RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1955
(512 letters)
>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 241 bits (618), Expect = 1e-72
Identities = 99/344 (28%), Positives = 165/344 (47%), Gaps = 67/344 (19%)
Query: 5 PKIKKLDETVVNRIAAGEVIQRPANALKELLENSLDAKSTSIQVTVKQGGLKLLQIQDNG 64
I+ L + N+IAAGEV++RPA+ +KEL+EN+LDA +T I + +++GGLKL++++DNG
Sbjct: 1 MPIQLLPPQLANQIAAGEVVERPASVVKELVENALDAGATRIDIEIEEGGLKLIRVRDNG 60
Query: 65 TGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSPCA 124
GI KED+ + R TSK+ +DL +I T GFRGEAL SI+ V+ LT+ ++T +
Sbjct: 61 CGISKEDLALALARHATSKIASLDDLEAIRTLGFRGEALPSIASVSRLTLTSRTADAAEG 120
Query: 125 YRWCTYLADLMALALMEMS--------------------QYLQRDKEQ---IGD------ 155
W + + + ++L+ +K + I D
Sbjct: 121 --WQIVYEGGEIVEVKPAAHPVGTTIEVRDLFFNTPARRKFLKSEKTELGHIDDVVNRLA 178
Query: 156 -----------KEEKQWYRTVEHTLVPLMKSQYQPSEKIVER-ACLLEIASLNNLELLSV 203
K Q + + ++++R A +L N L +
Sbjct: 179 LAHPDVAFTLTHNGKLVL-------------QTRGAGQLLQRLAAILGREFAEN--ALPI 223
Query: 204 EGTDDAFQLKVTGWITNVNFSTKKMTFL-LFINN-PIK-RM----IEQVYSIYLPKGSFP 256
+ L+++G++ S + LF+N ++ ++ I Q Y LP+G +P
Sbjct: 224 DAEHG--DLRLSGYVGLPTLSRANRDYQYLFVNGRYVRDKLLNHAIRQAYHDLLPRGRYP 281
Query: 257 FVYLSLCMDPKNVDVNVHPTKHEVHFLHEDTIIERVQSMLEKTL 300
L L +DP VDVNVHP KHEV F E + + + +++ L
Sbjct: 282 AFVLFLELDPHQVDVNVHPAKHEVRFRDERLVHDLIVQAIQEAL 325
Score = 200 bits (510), Expect = 5e-57
Identities = 68/183 (37%), Positives = 104/183 (56%), Gaps = 3/183 (1%)
Query: 313 STSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEA 372
+T I + +++GGLKL++++DNG GI KED+ + R TSK+ +DL +I T GFRGEA
Sbjct: 39 ATRIDIEIEEGGLKLIRVRDNGCGISKEDLALALARHATSKIASLDDLEAIRTLGFRGEA 98
Query: 373 LASISHVAHLTIITKTKTSPCAYRASYIDSKLKDPIKPCAGNQGTQIIAEDLFYNIPTRR 432
L SI+ V+ LT+ ++T + ++ Y ++ +KP A GT I DLF+N P RR
Sbjct: 99 LPSIASVSRLTLTSRTADAAEGWQIVYEGGEIV-EVKPAAHPVGTTIEVRDLFFNTPARR 157
Query: 433 KALKQPSEEYNKIADVVSRYAVHNPHVGFTLKKQNENLADIRTNVNSSHSEVIGNIYGNN 492
K LK E I DVV+R A+ +P V FTL + + ++T + + I G
Sbjct: 158 KFLKSEKTELGHIDDVVNRLALAHPDVAFTLTHNGKLV--LQTRGAGQLLQRLAAILGRE 215
Query: 493 ISR 495
+
Sbjct: 216 FAE 218
>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 = 217 bits (554), Expect = 1e-66
Identities = 84/187 (44%), Positives = 119/187 (63%), Gaps = 3/187 (1%)
Query: 312 QSTSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGE 371
+T I V +++GGLKL+++ DNG+GI KED+ + CER TSK+ FEDL I T GFRGE
Sbjct: 38 GATRIDVEIEEGGLKLIEVSDNGSGIDKEDLPLACERHATSKIQSFEDLERIETLGFRGE 97
Query: 372 ALASISHVAHLTIITKTKTSP-CAYRASYIDSKLKDPIKPCAGNQGTQIIAEDLFYNIPT 430
ALASIS V+ LTI TKT + AY+A ++ + + IKP GT + DLFYN+P
Sbjct: 98 ALASISSVSRLTITTKTSAADGLAYQA-LLEGGMIESIKPAPRPVGTTVEVRDLFYNLPV 156
Query: 431 RRKALKQPSEEYNKIADVVSRYAVHNPHVGFTLKKQNENLADIRTNVNSSHSE-VIGNIY 489
RRK LK P +E+ KI DV+ RYA+ +P + F+L + + + T N S E I +++
Sbjct: 157 RRKFLKSPKKEFRKILDVLQRYALIHPDISFSLTHDGKKVLQLSTKPNQSTKENRIRSVF 216
Query: 490 GNNISRR 496
G + R+
Sbjct: 217 GTAVLRK 223
Score = 192 bits (489), Expect = 5e-57
Identities = 72/123 (58%), Positives = 92/123 (74%), Gaps = 1/123 (0%)
Query: 6 KIKKLDETVVNRIAAGEVIQRPANALKELLENSLDAKSTSIQVTVKQGGLKLLQIQDNGT 65
IK L +VN+IAAGEVI+RPA+ +KEL+ENSLDA +T I V +++GGLKL+++ DNG+
Sbjct: 2 TIKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNGS 61
Query: 66 GIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSP-CA 124
GI KED+ + CER TSK+ FEDL I T GFRGEALASIS V+ LTI TKT + A
Sbjct: 62 GIDKEDLPLACERHATSKIQSFEDLERIETLGFRGEALASISSVSRLTITTKTSAADGLA 121
Query: 125 YRW 127
Y+
Sbjct: 122 YQA 124
Score = 78.5 bits (194), Expect = 6e-16
Identities = 36/97 (37%), Positives = 50/97 (51%), Gaps = 11/97 (11%)
Query: 193 ASLNNLELLSVEGTDDAFQLKVTGWITNVNFSTKKMT--FLLFINN------PIKRMIEQ 244
A L L L D L++ G+I+ N + + + LFIN + + I +
Sbjct: 219 AVLRKLIPLDEWEDLD---LQLEGFISQPNVTRSRRSGWQFLFINGRPVELKLLLKAIRE 275
Query: 245 VYSIYLPKGSFPFVYLSLCMDPKNVDVNVHPTKHEVH 281
VY YLPKG +P L+L +DP+ VDVNVHP K EV
Sbjct: 276 VYHEYLPKGQYPVFVLNLEIDPELVDVNVHPDKKEVR 312
>gnl|CDD|223400 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA
replication, recombination, and repair].
Length = 638
Score = 214 bits (547), Expect = 3e-62
Identities = 68/189 (35%), Positives = 103/189 (54%), Gaps = 1/189 (0%)
Query: 313 STSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEA 372
+T I + V+ GGLKL++++DNG+GI KED+ + R TSK+ EDL I T GFRGEA
Sbjct: 40 ATRIDIEVEGGGLKLIRVRDNGSGIDKEDLPLALLRHATSKIASLEDLFRIRTLGFRGEA 99
Query: 373 LASISHVAHLTIITKTKTSPCAYRASYIDSKLKDPIKPCAGNQGTQIIAEDLFYNIPTRR 432
LASI+ V+ LTI ++T + + ++ +KP A GT + DLFYN P RR
Sbjct: 100 LASIASVSRLTITSRTAEASEGTQIYAEGGGMEVTVKPAAHPVGTTVEVRDLFYNTPARR 159
Query: 433 KALKQPSEEYNKIADVVSRYAVHNPHVGFTLKKQNENLADIR-TNVNSSHSEVIGNIYGN 491
K LK E+ I ++++RYA+ +P + F+L + ++ E I +YG
Sbjct: 160 KFLKSEKTEFGHITELINRYALAHPDISFSLSHNGKLRIELLKLPGTGDLEERIAAVYGT 219
Query: 492 NISRRVRRF 500
+
Sbjct: 220 EFLKNALPI 228
Score = 199 bits (509), Expect = 8e-57
Identities = 65/123 (52%), Positives = 90/123 (73%)
Query: 5 PKIKKLDETVVNRIAAGEVIQRPANALKELLENSLDAKSTSIQVTVKQGGLKLLQIQDNG 64
PKI++L +VN+IAAGEVI+RPA+ +KEL+ENSLDA +T I + V+ GGLKL++++DNG
Sbjct: 2 PKIRQLPPDLVNQIAAGEVIERPASVVKELVENSLDAGATRIDIEVEGGGLKLIRVRDNG 61
Query: 65 TGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSPCA 124
+GI KED+ + R TSK+ EDL I T GFRGEALASI+ V+ LTI ++T +
Sbjct: 62 SGIDKEDLPLALLRHATSKIASLEDLFRIRTLGFRGEALASIASVSRLTITSRTAEASEG 121
Query: 125 YRW 127
+
Sbjct: 122 TQI 124
Score = 90.1 bits (224), Expect = 5e-19
Identities = 32/108 (29%), Positives = 56/108 (51%), Gaps = 9/108 (8%)
Query: 200 LLSVEGTDDAFQLKVTGWITNVNFSTKKMTFL-LFINN-PIK-----RMIEQVYSIYLPK 252
L +E + +L G+++ F+ + LF+N P++ + + Y+ YLP+
Sbjct: 225 ALPIENEHEDLRLS--GYVSLPEFTRASRDYQYLFVNGRPVRDKLLNHALREAYADYLPR 282
Query: 253 GSFPFVYLSLCMDPKNVDVNVHPTKHEVHFLHEDTIIERVQSMLEKTL 300
G +P L L +DP+ VDVNVHP K EV F E + + + +++ L
Sbjct: 283 GRYPVFVLFLELDPELVDVNVHPAKKEVRFSDERLVHDLIYEAIKEAL 330
>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 = 157 bits (399), Expect = 3e-46
Identities = 60/112 (53%), Positives = 77/112 (68%), Gaps = 6/112 (5%)
Query: 196 NNLELLSVEGTDDAFQLKVTGWITNVNFSTKKMTFLLFINN------PIKRMIEQVYSIY 249
N L + + DD KV G I+N N+S KK+ F+LFINN ++R IE VY+ Y
Sbjct: 16 NELIEVEISDDDDDLGFKVKGLISNANYSKKKIIFILFINNRLVECSALRRAIENVYANY 75
Query: 250 LPKGSFPFVYLSLCMDPKNVDVNVHPTKHEVHFLHEDTIIERVQSMLEKTLL 301
LPKG+ PFVYLSL + P+NVDVNVHPTK EVHFL+E+ IIER+Q ++E L
Sbjct: 76 LPKGAHPFVYLSLEIPPENVDVNVHPTKREVHFLNEEEIIERIQKLVEDKLS 127
>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 = 118 bits (299), Expect = 5e-32
Identities = 33/110 (30%), Positives = 54/110 (49%), Gaps = 9/110 (8%)
Query: 199 ELLSVEGTDDAFQLKVTGWITNVNFSTKKMTFL-LFINN------PIKRMIEQVYSIYLP 251
LL ++ D+ +++G+I+ S + LF+N + I + Y LP
Sbjct: 12 NLLPIDAEDEGL--RLSGFISKPELSRSNRDYQYLFVNGRPVRDKLLSHAIREAYRDLLP 69
Query: 252 KGSFPFVYLSLCMDPKNVDVNVHPTKHEVHFLHEDTIIERVQSMLEKTLL 301
KG +P L L +DP+ VDVNVHP K EV F E + + ++ + + L
Sbjct: 70 KGRYPVAVLFLEIDPELVDVNVHPAKREVRFRDEREVHDFIEEAVREALA 119
>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 = 112 bits (282), Expect = 1e-29
Identities = 40/110 (36%), Positives = 61/110 (55%), Gaps = 11/110 (10%)
Query: 199 ELLSVEGTDDAFQLKVTGWITNVNF--STKKMTFLLFINN------PIKRMIEQVYSIYL 250
L+ VE F +++G+I+ +F S+K FL F+N + + I + Y YL
Sbjct: 16 NLIEVELESGDF--RISGYISKPDFGRSSKDRQFL-FVNGRPVRDKLLSKAINEAYRSYL 72
Query: 251 PKGSFPFVYLSLCMDPKNVDVNVHPTKHEVHFLHEDTIIERVQSMLEKTL 300
PKG +P L+L + P+ VDVNVHPTK EV F E+ ++E ++ L L
Sbjct: 73 PKGRYPVFVLNLELPPELVDVNVHPTKREVRFSDEEEVLELIREALRSAL 122
>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 = 66.1 bits (162), Expect = 2e-13
Identities = 30/94 (31%), Positives = 42/94 (44%), Gaps = 13/94 (13%)
Query: 199 ELLSVEGTDDAFQLKVTGWITNVNFST-KKMTFLLFINN-------PIKRMIEQVYSIYL 250
+L+ VEG D F +V G I+ + K F+N + + + Y+ L
Sbjct: 16 KLIYVEGESDGF--RVEGAISYPDSGRSSKDRQFSFVNGRPVREGGTHVKAVREAYTRAL 73
Query: 251 ---PKGSFPFVYLSLCMDPKNVDVNVHPTKHEVH 281
+P LSL + P VDVNVHPTK EV
Sbjct: 74 NGDDVRRYPVAVLSLKIPPSLVDVNVHPTKEEVR 107
>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 = 62.6 bits (153), Expect = 4e-12
Identities = 34/97 (35%), Positives = 46/97 (47%), Gaps = 13/97 (13%)
Query: 212 LKVTGWITNVNFSTKKMTF-LLFINNPIKR------MIEQVYSIYLPKGSFPFVYLSLCM 264
L+++GWI F+ + ++N + R + Q YS L G P L L +
Sbjct: 27 LRLSGWIALPTFARSQADIQYFYVNGRMVRDKLISHAVRQAYSDVLHGGRHPAYVLYLEL 86
Query: 265 DPKNVDVNVHPTKHEVHF-----LHEDTIIERVQSML 296
DP VDVNVHP KHEV F +H D I V+ L
Sbjct: 87 DPAQVDVNVHPAKHEVRFRDSRLVH-DFIYHAVKKAL 122
>gnl|CDD|222246 pfam13589, HATPase_c_3, Histidine kinase-, DNA gyrase B-, and
HSP90-like ATPase. This family represents,
additionally, the structurally related ATPase domains of
histidine kinase, DNA gyrase B and HSP90.
Length = 134
Score = 63.1 bits (154), Expect = 5e-12
Identities = 25/103 (24%), Positives = 53/103 (51%), Gaps = 3/103 (2%)
Query: 26 RPANALKELLENSLDAKSTSIQVTVKQG-GLKLLQIQDNGTGIRKEDMDIVCERFTTSKL 84
+A+ EL++NS+DA +T++++++ G + I+DNG G+ E++ + +SK
Sbjct: 2 TLEDAIAELIDNSIDADATNVKISIDPDRGEDGISIEDNGGGMSYEELRNALKLGRSSKE 61
Query: 85 TQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSPCAYRW 127
+ + ++ G + LAS+S LT+ +K +
Sbjct: 62 GERDS-TTLGRKGIGMK-LASLSLGRKLTVTSKKEGESSTLTL 102
Score = 41.1 bits (97), Expect = 2e-04
Identities = 18/88 (20%), Positives = 41/88 (46%), Gaps = 3/88 (3%)
Query: 313 STSIQVTVKQG-GLKLLQIQDNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTFGFRGE 371
+T++++++ G + I+DNG G+ E++ + +SK + + ++ G +
Sbjct: 19 ATNVKISIDPDRGEDGISIEDNGGGMSYEELRNALKLGRSSKEGERDS-TTLGRKGIGMK 77
Query: 372 ALASISHVAHLTIITKTKTSPCAYRASY 399
LAS+S LT+ +K +
Sbjct: 78 -LASLSLGRKLTVTSKKEGESSTLTLDL 104
>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 = 59.6 bits (145), Expect = 8e-11
Identities = 27/118 (22%), Positives = 60/118 (50%), Gaps = 15/118 (12%)
Query: 197 NLELLSVEGTDDAFQLKVTGWI----TNVNFSTKKMTFLLFINN-PIKR------MIEQV 245
++ V+ TD+ Q+ + G++ ++V+ + F+ +N+ P+ ++ Q
Sbjct: 15 AANMVPVQSTDEDPQISLEGFLPKPGSDVSKTKSDGKFI-SVNSRPVSLGKDIGKLLRQY 73
Query: 246 YSIYLPKGS---FPFVYLSLCMDPKNVDVNVHPTKHEVHFLHEDTIIERVQSMLEKTL 300
YS K S +P +L++ P VDVN+ P K +V +++ +++ V+++LE
Sbjct: 74 YSSAYRKSSLRRYPVFFLNILCPPGLVDVNIEPDKDDVLLQNKEAVLQAVENLLESLY 131
>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 = 57.7 bits (140), Expect = 4e-10
Identities = 29/120 (24%), Positives = 54/120 (45%), Gaps = 12/120 (10%)
Query: 190 LEIASLNNLELLSVEGTDDAFQLKVTGWITNVNF----STKKMTFLLFINN------PIK 239
LE+ E L + ++K+TG+I+ + S+ F +IN +
Sbjct: 23 LELDVNPTKEELDSDEDLADSEVKITGYISKPSHGCGRSSSDRQFF-YINGRPVDLKKVA 81
Query: 240 RMIEQVYSIYLPKGSFPFVYLSLCMDPKNVDVNVHPTKHEVHFLHEDTIIERVQSMLEKT 299
++I +VY + +PF L++ + DVNV P K V ED +I+ +++ L +
Sbjct: 82 KLINEVYKSF-NSRQYPFFILNISLPTSLYDVNVTPDKRTVLLHDEDRLIDTLKTSLSEL 140
>gnl|CDD|238030 cd00075, HATPase_c, Histidine kinase-like ATPases; This family
includes several ATP-binding proteins for example:
histidine kinase, DNA gyrase B, topoisomerases, heat
shock protein HSP90, phytochrome-like ATPases and DNA
mismatch repair proteins.
Length = 103
Score = 50.0 bits (120), Expect = 1e-07
Identities = 23/87 (26%), Positives = 41/87 (47%), Gaps = 12/87 (13%)
Query: 30 ALKELLENSLDA---KSTSIQVTVKQGGLKL-LQIQDNGTGIRKEDMDIVCERFTTSKLT 85
L LL N++ I ++V++ G L ++++DNG GI +ED++ + ER
Sbjct: 4 VLLNLLSNAIKHTPEGGGRITISVERDGDHLEIRVEDNGPGIPEEDLERIFER------- 56
Query: 86 QFEDLNSISTFGFRGEALASISHVAHL 112
F D + G G L+ + + L
Sbjct: 57 -FSDGSRSRKGGGTGLGLSIVKKLVEL 82
Score = 38.4 bits (90), Expect = 9e-04
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 11/76 (14%)
Query: 310 YTQSTSIQVTV---KQGGLKLLQIQDNGTGIRKEDMDIVCERFTTSKLTQFEDLNSISTF 366
+T ++T+ + G ++++DNG GI +ED++ + ER F D +
Sbjct: 15 HTPEGGGRITISVERDGDHLEIRVEDNGPGIPEEDLERIFER--------FSDGSRSRKG 66
Query: 367 GFRGEALASISHVAHL 382
G G L+ + + L
Sbjct: 67 GGTGLGLSIVKKLVEL 82
>gnl|CDD|217081 pfam02518, HATPase_c, Histidine kinase-, DNA gyrase B-, and
HSP90-like ATPase. This family represents the
structurally related ATPase domains of histidine
kinase, DNA gyrase B and HSP90.
Length = 111
Score = 47.3 bits (113), Expect = 1e-06
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 30 ALKELLENSLDA--KSTSIQVTVKQGGLKL-LQIQDNGTGIRKEDMDIVCERFTTSK 83
L LL+N++ I+VT+++ G +L + ++DNG GI ED+ + E F +
Sbjct: 9 VLSNLLDNAIKHAPAGGEIEVTLERDGGRLRITVEDNGIGIPPEDLPKIFEPFFRTD 65
Score = 36.9 bits (86), Expect = 0.004
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 312 QSTSIQVTVKQGGLKL-LQIQDNGTGIRKEDMDIVCERFTTSK 353
I+VT+++ G +L + ++DNG GI ED+ + E F +
Sbjct: 23 AGGEIEVTLERDGGRLRITVEDNGIGIPPEDLPKIFEPFFRTD 65
>gnl|CDD|214643 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine
kinase-, DNA gyrase B-, phytochrome-like ATPases.
Length = 111
Score = 43.0 bits (102), Expect = 3e-05
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 30 ALKELLENSLDA--KSTSIQVTVKQGGLKL-LQIQDNGTGIRKEDMDIVCERFTTSK 83
L LL+N++ + I VT+++ G + + ++DNG GI ED++ + E F +
Sbjct: 9 VLSNLLDNAIKYTPEGGRITVTLERDGDHVEITVEDNGPGIPPEDLEKIFEPFFRTD 65
Score = 34.2 bits (79), Expect = 0.034
Identities = 13/43 (30%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 312 QSTSIQVTVKQGGLKL-LQIQDNGTGIRKEDMDIVCERFTTSK 353
+ I VT+++ G + + ++DNG GI ED++ + E F +
Sbjct: 23 EGGRITVTLERDGDHVEITVEDNGPGIPPEDLEKIFEPFFRTD 65
>gnl|CDD|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 336
Score = 40.9 bits (95), Expect = 0.001
Identities = 15/61 (24%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 25 QRPANALKELLENSLDA-KSTSIQVTVKQGGLKL-LQIQDNGTGIRKEDMDIVCERFTTS 82
+R L LL N++ I ++V+Q ++ + ++D G GI +E+++ + E F +
Sbjct: 227 ERLRQVLVNLLSNAIKYTPGGEITISVRQDDEQVTISVEDTGPGIPEEELERIFEPFFRT 286
Query: 83 K 83
Sbjct: 287 D 287
Score = 37.0 bits (85), Expect = 0.018
Identities = 12/45 (26%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 310 YTQSTSIQVTVKQGGLKL-LQIQDNGTGIRKEDMDIVCERFTTSK 353
YT I ++V+Q ++ + ++D G GI +E+++ + E F +
Sbjct: 243 YTPGGEITISVRQDDEQVTISVEDTGPGIPEEELERIFEPFFRTD 287
>gnl|CDD|224307 COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA replication,
recombination, and repair].
Length = 538
Score = 34.7 bits (80), Expect = 0.12
Identities = 29/112 (25%), Positives = 46/112 (41%), Gaps = 13/112 (11%)
Query: 27 PANAL----KELLENSLDAKSTS-----IQVTVKQGGLKL--LQIQDNGTGIRKEDMDIV 75
P +L EL+ NSLDA + I+V +++ G + ++DNG GI +E + V
Sbjct: 33 PIRSLTTTVHELVTNSLDACEEAGILPDIKVEIERIGKDHYKVIVEDNGPGIPEEQIPKV 92
Query: 76 -CERFTTSKLTQFEDLNSISTFGFRGEALASISHVA-HLTIITKTKTSPCAY 125
+ SK + G L S + +I+ T S AY
Sbjct: 93 FGKMLYGSKFHRNIQSRGQQGIGISAAVLYSQMTTGKPVRVISSTGDSGTAY 144
>gnl|CDD|235246 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
Length = 535
Score = 33.3 bits (77), Expect = 0.30
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 13/59 (22%)
Query: 27 PANAL----KELLENSLDAKST-----SIQVTVK----QGGLKLLQIQDNGTGIRKEDM 72
PA AL KEL++NSLDA I++ +K + ++DNG GI E++
Sbjct: 33 PARALYTTVKELVDNSLDACEEAGILPDIKIEIKRVDEGKDHYRVTVEDNGPGIPPEEI 91
>gnl|CDD|225827 COG3290, CitA, Signal transduction histidine kinase regulating
citrate/malate metabolism [Signal transduction
mechanisms].
Length = 537
Score = 32.3 bits (74), Expect = 0.59
Identities = 15/59 (25%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 34 LLENSLDAKST-----SIQVTVKQ-GGLKLLQIQDNGTGIRKEDMDIVCERFTTSKLTQ 86
L++N+L+A I++++ G ++++ D G GI E D + E+ ++K T
Sbjct: 435 LIDNALEALLAPEENKEIELSLSDRGDELVIEVADTGPGIPPEVRDKIFEKGVSTKNTG 493
>gnl|CDD|226654 COG4191, COG4191, Signal transduction histidine kinase regulating
C4-dicarboxylate transport system [Signal transduction
mechanisms].
Length = 603
Score = 32.3 bits (74), Expect = 0.60
Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 5/55 (9%)
Query: 34 LLENSLDAKSTS----IQVTVKQ-GGLKLLQIQDNGTGIRKEDMDIVCERFTTSK 83
LL+N+LDA + + + ++ GG +L ++DNG GI E + + E F T+K
Sbjct: 505 LLQNALDAMAGQEDRRLSIRAQREGGQVVLTVRDNGPGIAPEALPHLFEPFFTTK 559
>gnl|CDD|233250 TIGR01052, top6b, DNA topoisomerase VI, B subunit. This model
describes DNA topoisomerase VI, an archaeal type II DNA
topoisomerase (DNA gyrase) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 488
Score = 31.7 bits (72), Expect = 1.0
Identities = 24/98 (24%), Positives = 44/98 (44%), Gaps = 9/98 (9%)
Query: 31 LKELLENSLDAKSTS-----IQVTVKQGGLK--LLQIQDNGTGIRKEDMDIV-CERFTTS 82
+ EL+ NSLDA + I+V +++ G + ++DNG GI +E + V + S
Sbjct: 33 IHELVTNSLDACEEAGILPDIKVEIEKIGKDHYKVTVEDNGPGIPEEYIPKVFGKMLAGS 92
Query: 83 KLTQFEDLNSISTFGFRGEAL-ASISHVAHLTIITKTK 119
K + G G L + ++ + +I+ T
Sbjct: 93 KFHRIIQSRGQQGIGISGAVLYSQMTTGKPVKVISSTG 130
>gnl|CDD|224086 COG1164, COG1164, Oligoendopeptidase F [Amino acid transport and
metabolism].
Length = 598
Score = 31.5 bits (72), Expect = 1.3
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 246 YSIYLPKGSFPFVYLSLCMDPKNVDVNVHPTKHEVHF 282
YSI KG PF+ ++ ++V H H VH
Sbjct: 358 YSIGFYKGDHPFILMNYDGTLRDVFTLAHELGHSVHS 394
>gnl|CDD|225960 COG3426, COG3426, Butyrate kinase [Energy production and
conversion].
Length = 358
Score = 31.2 bits (71), Expect = 1.3
Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 4/70 (5%)
Query: 429 PTRRKALKQPSEEYN----KIADVVSRYAVHNPHVGFTLKKQNENLADIRTNVNSSHSEV 484
R+ A+ + +E K VV R + P G T + L D++ V H+
Sbjct: 49 EFRKDAILEFIDEQGYNISKFDAVVGRGGLLRPIPGGTYVVNEKMLKDLKNGVQGEHASN 108
Query: 485 IGNIYGNNIS 494
+G I N I+
Sbjct: 109 LGAIIANRIA 118
>gnl|CDD|233811 TIGR02289, M3_not_pepF, oligoendopeptidase, M3 family. This family
consists of probable oligoendopeptidases in the M3
family, related to lactococcal PepF and group B
streptococcal PepB (TIGR00181) but in a distinct clade
with considerable sequence differences. The likely
substrate is small peptides and not whole proteins, as
with PepF, but members are not characterized and the
activity profile may differ. Several bacteria have both
a member of this family and a member of the PepF family.
Length = 549
Score = 30.9 bits (70), Expect = 1.7
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 246 YSIYLPKGSFPFVYLSLCMDPKNVDVNVHPTKHEVHF 282
Y YLPK PF++ + ++DV H H H
Sbjct: 315 YCTYLPKYKAPFIFSNFNGTSGDIDVLTHEAGHAFHV 351
>gnl|CDD|237603 PRK14083, PRK14083, HSP90 family protein; Provisional.
Length = 601
Score = 31.1 bits (71), Expect = 1.7
Identities = 14/51 (27%), Positives = 28/51 (54%), Gaps = 10/51 (19%)
Query: 31 LKELLENSLDAKST----------SIQVTVKQGGLKLLQIQDNGTGIRKED 71
++ELL+N++DA + I++ + G L ++DNG G+ +E+
Sbjct: 28 VRELLQNAVDAITARRALDPTAPGRIRIELTDAGGGTLIVEDNGIGLTEEE 78
>gnl|CDD|237842 PRK14868, PRK14868, DNA topoisomerase VI subunit B; Provisional.
Length = 795
Score = 30.9 bits (70), Expect = 1.8
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 6/47 (12%)
Query: 30 ALKELLENSLDAKSTS-----IQVTVKQGG-LKLLQIQDNGTGIRKE 70
A+KE ++N+LDA + I V +++ G L ++DNG GI KE
Sbjct: 50 AVKEAVDNALDATEEAGILPDIYVEIEEVGDYYRLVVEDNGPGITKE 96
>gnl|CDD|181911 PRK09498, sifA, secreted effector protein SifA; Reviewed.
Length = 336
Score = 30.4 bits (68), Expect = 2.3
Identities = 27/96 (28%), Positives = 43/96 (44%), Gaps = 9/96 (9%)
Query: 403 KLKDPIKPCAGNQGTQIIAEDLFYNIPTRRKALKQPSEEYNKIA--DVVSRYAVHNPH-- 458
K+KD + + + E LF + R+ L + E ++A R+ VHNPH
Sbjct: 33 KIKDFFFSTGKAKADRCLHEMLFADRAPTRERLTEIFFELKELACASQRDRFQVHNPHEN 92
Query: 459 ---VGFTLKKQNEN--LADIRTNVNSSHSEVIGNIY 489
+ + QNE L I N ++ EV+GN+Y
Sbjct: 93 DATIILRIMDQNEENELLRITQNTDTFSCEVMGNLY 128
>gnl|CDD|119345 cd06553, ASCH_Ef3133_like, ASC-1 homology domain, subfamily similar
to Enterococcus faecalis Ef3133. The ASCH domain, a
small beta-barrel domain found in all three kingdoms of
life, resembles the RNA-binding PUA domain and may also
interact with RNA. ASCH has been proposed to function as
an RNA-binding domain during coactivation,
RNA-processing and the regulation of prokaryotic
translation.
Length = 127
Score = 29.1 bits (66), Expect = 2.5
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 70 EDMDIVCERF 79
EDM +VCERF
Sbjct: 114 EDMLVVCERF 123
Score = 29.1 bits (66), Expect = 2.5
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 340 EDMDIVCERF 349
EDM +VCERF
Sbjct: 114 EDMLVVCERF 123
>gnl|CDD|236846 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional.
Length = 475
Score = 30.2 bits (69), Expect = 3.0
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 5/54 (9%)
Query: 30 ALKELLENSLD---AKSTSIQVTV-KQGGLKLLQIQDNGTGIRKEDMDIVCERF 79
AL LL+N++D T I ++ G L ++D G GI + + ERF
Sbjct: 372 ALGNLLDNAIDFSPEGGT-ITLSAEVDGEQVALSVEDQGPGIPDYALPRIFERF 424
>gnl|CDD|182539 PRK10549, PRK10549, signal transduction histidine-protein kinase
BaeS; Provisional.
Length = 466
Score = 29.6 bits (67), Expect = 4.1
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 3/49 (6%)
Query: 34 LLENSL---DAKSTSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCERF 79
LLENSL D+ + ++ L D+ G+ E + + ERF
Sbjct: 360 LLENSLRYTDSGGSLHISAEQRDKTLRLTFADSAPGVSDEQLQKLFERF 408
>gnl|CDD|236901 PRK11360, PRK11360, sensory histidine kinase AtoS; Provisional.
Length = 607
Score = 29.6 bits (67), Expect = 4.6
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 30 ALKELLENSLDAKSTSIQVTVKQGGLK----LLQIQDNGTGIRKEDMDIVCERFTTSK 83
L +L N++ A S ++ ++ + I+DNG GI E + + + F T+K
Sbjct: 504 VLLNILINAVQAISARGKIRIRTWQYSDGQVAVSIEDNGCGIDPELLKKIFDPFFTTK 561
>gnl|CDD|236724 PRK10604, PRK10604, sensor protein RstB; Provisional.
Length = 433
Score = 29.6 bits (67), Expect = 4.7
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 30 ALKELLENSLDAKSTSIQVTV-KQGGLKLLQIQDNGTGIRKEDMDIVCERFT 80
L LL N+L + ++V++ G L ++D+G GI E+ + V E F
Sbjct: 323 VLDNLLNNALRYAHSRVRVSLLLDGNQACLIVEDDGPGIPPEERERVFEPFV 374
>gnl|CDD|225866 COG3329, COG3329, Predicted permease [General function prediction
only].
Length = 372
Score = 29.4 bits (66), Expect = 4.9
Identities = 15/64 (23%), Positives = 32/64 (50%), Gaps = 8/64 (12%)
Query: 78 RFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSPCAYRWCTYLADLMAL 137
F KL + + +++ +T G G ++++++ A +T + ++ + AY L
Sbjct: 89 YFLLRKLPKVDTVDAAATAGTYG-SVSAVTFAAAVTFLEESGIAYEAYM-------PAML 140
Query: 138 ALME 141
ALME
Sbjct: 141 ALME 144
Score = 28.6 bits (64), Expect = 9.2
Identities = 10/48 (20%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 348 RFTTSKLTQFEDLNSISTFGFRGEALASISHVAHLTIITKTKTSPCAY 395
F KL + + +++ +T G G ++++++ A +T + ++ + AY
Sbjct: 89 YFLLRKLPKVDTVDAAATAGTYG-SVSAVTFAAAVTFLEESGIAYEAY 135
>gnl|CDD|226655 COG4192, COG4192, Signal transduction histidine kinase regulating
phosphoglycerate transport system [Signal transduction
mechanisms].
Length = 673
Score = 29.5 bits (66), Expect = 5.7
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 31 LKELLENSLDAKSTS---IQVTV--KQGGLKLLQIQDNGTGIRKEDMDIVCERFTTSK 83
L L+ N+LDA + I++ + + + I DNG G E +D + FTTSK
Sbjct: 569 LVNLIVNALDASTHFAPWIKLIALGTEQEMLRIAIIDNGQGWPHELVDKLLTPFTTSK 626
>gnl|CDD|148397 pfam06767, Sif, Sif protein. This family consists of several SifA
and SifB and SseJ proteins which seem to be specific to
the Salmonella species. SifA, SifB and SseJ have been
demonstrated to localise to the Salmonella-containing
vacuole (SCV) and to Salmonella-induced filaments
(Sifs). Trafficking of SseJ and SifB away from the SCV
requires the SPI-2 effector SifA. SseJ trafficking away
from the SCV along Sifs is unnecessary for its virulence
function.
Length = 336
Score = 29.1 bits (65), Expect = 6.3
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 9/79 (11%)
Query: 420 IAEDLFYNIPTRRKALKQPSEEYNKIA--DVVSRYAVHNPH-----VGFTLKKQNE--NL 470
+ E LF + P R+ L + E +A R+ V+NPH + F + +NE L
Sbjct: 50 LHEMLFADPPPTRERLTEIFFELKALACASHKDRFQVYNPHENDATIIFRIMDENEEDEL 109
Query: 471 ADIRTNVNSSHSEVIGNIY 489
I N ++ +++GN Y
Sbjct: 110 LRITQNTDTFSCKIMGNSY 128
>gnl|CDD|236839 PRK11086, PRK11086, sensory histidine kinase DcuS; Provisional.
Length = 542
Score = 29.1 bits (66), Expect = 6.9
Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 7/56 (12%)
Query: 34 LLENSLDA------KSTSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCERFTTSK 83
L+EN+L+A S+ + + G L ++ D+G GI +++D + ++ ++K
Sbjct: 441 LIENALEAVGGEEGGEISVSLHYRNGWL-HCEVSDDGPGIAPDEIDAIFDKGYSTK 495
>gnl|CDD|236701 PRK10490, PRK10490, sensor protein KdpD; Provisional.
Length = 895
Score = 28.8 bits (65), Expect = 8.6
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 5/51 (9%)
Query: 34 LLENSL----DAKSTSIQVTVKQGGLKLLQIQDNGTGIRKEDMDIVCERFT 80
LLEN++ I V+ L+L + DNG GI ++ ++F
Sbjct: 786 LLENAVKYAGAQAEIGIDAHVEGERLQL-DVWDNGPGIPPGQEQLIFDKFA 835
>gnl|CDD|216484 pfam01411, tRNA-synt_2c, tRNA synthetases class II (A). Other tRNA
synthetase sub-families are too dissimilar to be
included. This family includes only alanyl-tRNA
synthetases.
Length = 551
Score = 28.8 bits (65), Expect = 8.8
Identities = 23/92 (25%), Positives = 40/92 (43%), Gaps = 25/92 (27%)
Query: 130 YLADLMALALMEMSQY---LQRDKEQIG---DKEEKQWYRTVEHTLVPLMKSQYQPSEKI 183
+L L+ + EM L+ ++ I + EE+++ +T+E L ++
Sbjct: 321 FLYKLVPTVIEEMGDAYPELKEKEDTIQEILELEEERFAKTLERGL------------RL 368
Query: 184 VERACLLEIASLNNLELLSVEGTDDAFQLKVT 215
+ER I SL + L E DAF+L T
Sbjct: 369 LERL----IKSLKKSKTLPGE---DAFKLYDT 393
>gnl|CDD|220107 pfam09090, MIF4G_like_2, MIF4G like. Members of this family are
involved in mediating U snRNA export from the nucleus.
They adopt a highly helical structure, wherein the
polypeptide chain forms a right-handed solenoid. At the
tertiary level, the domain is composed of a superhelical
arrangement of successive antiparallel pairs of helices.
Length = 250
Score = 28.2 bits (63), Expect = 9.2
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 433 KALKQPSEEY-NKIADVVSRYAVHNPHVGF 461
K L SEE I + V Y + P +GF
Sbjct: 83 KTLSAESEEKQQWIIEAVFEYWKNQPQMGF 112
>gnl|CDD|182581 PRK10600, PRK10600, nitrate/nitrite sensor protein NarX;
Provisional.
Length = 569
Score = 28.5 bits (64), Expect = 9.7
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 4/39 (10%)
Query: 32 KELLENSL---DAKSTSIQVTVKQGGLKLLQIQDNGTGI 67
+E L N+L A + V Q +KL +QDNG G+
Sbjct: 475 REALSNALKHAQASEVVVTVAQNQNQVKL-SVQDNGCGV 512
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 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,183,922
Number of extensions: 2400263
Number of successful extensions: 1792
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1776
Number of HSP's successfully gapped: 60
Length of query: 512
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 411
Effective length of database: 6,457,848
Effective search space: 2654175528
Effective search space used: 2654175528
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: 61 (27.2 bits)