RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13670
(380 letters)
>gnl|CDD|223400 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA
replication, recombination, and repair].
Length = 638
Score = 162 bits (412), Expect = 1e-44
Identities = 81/378 (21%), Positives = 151/378 (39%), Gaps = 36/378 (9%)
Query: 2 KLVNEVYHQFN-NHQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDS 60
+ E Y + +YP +L +E+ + VDVNV P K+++ E+L+ + I ++
Sbjct: 270 HALREAYADYLPRGRYPVFVLFLELDPELVDVNVHPAKKEVRFSDERLVHDLIYEAIKEA 329
Query: 61 YAIGFTVDGNNMNQSMEQDPSSDVDMEKIQRSNSEEVEHETIPVPSEDNSNFSHEANLQQ 120
A G S+E +S S+ + P P ++ +
Sbjct: 330 LAQ----QGLIPPASVEA-----------PKSASQPLPAFQEPSPLPESRIQKSKVAKSG 374
Query: 121 SPETVEPDTPDETIEVIDDMPRLQGSYRQSTPVTLSLDIIQDQLKARYARRTVQAQDRCV 180
S ++ P + S + LS I + + +DR
Sbjct: 375 SSKSDAPSIAEPA-------SGASPSPASPSIRPLSK-NILPESSPGSL----KNEDRSY 422
Query: 181 ENRFHANIDPSKNKEAESELNRVIKKSMFEKMKIVGQFNLGFIIVKYDSDLFIIDQHATD 240
++ + E + I + +F + +GQ + +I+ +++ L ++DQHA
Sbjct: 423 DDLL--EEPAESEDKQEEAEQKAISEDVFPLGEAIGQVHGTYILAEHEDGLVLVDQHAAH 480
Query: 241 EKYNFETLQKT--TLIKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEFSFDSSDDGN 298
E+ +E L+ + + Q L++P L L+ +L+++ K GFE S + +
Sbjct: 481 ERILYEKLKNELGNVGELQPLLIPIRLELSPEEADVLEEHKEELEKLGFEIE--SFGENS 538
Query: 299 VLLTSLPMSKNTTLGREDIEELLFMLQHTNSTEHCRPSRIRAMFASRACRKSVMIGRALS 358
V + S+P +E I ELL L + + + A+ ACR +V GR LS
Sbjct: 539 VAVRSVPAMLGKAEVQELIRELLDDLLEGKLKDL--KELLEELAATMACRSAVKAGRELS 596
Query: 359 VGEMTGLVRNMGRIDQPW 376
EM L+R++ PW
Sbjct: 597 AEEMNALLRDLEACPNPW 614
>gnl|CDD|214857 smart00853, MutL_C, MutL C terminal dimerisation domain. MutL and
MutS are key components of the DNA repair machinery that
corrects replication errors. MutS recognises mispaired
or unpaired bases in a DNA duplex and in the presence of
ATP, recruits MutL to form a DNA signaling complex for
repair. The N terminal region of MutL contains the
ATPase domain and the C terminal is involved in
dimerisation.
Length = 140
Score = 122 bits (308), Expect = 5e-34
Identities = 41/144 (28%), Positives = 74/144 (51%), Gaps = 5/144 (3%)
Query: 214 IVGQFNLGFIIVKYDSDLFIIDQHATDEKYNFETLQ-KTTLIKSQKLVVPQNLHLTKINQ 272
+GQ +I+ + + L+++DQHA E+ +E L + ++SQ L++P L L+
Sbjct: 1 ALGQVAGTYILAEREDGLYLLDQHAAHERILYEQLLKQAGGLESQPLLIPVRLELSPQEA 60
Query: 273 CILKDNLPVFYKNGFEFSFDSSDDGNVLLTSLPMSKNTTLGREDIEELLFMLQHTNSTEH 332
+L+++L + + GFE +++L S+P ++ I ELL +L
Sbjct: 61 ALLEEHLELLRQLGFELEIFG--PQSLILRSVPALLRQQNLQKLIPELLDLLSDEEENAR 118
Query: 333 CRPSRIRAMFASRACRKSVMIGRA 356
PSR+ A+ AS ACR ++ G A
Sbjct: 119 --PSRLEALLASLACRSAIRAGDA 140
>gnl|CDD|219965 pfam08676, MutL_C, MutL C terminal dimerisation domain. MutL and
MutS are key components of the DNA repair machinery that
corrects replication errors. MutS recognises mispaired
or unpaired bases in a DNA duplex and in the presence of
ATP, recruits MutL to form a DNA signaling complex for
repair. The N terminal region of MutL contains the
ATPase domain and the C terminal is involved in
dimerisation.
Length = 144
Score = 95.0 bits (237), Expect = 1e-23
Identities = 37/147 (25%), Positives = 70/147 (47%), Gaps = 8/147 (5%)
Query: 213 KIVGQFNLGFIIVKYDSDLFIIDQHATDEKYNFETLQKTT--LIKSQKLVVPQNLHLTKI 270
K +GQ + +I+ + + L+++DQHA E+ +E L+ +SQ L++P L L+
Sbjct: 4 KALGQVHGTYILAENEDGLYLVDQHAAHERILYEKLKSKLKEGGQSQPLLIPLTLELSPE 63
Query: 271 NQCILKDNLPVFYKNGFEFSFDSSDDGNVLLTSLPMSKNTTLGREDIEELLFMLQHTNST 330
+L+++ + + GFE ++++ S+P E I ELL L +
Sbjct: 64 EAALLEEHKELLARLGFELE--EFGPNSLIVRSVPALLRQQNLEELIRELLDELAEKGES 121
Query: 331 EHCRPSRIRAMFASRACRKSVMIGRAL 357
E + + A+ AC ++ GR L
Sbjct: 122 E----ELLEELLATMACHSAIRAGRRL 144
>gnl|CDD|239566 cd03484, MutL_Trans_hPMS_2_like, MutL_Trans_hPMS2_like: transducer
domain, having a ribosomal S5 domain 2-like fold, found
in proteins similar to human PSM2 (hPSM2). hPSM2 belongs
to the DNA mismatch repair (MutL/MLH1/PMS2) family.
This transducer domain is homologous to the second
domain of the DNA gyrase B subunit, which is known to be
important in nucleotide hydrolysis and the transduction
of structural signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes. Included in
this group are proteins similar to yeast PMS1. The yeast
MLH1-PMS1 and the human MLH1-PMS2 heterodimers play a
role in meiosis. hMLH1-hPMS2 also participates in the
repair of all DNA mismatch repair (MMR) substrates.
Cells lacking hPMS2 have a strong mutator phenotype and
display microsatellite instability (MSI). Mutation in
hPMS2 causes predisposition to HPNCC and Turcot
syndrome.
Length = 142
Score = 90.4 bits (225), Expect = 6e-22
Identities = 29/61 (47%), Positives = 40/61 (65%)
Query: 2 KLVNEVYHQFNNHQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDSY 61
KL+NEVY FN+ QYPF ILNI + DVNVTPDKR + + E L+ T+K +++ +
Sbjct: 82 KLINEVYKSFNSRQYPFFILNISLPTSLYDVNVTPDKRTVLLHDEDRLIDTLKTSLSELF 141
Query: 62 A 62
Sbjct: 142 E 142
>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 88.7 bits (221), Expect = 4e-19
Identities = 68/383 (17%), Positives = 142/383 (37%), Gaps = 60/383 (15%)
Query: 2 KLVN----EVYHQF-NNHQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVH 56
KL+N + YH +YP +L +E+ VDVNV P K ++ E+L+ +
Sbjct: 261 KLLNHAIRQAYHDLLPRGRYPAFVLFLELDPHQVDVNVHPAKHEVRFRDERLVHDLIVQA 320
Query: 57 ITDSYAIGFTVDGNNMNQSMEQDPSSDVDMEKIQRSNSEEVEHETIPVPSEDNSNFSHEA 116
I ++ A + + + + ++ + S +
Sbjct: 321 IQEALAQ----------SGLIPAAAGANQVLEPAEPEPLPLQQTPLYASGSSPPASSPSS 370
Query: 117 NLQQSPETVEPDTPDETIEVIDDMPRLQGSYRQSTPVTLSLDIIQDQLKARYARRTVQAQ 176
+ E + ++ E + + + + + S +
Sbjct: 371 APPEQSEESQEESSAEKNPLQPNASQSEAAAAASAEAAAA-------------------- 410
Query: 177 DRCVENRFHANIDPSKNKEAESELNRVIKKSMFEKMKIVGQFNLGFIIVKYDSDLFIIDQ 236
A + EA E + F +GQ + +I+ + + L+++DQ
Sbjct: 411 ---------APAAAPEPAEAAEEADS------FPLGYALGQLHGTYILAENEDGLYLVDQ 455
Query: 237 HATDEKYNFETLQ---KTTLIKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEFSFDS 293
HA E+ +E L+ + SQ L++P L L++ L+++ + + G E
Sbjct: 456 HAAHERLLYEQLKDKLAEVGLASQPLLIPLVLELSEDEADRLEEHKELLARLGLELE--P 513
Query: 294 SDDGNVLLTSLPMSKNTTLGREDIEELLF-MLQHTNSTEHCRPSRIRAMFASRACRKSVM 352
+ + +P LG++++EEL+ +L + R + A+ AC ++
Sbjct: 514 FGPNSFAVREVP----ALLGQQELEELIRDLLDELAEEGDSDTLKERELLATMACHGAIR 569
Query: 353 IGRALSVGEMTGLVRNMGRIDQP 375
GR L++ EM L+R + + P
Sbjct: 570 AGRRLTLEEMNALLRQLEATENP 592
>gnl|CDD|238405 cd00782, MutL_Trans, MutL_Trans: transducer domain, having a
ribosomal S5 domain 2-like fold, conserved in the
C-terminal domain of DNA mismatch repair
(MutL/MLH1/PMS2) family. This transducer domain is
homologous to the second domain of the DNA gyrase B
subunit, which is known to be important in nucleotide
hydrolysis and the transduction of structural signals
from ATP-binding site to the DNA breakage/reunion
regions of the enzymes. Included in this group are
proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and
E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1
and MLH3. These three complexes have distinct functions
in meiosis. hMLH1-hPMS2 also participates in the repair
of all DNA mismatch repair (MMR) substrates. Roles for
hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been
established. Cells lacking either hMLH1 or hPMS2 have a
strong mutator phenotype and display microsatellite
instability (MSI). Mutation in hMLH1 causes
predisposition to HNPCC, Muir-Torre syndrome and Turcot
syndrome (HNPCC variant). Mutation in hPMS2 causes
predisposition to HPNCC and Turcot syndrome. Mutation in
hMLH1 accounts for a large fraction of HNPCC families.
There is no convincing evidence to support hPMS1 having
a role in HNPCC predisposition. It has been suggested
that hMLH3 may be a low risk gene for colorectal cancer;
however there is little evidence to support it having a
role in classical HNPCC. It has been suggested that
during initiation of DNA mismatch repair in E. coli, the
mismatch recognition protein MutS recruits MutL in the
presence of ATP. The MutS(ATP)-MutL ternary complex
formed, then recruits the latent endonuclease MutH.
Length = 122
Score = 69.1 bits (170), Expect = 2e-14
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 1 MKLVNEVYHQFNN-HQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITD 59
K +NE Y + +YP +LN+E+ + VDVNV P KR++ E+ +L ++ +
Sbjct: 61 SKAINEAYRSYLPKGRYPVFVLNLELPPELVDVNVHPTKREVRFSDEEEVLELIREALRS 120
Query: 60 SY 61
+
Sbjct: 121 AL 122
>gnl|CDD|201604 pfam01119, DNA_mis_repair, DNA mismatch repair protein, C-terminal
domain. This family represents the C-terminal domain of
the mutL/hexB/PMS1 family. This domain has a ribosomal
S5 domain 2-like fold.
Length = 119
Score = 56.7 bits (138), Expect = 3e-10
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 1 MKLVNEVYHQF-NNHQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITD 59
+ E Y +YP +L +E+ + VDVNV P KR++ E+ + ++ + +
Sbjct: 57 SHAIREAYRDLLPKGRYPVAVLFLEIDPELVDVNVHPAKREVRFRDEREVHDFIEEAVRE 116
Query: 60 SYA 62
+ A
Sbjct: 117 ALA 119
>gnl|CDD|233035 TIGR00585, mutl, DNA mismatch repair protein MutL. All proteins in
this family for which the functions are known are
involved in the process of generalized mismatch 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 = 312
Score = 50.7 bits (122), Expect = 4e-07
Identities = 19/42 (45%), Positives = 29/42 (69%), Gaps = 1/42 (2%)
Query: 2 KLVNEVYHQFN-NHQYPFIILNIEMSRDSVDVNVTPDKRQIF 42
K + EVYH++ QYP +LN+E+ + VDVNV PDK+++
Sbjct: 271 KAIREVYHEYLPKGQYPVFVLNLEIDPELVDVNVHPDKKEVR 312
>gnl|CDD|238202 cd00329, TopoII_MutL_Trans, MutL_Trans: transducer domain, having a
ribosomal S5 domain 2-like fold, conserved in the
C-terminal domain of type II DNA topoisomerases (Topo
II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins.
This transducer domain is homologous to the second
domain of the DNA gyrase B subunit, which is known to be
important in nucleotide hydrolysis and the transduction
of structural signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes. The GyrB
dimerizes in response to ATP binding, and is homologous
to the N-terminal half of eukaryotic Topo II and the
ATPase fragment of MutL. Type II DNA topoisomerases
catalyze the ATP-dependent transport of one DNA duplex
through another, in the process generating transient
double strand breaks via covalent attachments to both
DNA strands at the 5' positions. Included in this group
are proteins similar to human MLH1 and PMS2. MLH1 forms
a heterodimer with PMS2 which functions in meiosis and
in DNA mismatch repair (MMR). Cells lacking either hMLH1
or hPMS2 have a strong mutator phenotype and display
microsatellite instability (MSI). Mutation in hMLH1
accounts for a large fraction of Lynch syndrome (HNPCC)
families.
Length = 107
Score = 44.2 bits (105), Expect = 6e-06
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 2 KLVNEVYHQFNN----HQYPFIILNIEMSRDSVDVNVTPDKRQIF 42
K V E Y + N +YP +L++++ VDVNV P K ++
Sbjct: 63 KAVREAYTRALNGDDVRRYPVAVLSLKIPPSLVDVNVHPTKEEVR 107
>gnl|CDD|239567 cd03485, MutL_Trans_hPMS_1_like, MutL_Trans_hPMS1_like: transducer
domain, having a ribosomal S5 domain 2-like fold, found
in proteins similar to human PSM1 (hPSM1) and yeast
MLH2. hPSM1 and yMLH2 are members of the DNA mismatch
repair (MutL/MLH1/PMS2) family. This transducer domain
is homologous to the second domain of the DNA gyrase B
subunit, which is known to be important in nucleotide
hydrolysis and the transduction of structural signals
from ATP-binding site to the DNA breakage/reunion
regions of the enzymes. PMS1 forms a heterodimer with
MLH1. The MLH1-PMS1 complex functions in meiosis. Loss
of yMLH2 results in a small but significant decrease in
spore viability and a significant increase in gene
conversion frequencies. A role for hMLH1-hPMS1 in DNA
mismatch repair has not been established. Mutation in
hMLH1 accounts for a large fraction of Lynch syndrome
(HNPCC) families, however there is no convincing
evidence to support hPMS1 having a role in HNPCC
predisposition.
Length = 132
Score = 41.5 bits (98), Expect = 9e-05
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 1 MKLVNEVYHQ----FNNHQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLL 50
KL+ + Y + +YP LNI VDVN+ PDK + + +++ +L
Sbjct: 67 GKLLRQYYSSAYRKSSLRRYPVFFLNILCPPGLVDVNIEPDKDDVLLQNKEAVL 120
>gnl|CDD|239565 cd03483, MutL_Trans_MLH1, MutL_Trans_MLH1: transducer domain,
having a ribosomal S5 domain 2-like fold, found in
proteins similar to yeast and human MLH1 (MutL homologue
1). This transducer domain is homologous to the second
domain of the DNA gyrase B subunit, which is known to be
important in nucleotide hydrolysis and the transduction
of structural signals from ATP-binding site to the DNA
breakage/reunion regions of the enzymes. MLH1 forms
heterodimers with PMS2, PMS1 and MLH3. These three
complexes have distinct functions in meiosis.
hMLH1-hPMS2 also participates in the repair of all DNA
mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1
or hMLH1-hMLH3 in MMR have not been established. Cells
lacking hMLH1 have a strong mutator phenotype and
display microsatellite instability (MSI). Mutation in
hMLH1 causes predisposition to HNPCC, Muir-Torre
syndrome and Turcot syndrome (HNPCC variant). Mutation
in hMLH1 accounts for a large fraction of HNPCC
families.
Length = 127
Score = 38.8 bits (91), Expect = 8e-04
Identities = 16/59 (27%), Positives = 35/59 (59%), Gaps = 1/59 (1%)
Query: 2 KLVNEVYHQF-NNHQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITD 59
+ + VY + +PF+ L++E+ ++VDVNV P KR++ +E+ ++ ++ + D
Sbjct: 66 RAIENVYANYLPKGAHPFVYLSLEIPPENVDVNVHPTKREVHFLNEEEIIERIQKLVED 124
>gnl|CDD|173181 PRK14718, PRK14718, ribonuclease III; Provisional.
Length = 467
Score = 31.7 bits (71), Expect = 0.71
Identities = 19/64 (29%), Positives = 25/64 (39%), Gaps = 7/64 (10%)
Query: 80 PSSDVDMEKIQRSNSEEVEHETIPVPSEDNSNFSHEANLQQSPETVEPDTPDETIEVIDD 139
++D EK S E E P + SHE L +S E V D+T + D
Sbjct: 377 AATDKPPEKASDKPSPEKTSEKTP-------DKSHEKQLDKSSEPVAEKALDKTADKPDA 429
Query: 140 MPRL 143
RL
Sbjct: 430 AARL 433
>gnl|CDD|150663 pfam10015, DUF2258, Uncharacterized protein conserved in archaea
(DUF2258). Members of this family of hypothetical
bacterial archaeal have no known function. Structural
modelling suggests this domain may bind nucleic acids.
Length = 75
Score = 28.9 bits (65), Expect = 0.95
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 11/66 (16%)
Query: 166 ARYA---RRTVQAQDRCVENRFHANIDPSKNKEAESELNRVIKKSMFEKMKIVGQFNLGF 222
A YA RR + A + P + A SELN+ + + + E+MKI + ++
Sbjct: 10 AGYADKLRRVLFAA-------LSGKVPPKEIVRAISELNKKLFEKLVEEMKI-DKLDVVR 61
Query: 223 IIVKYD 228
I V Y+
Sbjct: 62 ISVDYE 67
>gnl|CDD|223062 PHA03373, PHA03373, tegument protein; Provisional.
Length = 247
Score = 30.2 bits (68), Expect = 1.6
Identities = 22/101 (21%), Positives = 43/101 (42%), Gaps = 15/101 (14%)
Query: 65 FTV-DGNNMNQSMEQ---DPSSDVDMEKIQR------SNS----EEVEHETIPVPSEDNS 110
FT+ + +++N+ +E+ D S+ ++EKI R NS E+ +
Sbjct: 127 FTMSETDSLNRLLEKFSTDQSTLCEVEKINRLVDMDGENSKRLLTELASADEAEVESASD 186
Query: 111 NFSHE-ANLQQSPETVEPDTPDETIEVIDDMPRLQGSYRQS 150
HE L Q+P ++ D + T + + P + R+
Sbjct: 187 PLLHEETGLPQAPPNLQQDEREGTGPPVTEQPSGRRKSRRK 227
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 30.7 bits (69), Expect = 1.7
Identities = 24/99 (24%), Positives = 47/99 (47%), Gaps = 9/99 (9%)
Query: 68 DGNNMNQSMEQDPSSDVDMEKIQRSNSEEVEH-ETIPVPSEDNSNFSHEANLQQSPETVE 126
N++N+ + +P+ + +E Q+SN + + E+ V ED++ L+ +
Sbjct: 3899 LSNSLNEKLWDEPNEEDLLETEQKSNEQSAANNESDLVSKEDDNK-----ALEDKDRQEK 3953
Query: 127 PDTPDETIEV-IDD--MPRLQGSYRQSTPVTLSLDIIQD 162
D + + +V IDD P +Q + Q P LD+ +D
Sbjct: 3954 EDEEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPED 3992
>gnl|CDD|238198 cd00321, SO_family_Moco, Sulfite oxidase (SO) family, molybdopterin
binding domain. This molybdopterin cofactor (Moco)
binding domain is found in a variety of oxidoreductases,
main members of this family are nitrate reductase (NR)
and sulfite oxidase (SO). SO catalyzes the terminal
reaction in the oxidative degradation of the
sulfur-containing amino acids cysteine and methionine.
Assimilatory NRs catalyze the reduction of nitrate to
nitrite which is subsequently converted to NH4+ by
nitrite reductase. Common features of all known members
of this family are that they contain one single pterin
cofactor and part of the coordination of the metal (Mo)
is a cysteine ligand of the protein and that they
catalyze the transfer of an oxygen to or from a lone
pair of electrons on the substrate.
Length = 156
Score = 28.3 bits (64), Expect = 4.4
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 5/34 (14%)
Query: 151 TPVTLSLDIIQDQLKARYARRTVQAQDRCVENRF 184
P++L+LD ++ + V A CV NR+
Sbjct: 27 KPLSLTLDDLK-----ALPQVEVIATLHCVGNRW 55
>gnl|CDD|185282 PRK15384, PRK15384, type III secretion system protein; Provisional.
Length = 336
Score = 28.1 bits (62), Expect = 7.4
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 9/68 (13%)
Query: 183 RFHANIDPSKNKEAESELNRVIKKSMFEKMKIVGQFNLGFIIVKYDSDLFIIDQHATDE- 241
RF N P N E LN +IK + EK +++G F D D F + A +
Sbjct: 58 RFGKNDIPIINTEKNPYLNNIIKAATIEKERLIGIF--------VDGDFFPGQKDAFSKL 109
Query: 242 KYNFETLQ 249
+Y++E ++
Sbjct: 110 EYDYENIK 117
>gnl|CDD|239564 cd03482, MutL_Trans_MutL, MutL_Trans_MutL: transducer domain,
having a ribosomal S5 domain 2-like fold, found in
proteins similar to Escherichia coli MutL. EcMutL
belongs to the DNA mismatch repair (MutL/MLH1/PMS2)
family. This transducer domain is homologous to the
second domain of the DNA gyrase B subunit, which is
known to be important in nucleotide hydrolysis and the
transduction of structural signals from the ATP-binding
site to the DNA breakage/reunion regions of the enzymes.
It has been suggested that during initiation of DNA
mismatch repair in E. coli, the mismatch recognition
protein MutS recruits MutL in the presence of ATP. The
MutS(ATP)-MutL ternary complex formed, then recruits the
latent endonuclease MutH. Prokaryotic MutS and MutL are
homodimers.
Length = 123
Score = 26.8 bits (60), Expect = 9.7
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 13 NHQYPFIILNIEMSRDSVDVNVTPDKRQI 41
++P +L +E+ VDVNV P K ++
Sbjct: 74 GGRHPAYVLYLELDPAQVDVNVHPAKHEV 102
>gnl|CDD|178532 PLN02946, PLN02946, cysteine-tRNA ligase.
Length = 557
Score = 28.0 bits (62), Expect = 9.7
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 82 SDVDMEKIQRSNSEEVEHETIPVPSEDNSNFSHE-ANLQQSPETVEPDTPDETIEVID 138
+DVD + I R+N E+ + I + F + A L P +VEP D ++ID
Sbjct: 126 TDVDDKIIARAN--ELGEDPISLSRRYCEEFLSDMAYLHCLPPSVEPRVSDHIPQIID 181
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
0.317 0.132 0.372
Gapped
Lambda K H
0.267 0.0707 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,896,659
Number of extensions: 1801176
Number of successful extensions: 1575
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1561
Number of HSP's successfully gapped: 40
Length of query: 380
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 281
Effective length of database: 6,546,556
Effective search space: 1839582236
Effective search space used: 1839582236
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 (21.7 bits)
S2: 60 (26.9 bits)