RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8492
(489 letters)
>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 = 68.9 bits (169), Expect = 4e-14
Identities = 31/96 (32%), Positives = 40/96 (41%), Gaps = 4/96 (4%)
Query: 279 VIAQVDKKYIVVLLNKTLLVAFDQHAVDERIRVEKLFS-YGAFLSHPI-TPCVLNLTPQE 336
+ QV YI+ L + DQHA ERI E+L G S P+ P L L+PQE
Sbjct: 1 ALGQVAGTYILAEREDGLYL-LDQHAAHERILYEQLLKQAGGLESQPLLIPVRLELSPQE 59
Query: 337 INTLSNRQTCLQYYGLEFEFKNTGKCVKVTHVPKCL 372
L L+ G E E + + VP L
Sbjct: 60 AALLEEHLELLRQLGFELEIFGPQS-LILRSVPALL 94
>gnl|CDD|239568 cd03486, MutL_Trans_MLH3, MutL_Trans_MLH3: transducer domain,
having a ribosomal S5 domain 2-like fold, found in
proteins similar to yeast and human MLH3 (MutL homologue
3). MLH3 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. MLH1 forms heterodimers with
MLH3. The MLH1-MLH3 complex plays a role in meiosis. A
role for hMLH1-hMLH3 in DNA mismatch repair (MMR) has
not been established. 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.
Length = 141
Score = 56.2 bits (136), Expect = 1e-09
Identities = 23/59 (38%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 219 HKREDYEVDGYISREPISQPQYQNIYINKRLVTNTILHDTINKLLVKSFYLNITKESNK 277
K ++YEV GYIS E +Q IY+N RL T H INKL K+ + K +
Sbjct: 23 AKFQEYEVSGYISSEGHYSKSFQFIYVNGRLYLKTRFHKLINKLFRKTSA--VAKNKSS 79
>gnl|CDD|143944 pfam00178, Ets, Ets-domain.
Length = 85
Score = 52.3 bits (126), Expect = 7e-09
Identities = 20/36 (55%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 430 PNVCLSKFTR--RYYYDKNIIHKTAGKRYVYRFVCD 463
PN+ K +R RYYY K II K GKR VY+FV D
Sbjct: 50 PNMNYDKLSRALRYYYKKGIIRKVKGKRLVYKFVSD 85
>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 = 52.6 bits (127), Expect = 2e-08
Identities = 30/97 (30%), Positives = 38/97 (39%), Gaps = 5/97 (5%)
Query: 279 VIAQVDKKYIVVLLNKTLLVAFDQHAVDERIRVEKLFSYGAFLSHP---ITPCVLNLTPQ 335
+ QV YI+ L + DQHA ERI EKL S + P L L+P+
Sbjct: 5 ALGQVHGTYILAENEDGLYL-VDQHAAHERILYEKLKSKLKEGGQSQPLLIPLTLELSPE 63
Query: 336 EINTLSNRQTCLQYYGLEFEFKNTGKCVKVTHVPKCL 372
E L + L G E E + V VP L
Sbjct: 64 EAALLEEHKELLARLGFELEEFGPNS-LIVRSVPALL 99
>gnl|CDD|197710 smart00413, ETS, erythroblast transformation specific domain.
variation of the helix-turn-helix motif.
Length = 87
Score = 50.0 bits (120), Expect = 5e-08
Identities = 19/37 (51%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 430 PNVCLSKFTR--RYYYDKNIIHKTAGKRYVYRFVCDL 464
PN+ K +R RYYY KNI+ K GKR VY+FV +
Sbjct: 50 PNMNYEKLSRALRYYYKKNILEKVPGKRLVYKFVKNP 86
>gnl|CDD|223400 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA
replication, recombination, and repair].
Length = 638
Score = 53.9 bits (130), Expect = 1e-07
Identities = 32/97 (32%), Positives = 43/97 (44%), Gaps = 5/97 (5%)
Query: 279 VIAQVDKKYIVVLLNKTLLVAFDQHAVDERIRVEKLFSYGAFLSH---PITPCVLNLTPQ 335
I QV YI+ ++ LV DQHA ERI EKL + + + P L L+P+
Sbjct: 454 AIGQVHGTYILAE-HEDGLVLVDQHAAHERILYEKLKNELGNVGELQPLLIPIRLELSPE 512
Query: 336 EINTLSNRQTCLQYYGLEFEFKNTGKCVKVTHVPKCL 372
E + L + L+ G E E V V VP L
Sbjct: 513 EADVLEEHKEELEKLGFEIE-SFGENSVAVRSVPAML 548
Score = 36.2 bits (84), Expect = 0.042
Identities = 16/67 (23%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 200 QLEVAKDIYAMKMVENF--PEHKREDYEVDGYISREPI---SQPQYQNIYINKRLVTNTI 254
E +Y + ++N E++ ED + GY+S P + YQ +++N R V + +
Sbjct: 209 LEERIAAVYGTEFLKNALPIENEHEDLRLSGYVSL-PEFTRASRDYQYLFVNGRPVRDKL 267
Query: 255 LHDTINK 261
L+ + +
Sbjct: 268 LNHALRE 274
>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 = 44.1 bits (105), Expect = 1e-05
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 10/65 (15%)
Query: 218 EHKREDYEVDGYISREPI--SQPQYQNIYINKRLVTNTILHDTINKLLVKS--------F 267
E + D+ + GYIS+ S Q +++N R V + +L IN+ F
Sbjct: 21 ELESGDFRISGYISKPDFGRSSKDRQFLFVNGRPVRDKLLSKAINEAYRSYLPKGRYPVF 80
Query: 268 YLNIT 272
LN+
Sbjct: 81 VLNLE 85
>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 = 40.2 bits (95), Expect = 3e-04
Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 10/65 (15%)
Query: 218 EHKREDYEVDGYISREPI--SQPQYQNIYINKRLVTNTILHDTINK----LLVK----SF 267
+ + E + G+IS+ + S YQ +++N R V + +L I + LL K
Sbjct: 17 DAEDEGLRLSGFISKPELSRSNRDYQYLFVNGRPVRDKLLSHAIREAYRDLLPKGRYPVA 76
Query: 268 YLNIT 272
L +
Sbjct: 77 VLFLE 81
>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 42.1 bits (100), Expect = 6e-04
Identities = 26/81 (32%), Positives = 37/81 (45%), Gaps = 5/81 (6%)
Query: 279 VIAQVDKKYIVVLLNKTLLVAFDQHAVDERIRVEKL---FSYGAFLSHP-ITPCVLNLTP 334
+ Q+ YI+ N+ L DQHA ER+ E+L + S P + P VL L+
Sbjct: 433 ALGQLHGTYIL-AENEDGLYLVDQHAAHERLLYEQLKDKLAEVGLASQPLLIPLVLELSE 491
Query: 335 QEINTLSNRQTCLQYYGLEFE 355
E + L + L GLE E
Sbjct: 492 DEADRLEEHKELLARLGLELE 512
Score = 33.7 bits (78), Expect = 0.26
Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 8/38 (21%)
Query: 218 EHKREDYEVDGYI-----SREPISQPQYQNIYINKRLV 250
+ + D + GY+ SR + YQ +++N R V
Sbjct: 224 DAEHGDLRLSGYVGLPTLSR---ANRDYQYLFVNGRYV 258
>gnl|CDD|212475 cd01728, LSm1, Like-Sm protein 1. The eukaryotic LSm proteins
(LSm1-7) assemble into a hetero-heptameric ring around
the 3'-terminus of the gamma-methyl triphosphate
(gamma-m-P3) capped U6 snRNA. Accumulation of uridylated
RNAs in an lsm1 mutant suggests an involvement of the
LSm1-7 complex in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. LSm1-7,
together with Pat1, are also called the decapping
activator. Members of this family share a highly
conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet.
Length = 74
Score = 31.7 bits (73), Expect = 0.11
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 10/47 (21%)
Query: 280 IAQVDKKYIVVLLNKTLLV----AFDQHA------VDERIRVEKLFS 316
++DKK +VVL + L+ +FDQ A ERI V +
Sbjct: 8 EEELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYG 54
>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 = 31.5 bits (72), Expect = 0.23
Identities = 12/69 (17%), Positives = 23/69 (33%), Gaps = 14/69 (20%)
Query: 218 EHKREDYEVDGYISREPISQPQ--YQNIYINKRLVT---------NTILHDTINKLLVK- 265
E + + + V+G IS + Q ++N R V +N V+
Sbjct: 21 EGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREGGTHVKAVREAYTRALNGDDVRR 80
Query: 266 --SFYLNIT 272
L++
Sbjct: 81 YPVAVLSLK 89
>gnl|CDD|217496 pfam03327, Herpes_VP19C, Herpesvirus capsid shell protein VP19C.
Length = 266
Score = 31.5 bits (72), Expect = 0.74
Identities = 29/171 (16%), Positives = 48/171 (28%), Gaps = 55/171 (32%)
Query: 323 HPITPCVLNLTPQEINTLSNRQTCL----QYYGLEFEFKNTGK---CVKVTHVPKCLFVK 375
P+ P V N++ + + TC+ N K VK+ VP F+
Sbjct: 99 TPVGPLVSNVSSTFLALI----TCVMRGPVE--------NARKPEIRVKL-VVPADAFLD 145
Query: 376 VHKEEDRIRENQTSREPTSTVYDKVCLG-RESNPQSSACKHVF--PRKHHVLRSPMYPNV 432
+ + RE R S VY + + + +VF L
Sbjct: 146 L--DATLGRE---PRGGLSYVY--LVFVYTQRLNREGPRLYVFKSILGESTLLD------ 192
Query: 433 CLSKFTRRYYYDKNIIHKTAGKRYVYRFVCDLQ---------TLLGYSPEE 474
L RYY+ + + + LG P +
Sbjct: 193 LL-----RYYFSRERFNN-----LIRDLRGRPTINSLCYGAVCRLGTCPSD 233
>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 = 29.9 bits (68), Expect = 1.3
Identities = 17/79 (21%), Positives = 29/79 (36%), Gaps = 13/79 (16%)
Query: 206 DIYAMKMVENFPEHKREDYEVDGYISREPI----SQPQYQNIYINKRLVT--------NT 253
+ +++ + + ++ GYIS+ S Q YIN R V N
Sbjct: 27 VNPTKEELDSDEDLADSEVKITGYISKPSHGCGRSSSDRQFFYINGRPVDLKKVAKLINE 86
Query: 254 ILHDTINKLLVKSFYLNIT 272
+ + N F LNI+
Sbjct: 87 VYK-SFNSRQYPFFILNIS 104
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains
separated by a hinge in the middle. The eukaryotic SMC
proteins form two kind of heterodimers: the SMC1/SMC3
and the SMC2/SMC4 types. These heterodimers constitute
an essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 31.1 bits (70), Expect = 1.9
Identities = 29/210 (13%), Positives = 75/210 (35%), Gaps = 1/210 (0%)
Query: 2 VENFPEHKREVKRRDISRTREKIKPKIVQQQEKENTDTLVKENKCQPNEPKNYAREVKRS 61
+ +R + + +REK K K ++ E T+ L + + ++
Sbjct: 148 IAMMKPERRLEIEEEAAGSREKRKKKERLKKLIEETENLAELIIDLEELKLQELKLKEQ- 206
Query: 62 EMVTASHSDPSPRNEMVKETRASVTSLKSKIQQLKEENRKRKRKDIKKIATSFHNKRNLQ 121
+ + E+ +E + LK +++ + + + ++ ++ +
Sbjct: 207 AKKALEYYQLKEKLELEEENLLYLDYLKLNEERIDLLQELLRDEQEEIESSKQELEKEEE 266
Query: 122 YLDERPKITHSNGKNDQNYRKQRKEQSLPTEQSNVTLNNERKYCEDNIKVDNNLERKTKY 181
L + K K + ++ K + E+ L + D+ + E++ K
Sbjct: 267 ILAQVLKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKK 326
Query: 182 CLEANEQKPEEAEEIAIEQLEVAKDIYAMK 211
+ +++ EE EE+ E E+ A +
Sbjct: 327 LEKELKKEKEEIEELEKELKELEIKREAEE 356
>gnl|CDD|223036 PHA03295, PHA03295, envelope glycoprotein H; Provisional.
Length = 714
Score = 30.8 bits (70), Expect = 2.1
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 7/54 (12%)
Query: 320 FLSHPITPCVLNLTPQEINTLSNRQTCLQYYGLEFEFKNTGKCVKVTHVPKCLF 373
FL T C +N N N QT ++ + F F G +V VP+CLF
Sbjct: 34 FLRSNSTRCCVN------NETRN-QTVVREGLITFNFYEDGNTYRVYQVPRCLF 80
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 30.3 bits (68), Expect = 2.7
Identities = 26/115 (22%), Positives = 56/115 (48%), Gaps = 5/115 (4%)
Query: 60 RSEMVTASHSDPSPRNEMVKETRASVTSLKSKIQQLKEENRKRKRKDIKKIATSFHNKRN 119
++E+ A ++ RN++ T SLKS + QLK+EN + K ++ +K++
Sbjct: 419 QAELQQARQNESELRNQISLLTSLE-RSLKSDLGQLKKENDMLQTKLNSMVSAKQKDKQS 477
Query: 120 LQYLDERPKITH----SNGKNDQNYRKQRKEQSLPTEQSNVTLNNERKYCEDNIK 170
+Q +++R K + K +K++KE+ ++ R+ C +++K
Sbjct: 478 MQSMEKRLKSEADSRVNAEKQLAEEKKRKKEEEETAARAAAQAAASREECAESLK 532
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 30.5 bits (68), Expect = 2.8
Identities = 39/219 (17%), Positives = 89/219 (40%), Gaps = 8/219 (3%)
Query: 7 EHKREVKRRDISRTREKIKPKIVQQQEKENTDTLVKENKCQPNEPKNYAREVKRSEMVTA 66
E K+ + ++++ + + K + + +E +E K + E K ++E +
Sbjct: 1568 EAKKAEEDKNMALRKAEEAKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKK 1627
Query: 67 SHSDPSPRNEMVKETRASVTSLKSKIQQLKEENRKRKRKDIKKIATSFHNKRNLQYLDER 126
+ + + V++ + K K ++LK+ + K K ++ + +K+ E
Sbjct: 1628 AEEE----KKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKA----EE 1679
Query: 127 PKITHSNGKNDQNYRKQRKEQSLPTEQSNVTLNNERKYCEDNIKVDNNLERKTKYCLEAN 186
K + K K+ E++ E+ E+K E+ K + + K + +
Sbjct: 1680 AKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEA 1739
Query: 187 EQKPEEAEEIAIEQLEVAKDIYAMKMVENFPEHKREDYE 225
E+ ++AEE ++ E K + K E E R++ E
Sbjct: 1740 EEDKKKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKE 1778
>gnl|CDD|224073 COG1151, COG1151, 6Fe-6S prismane cluster-containing protein
[Energy production and conversion].
Length = 576
Score = 30.1 bits (68), Expect = 3.1
Identities = 33/156 (21%), Positives = 51/156 (32%), Gaps = 45/156 (28%)
Query: 110 IATSFHNKRNLQYLDERPK---------ITHSNGKNDQNYRKQRKEQSL--------PTE 152
I + H+ +L+ L E+ + THS Y + RK + +
Sbjct: 252 ILITGHDLADLEELLEQAEGAGAKGINVYTHSEMLPAHGYPELRKYKHFVGNYGNWWQQQ 311
Query: 153 Q-------------SNVTLNNERKYCEDNIKVDNNLERKTKYCLEANEQKPEEAEEIAIE 199
SN L +KY D+ + + EEAEE E
Sbjct: 312 ALEFTGFVDPIVMTSNCILPPLKKYSYDDRIFTTGIAGLPGV-------EHEEAEEDFSE 364
Query: 200 QLEVAKDIYAMKMVENFPEHKREDYEVDGYISREPI 235
+E+A ENF K E +++ S E I
Sbjct: 365 VIEMAI--------ENFKNRKSEKHKIVVGFSHESI 392
>gnl|CDD|236370 PRK09064, PRK09064, 5-aminolevulinate synthase; Validated.
Length = 407
Score = 29.4 bits (67), Expect = 4.2
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 88 LKSKIQQLKEENRKRKRKDIKKIATSF 114
++ + +LK E R R D+++IA F
Sbjct: 7 FENALDRLKAEGRYRVFADLERIAGRF 33
>gnl|CDD|206729 cd04166, CysN_ATPS, CysN, together with protein CysD, forms the ATP
sulfurylase (ATPS) complex. CysN_ATPS subfamily. CysN,
together with protein CysD, form the ATP sulfurylase
(ATPS) complex in some bacteria and lower eukaryotes.
ATPS catalyzes the production of ATP sulfurylase (APS)
and pyrophosphate (PPi) from ATP and sulfate. CysD,
which catalyzes ATP hydrolysis, is a member of the ATP
pyrophosphatase (ATP PPase) family. CysN hydrolysis of
GTP is required for CysD hydrolysis of ATP; however,
CysN hydrolysis of GTP is not dependent on CysD
hydrolysis of ATP. CysN is an example of lateral gene
transfer followed by acquisition of new function. In
many organisms, an ATPS exists which is not
GTP-dependent and shares no sequence or structural
similarity to CysN.
Length = 209
Score = 29.1 bits (66), Expect = 4.3
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 5/37 (13%)
Query: 286 KYIVVLLNKTLLVAFDQHAVDERIRVEKLFSYGAFLS 322
+++VV +NK LV +D+ V E I+ + Y AF +
Sbjct: 132 RHVVVAVNKMDLVDYDE-EVFEEIKAD----YLAFAA 163
>gnl|CDD|139768 PRK13691, PRK13691, (3R)-hydroxyacyl-ACP dehydratase subunit HadC;
Provisional.
Length = 166
Score = 28.3 bits (63), Expect = 5.6
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 261 KLLVKSFYLNITKESNKLVIAQVDKKYIV---VLLNKTLLVAFDQHAVDER 308
K + F+ ++ + I QVD++++ VL L D H+VDER
Sbjct: 65 KYVQLDFFRHVDVGMETMQIVQVDQRFVFHKPVLAGDKLWARMDIHSVDER 115
>gnl|CDD|206643 cd00877, Ran, Ras-related nuclear proteins (Ran)/TC4 family of
small GTPases. Ran GTPase is involved in diverse
biological functions, such as nuclear transport, spindle
formation during mitosis, DNA replication, and cell
division. Among the Ras superfamily, Ran is a unique
small G protein. It does not have a lipid modification
motif at the C-terminus to bind to the membrane, which
is often observed within the Ras superfamily. Ran may
therefore interact with a wide range of proteins in
various intracellular locations. Like other GTPases, Ran
exists in GTP- and GDP-bound conformations that interact
differently with effectors. Conversion between these
forms and the assembly or disassembly of effector
complexes requires the interaction of regulator
proteins. The intrinsic GTPase activity of Ran is very
low, but it is greatly stimulated by a GTPase-activating
protein (RanGAP1) located in the cytoplasm. By contrast,
RCC1, a guanine nucleotide exchange factor that
generates RanGTP, is bound to chromatin and confined to
the nucleus. Ran itself is mobile and is actively
imported into the nucleus by a mechanism involving
NTF-2. Together with the compartmentalization of its
regulators, this is thought to produce a relatively high
concentration of RanGTP in the nucleus.
Length = 166
Score = 28.4 bits (64), Expect = 6.0
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 102 RKRKDIKKIATSFHNKRNLQYLD 124
K + +K +FH K+NLQY +
Sbjct: 116 IKDRKVKPKQITFHRKKNLQYYE 138
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 28.0 bits (63), Expect = 6.7
Identities = 11/60 (18%), Positives = 21/60 (35%), Gaps = 5/60 (8%)
Query: 269 LNITKESNKLVIAQVDKKYIVVLLNKTLLVAFDQHAVDERIRVEKLFSYGAFLSHPITPC 328
L +E KL + + K ++++LNK D E + + P+
Sbjct: 88 LTPVEEEAKLGLLRERGKPVLLVLNK-----IDLVPESEEEELLRERKLELLPDLPVIAV 142
>gnl|CDD|148511 pfam06936, Selenoprotein_S, Selenoprotein S (SelS). This family
consists of several mammalian selenoprotein S (SelS)
sequences. SelS is a plasma membrane protein and is
present in a variety of tissues and cell types. The
function of this family is unknown.
Length = 190
Score = 28.3 bits (63), Expect = 6.8
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 57 EVKRSEMVTASHSDPSPRNEMVKETRASVTSLKSKIQQLKEENRKRK 103
V+R E + A+ R M ++ A K K +QL+EE R++K
Sbjct: 78 VVRRQEALEAA------RLRMQEDLDAKAAKFKEKQKQLEEEKRRQK 118
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 29.1 bits (66), Expect = 7.0
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 286 KYIVVLLNKTLLVAFDQHAVDERIRVEKLFSYGAF 320
+++V+ +NK LV +DQ V + I + Y AF
Sbjct: 158 RHVVLAVNKMDLVDYDQ-EVFDEIVAD----YRAF 187
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 28.1 bits (63), Expect = 8.3
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 5/26 (19%)
Query: 99 NRKRKRKDIKKIATSFHNKRNLQYLD 124
+R+ K + I FH K+NLQY D
Sbjct: 127 DRQVKARQIT-----FHRKKNLQYYD 147
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 0.131 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: 24,089,084
Number of extensions: 2297594
Number of successful extensions: 2826
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2770
Number of HSP's successfully gapped: 140
Length of query: 489
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 388
Effective length of database: 6,457,848
Effective search space: 2505645024
Effective search space used: 2505645024
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 (21.5 bits)
S2: 61 (27.3 bits)