLPDRYVEGTCPYCGSEDARGDQCEVCGRPLEPT 162
Query: 173 DAKNEYLLKDCDLDKREPVLRFLRAKNPHNKHWGDMKLYLSLQVEQRAIEVWGSEEELEQ 232
+ N + P L+ +H+ + L Q + W E ++
Sbjct: 163 ELINPR----SAISGSTPELK-------EEEHY-----FFRLSKFQDKLLEWIKENP-DE 205
Query: 233 ERERRAEKASN 243
E +
Sbjct: 206 PPSNVNEVVLS 216
>gnl|CDD|234622 PRK00085, recO, DNA repair protein RecO; Reviewed.
Length = 247
Score = 29.8 bits (68), Expect = 1.6
Identities = 9/34 (26%), Positives = 12/34 (35%)
Query: 135 CVECKKKFPQSFLYDKFGHSVCDSCRDGESKHCL 168
C C + K G +VC C D + L
Sbjct: 152 CAVCGAPGDHRYFSPKEGGAVCSECGDPYAIKLL 185
>gnl|CDD|218217 pfam04700, Baculo_gp41, Structural glycoprotein p40/gp41 conserved
region. Family of viral structural glycoproteins.
Length = 186
Score = 29.2 bits (66), Expect = 1.7
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 57 VRQTASAPSSCPQSPNLRSTTRLGGARSPGTIRSIINAVGSKLFTDTGGGFLLDY 111
+ Q A P + Q+ N R+ +L I IIN V LFT TG + +Y
Sbjct: 96 LLQKADIPPNIQQAINSRNNPQLN------MINDIINNVVDDLFTGTGNDYYYNY 144
>gnl|CDD|227070 COG4726, PilX, Tfp pilus assembly protein PilX [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 196
Score = 29.0 bits (65), Expect = 2.2
Identities = 17/104 (16%), Positives = 31/104 (29%), Gaps = 8/104 (7%)
Query: 17 ISLSAMQ----KEQIERN---RQRAIQIQQTRTRDLYDPYPN-PVKAGVRQTASAPSSCP 68
+ L+A + +E+I N R A Q + R+ N ++C
Sbjct: 30 LGLAAARSVLLQERISANERDRSLAFQAAEAALREGELQINNATAYPTSSACNFTANNCG 89
Query: 69 QSPNLRSTTRLGGARSPGTIRSIINAVGSKLFTDTGGGFLLDYD 112
P RL G S ++ G + + +
Sbjct: 90 AGPCNAVNGRLNGDCSSAPDNPVVVPKGVEAWKRSSDALSTTTL 133
>gnl|CDD|178071 PLN02452, PLN02452, phosphoserine transaminase.
Length = 365
Score = 29.3 bits (66), Expect = 2.8
Identities = 25/99 (25%), Positives = 36/99 (36%), Gaps = 39/99 (39%)
Query: 19 LSAMQKEQIERNRQRAIQIQQTRTRDLYDP-------YPNPVKAGVRQTASAPSSCPQSP 71
L AM+K RN ++A + LYD Y PV+ VR + P + S
Sbjct: 264 LKAMEK----RNIRKA-DL-------LYDAIDESNGFYVCPVEKSVRSLMNVPFTLGGSE 311
Query: 72 ---------------NLRSTTRLGGARSPGTIRSIINAV 95
L+ +GG R+ SI NA+
Sbjct: 312 LEAEFVKEAAKAGMVQLKGHRSVGGMRA-----SIYNAM 345
>gnl|CDD|220204 pfam09362, DUF1996, Domain of unknown function (DUF1996). This
family of proteins are functionally uncharacterized.
Length = 228
Score = 28.8 bits (65), Expect = 3.3
Identities = 10/39 (25%), Positives = 14/39 (35%), Gaps = 4/39 (10%)
Query: 270 TSPSSHSHQF----GMEVHNEEDDTYTRKCSTCDFEETF 304
PS+H HQ + D C++C E F
Sbjct: 8 QIPSAHVHQIVGGNAFDATMTYDLLLASTCTSCTNAEDF 46
>gnl|CDD|216874 pfam02099, Josephin, Josephin.
Length = 158
Score = 28.1 bits (63), Expect = 3.9
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 11/50 (22%)
Query: 184 DLDKREPVL--------RFLRAKNPHNKHWGDMKLYLSLQVEQRAIEVWG 225
+LD++E + + HN D S+QV + A+EVWG
Sbjct: 32 ELDQKERNKLSVEHWTPKSFLDEPSHNV---DDTGNFSIQVLETALEVWG 78
>gnl|CDD|215053 PLN00094, PLN00094, aconitate hydratase 2; Provisional.
Length = 938
Score = 29.1 bits (65), Expect = 4.2
Identities = 26/110 (23%), Positives = 43/110 (39%), Gaps = 12/110 (10%)
Query: 57 VRQTASAPSSCPQSPNLRSTTRLGGA-------RSPGTIRSIINAVGSKLFTDTGGGFLL 109
VR + S T R RS G I +I+ S T + GFL
Sbjct: 14 VRVRSFGLLGTRLSRCTSDTARSSTTLLPLLRTRSTGVI-PVISLQSSASATVSASGFLA 72
Query: 110 DYDDKYEEKYIKQPAPLLLESEQPTCVECKKKFPQS----FLYDKFGHSV 155
+Y+ E+ + AP L+++Q + + + + P+S L D + V
Sbjct: 73 EYEAHVAERAQEGIAPKPLDAKQVSELIAQLEAPKSEDADRLVDLLVNRV 122
>gnl|CDD|217720 pfam03770, IPK, Inositol polyphosphate kinase. ArgRIII has has
been demonstrated to be an inositol polyphosphate
kinase.
Length = 183
Score = 28.3 bits (64), Expect = 4.4
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 267 KISTSPSSHSHQF---GMEVHNEEDDTYT-------RKCSTCDFEETFEKIF 308
+ +S S F GM+V+N ++D Y R S + +E ++ F
Sbjct: 40 RKCAQSTSASLGFRICGMKVYNVDEDGYIFRDKYYGRSLSAEEVKEALKRFF 91
>gnl|CDD|176137 cd08446, PBP2_Chlorocatechol, The C-terminal substrate binding
domain of LysR-type transcriptional regulators involved
in the chlorocatechol catabolism, contains the type 2
periplasmic binding fold. This CD includes the
substrate binding domain of LysR-type regulators CbnR,
ClcR and TfdR, which are involved in the regulation of
chlorocatechol breakdown. The
chlorocatechol-degradative pathway is often found in
bacteria that can use chlorinated aromatic compounds as
carbon and energy sources. CbnR is found in the
3-chlorobenzoate degradative bacterium Ralstonia
eutropha NH9 and forms a tetramer. CbnR activates the
expression of the cbnABCD genes, which are responsible
for the degradation of chlorocatechol converted from
3-chlorobenzoate and are transcribed divergently from
cbnR. In soil bacterium Pseudomonas putida, the
3-chlorocatechol-degradative pathway is encoded by
clcABD operon, which requires the divergently
transcribed clcR for activation. TfdR is involved in
the activation of tfdA and tfdB gene expression. These
genes encode enzymes for the conversion of
2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol.
The topology of this substrate-binding domain is most
similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake
of a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 198
Score = 28.0 bits (63), Expect = 4.6
Identities = 12/23 (52%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 16 TISLSAMQK-EQIERNRQRAIQI 37
T+SL M K EQIE R I I
Sbjct: 31 TVSLHNMTKDEQIEALRAGRIHI 53
>gnl|CDD|236130 PRK07914, PRK07914, hypothetical protein; Reviewed.
Length = 320
Score = 28.2 bits (63), Expect = 5.4
Identities = 11/38 (28%), Positives = 17/38 (44%), Gaps = 10/38 (26%)
Query: 78 RLGGARSPGTIRSIINAVGS----------KLFTDTGG 105
L T+ ++++AVGS +L DTGG
Sbjct: 143 SLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTGG 180
>gnl|CDD|218039 pfam04351, PilP, Pilus assembly protein, PilP. The PilP family
are periplasmic proteins involved in the biogenesis of
type IV pili.
Length = 148
Score = 27.5 bits (62), Expect = 6.2
Identities = 9/31 (29%), Positives = 12/31 (38%), Gaps = 1/31 (3%)
Query: 44 DLYDPYPNPVKAGVRQTASAPSSCPQSPNLR 74
L P+ P +A SC Q P+L
Sbjct: 35 GLRSPFSPPKPETDEAQEAAGKSCVQ-PDLN 64
>gnl|CDD|239642 cd03670, ADPRase_NUDT9, ADP-ribose pyrophosphatase (ADPRase)
catalyzes the hydrolysis of ADP-ribose to AMP and
ribose-5-P. Like other members of the Nudix hydrolase
superfamily of enzymes, it is thought to require a
divalent cation, such as Mg2+, for its activity. It also
contains a 23-residue Nudix motif (GX5EX7REUXEEXGU,
where U = I, L or V) which functions as a metal binding
site/catalytic site. In addition to the Nudix motif,
there are additional conserved amino acid residues,
distal from the signature sequence, that correlate with
substrate specificity. In humans, there are four
distinct ADPRase activities, three putative cytosolic
(ADPRase-I, -II, and -Mn) and a single mitochondrial
enzyme (ADPRase-m). ADPRase-m is also known as NUDT9. It
can be distinugished from the cytosolic ADPRase by a
N-terminal target sequence unique to mitochondrial
ADPRase. NUDT9 functions as a monomer.
Length = 186
Score = 27.5 bits (61), Expect = 6.9
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 9/59 (15%)
Query: 186 DKREPVLRFLRAKNPHNKHW---GDM-----KLYLSLQVEQRAIEVWGSEEELEQERER 236
+P+L+F+ K P + W G M K+ +L+ E E S ++ ++E+E
Sbjct: 43 KSGKPILQFVAIKRPDSGEWAIPGGMVDPGEKISATLKREFGE-EALNSLQKSDEEKEE 100
>gnl|CDD|235912 PRK07028, PRK07028, bifunctional hexulose-6-phosphate
synthase/ribonuclease regulator; Validated.
Length = 430
Score = 28.1 bits (63), Expect = 7.2
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 215 QVEQRAIEVWGSEEELEQERERRAEKASNSKLKQYNKK 252
++ +RA+EV +E+ + +E R + +LK++ KK
Sbjct: 392 EIARRALEVKKTEDRIREEIRRGRTLSEVIELKKWEKK 429
>gnl|CDD|181512 PRK08637, PRK08637, hypothetical protein; Provisional.
Length = 388
Score = 27.6 bits (62), Expect = 8.4
Identities = 10/49 (20%), Positives = 19/49 (38%), Gaps = 12/49 (24%)
Query: 14 SKTISLSAMQKEQIERNRQRAIQIQQTRTR------------DLYDPYP 50
S++ L A+ + ++ +Q QI + R D + YP
Sbjct: 274 SQSAVLRALNSPEFDKEKQEKFQILKERYEKTKEVLYDGKYDDAWQAYP 322
>gnl|CDD|222462 pfam13934, ELYS, Nuclear pore complex assembly. ELYS (embryonic
large molecule derived from yolk sac) is conserved from
fungi such Aspergillus nidulans and Schizosaccharomyces
pombe to human. It is important for the assembly of the
nuclear pore complex.
Length = 225
Score = 27.6 bits (62), Expect = 8.7
Identities = 13/37 (35%), Positives = 15/37 (40%), Gaps = 7/37 (18%)
Query: 161 DGESKHCLVTRTDAKNEYLLKDCDLDKREPVLRFLRA 197
D KH L+ YLL D D + E F RA
Sbjct: 42 DLLHKHALIY-------YLLLDLDQTRTELSEDFARA 71
>gnl|CDD|215072 PLN00141, PLN00141, Tic62-NAD(P)-related group II protein;
Provisional.
Length = 251
Score = 27.5 bits (61), Expect = 8.9
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 53 VKAGVRQTASAPSSCPQSPNLR 74
VKAGVR A +S PQ P+L+
Sbjct: 44 VKAGVRDVDKAKTSLPQDPSLQ 65
>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 558
Score = 27.6 bits (62), Expect = 9.6
Identities = 22/98 (22%), Positives = 33/98 (33%), Gaps = 26/98 (26%)
Query: 111 YDDKYEEKYIKQPAPLLLESEQPTCVECKKKFPQSFLYDKFGHSVCDSCRDGESK--HC- 167
+ YE I L E E CV C + FL D++ C C +++ C
Sbjct: 110 FLKLYENGDIY-----LREYEGLYCVSC-----ERFLPDRYVEGTCPKCGGEDARGDQCE 159
Query: 168 ----LVTRTDAKNEYLLKDCDLDKREPVLR-----FLR 196
+ T+ N C + P +R F R
Sbjct: 160 NCGRTLDPTELINPV----CVISGATPEVREEEHYFFR 193
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
0.315 0.130 0.380
Gapped
Lambda K H
0.267 0.0714 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,338,510
Number of extensions: 1417990
Number of successful extensions: 1780
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1770
Number of HSP's successfully gapped: 50
Length of query: 313
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 216
Effective length of database: 6,635,264
Effective search space: 1433217024
Effective search space used: 1433217024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.5 bits)