RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780814|ref|YP_003065227.1| DNA gyrase subunit B
[Candidatus Liberibacter asiaticus str. psy62]
(803 letters)
>gnl|CDD|30536 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 834 bits (2157), Expect = 0.0
Identities = 336/571 (58%), Positives = 429/571 (75%), Gaps = 5/571 (0%)
Query: 5 IQNSSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADII 64
+ ++YDA SIQ+L+GL+AV+KRP MYIG T GLHH+++EV+DN+IDE+L GYAD I
Sbjct: 1 SKTNNYDASSIQVLEGLEAVRKRPGMYIGSTGDGRGLHHLVWEVVDNSIDEALAGYADRI 60
Query: 65 TVTLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVG 124
VTL+ DGS +V DNGRGIP D+H +E +SA EVI T LHAGGKF+ SYKVSGGLHGVG
Sbjct: 61 DVTLHEDGSISVEDNGRGIPVDIHPKEKVSAVEVIFTVLHAGGKFDNDSYKVSGGLHGVG 120
Query: 125 VSVVNALSSWLKLRIKREGNIYEMSFINGILDNPLVVTGSAGND-TGTEVTFLPSSDIFS 183
VSVVNALS+WL++ +KR+G IY F G+ PL V GS TGT+V F P +IF
Sbjct: 121 VSVVNALSTWLEVEVKRDGKIYRQRFERGVPVTPLEVIGSTDTKKTGTKVRFKPDPEIFG 180
Query: 184 VQDFNYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPL 243
+F+Y+ L+ RLREL+FLN V+I+L D+R+ E + Y+GG++ +V YL++ K PL
Sbjct: 181 ETEFDYEILKRRLRELAFLNKGVKITLTDERTGEE-KKEFHYEGGLKDYVEYLNKGKTPL 239
Query: 244 MQSPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSY 303
+ G +D I++++A++WNDGY EN+L F NNIP ++GGTH +G RSALTR I Y
Sbjct: 240 HEEIFYFNGEKDGIAVEVALQWNDGYSENILSFVNNIPTREGGTHEAGFRSALTRAINEY 299
Query: 304 VEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDG 363
+K K+ + GDD REG T+V+S+K+PDP+F QTKEKL +SEVRS+VE V++
Sbjct: 300 AKKKNLLKEGD--LTGDDIREGLTAVISVKIPDPQFEGQTKEKLGNSEVRSIVEKLVSEA 357
Query: 364 LSAWLEEHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASLPGKLADCSERDPK 423
S +LEE+P EAK IV+K + A+ R+AAR+AR+LTRRK LDI LPGKLADC+ +DP+
Sbjct: 358 FSLFLEENPQEAKKIVEKAIAAAKAREAARKARELTRRKSALDIPGLPGKLADCTSKDPE 417
Query: 424 KSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGT 483
KSELFLVEGDSAGGSAKQGR RE QAILPLRGKILNVE+AR DK+L ++EI T+ITALGT
Sbjct: 418 KSELFLVEGDSAGGSAKQGRDREFQAILPLRGKILNVEKARLDKILKNEEIQTIITALGT 477
Query: 484 GIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKPPLYG 543
GIG+D FD+ KLRYHKIIIMTDADVDGAHIRTLLLTFF+R MP LI NG +YI +PPLY
Sbjct: 478 GIGKD-FDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFYRYMPPLIENGHVYIAQPPLYK 536
Query: 544 ITRGKSLQYVKDEESLEDYLINQSLSEEIEL 574
+ +GK Y D+E LE L + E+
Sbjct: 537 VKKGKKTFYAYDDEELEKLLERLGKKKGYEI 567
Score = 119 bits (301), Expect = 2e-27
Identities = 48/74 (64%), Positives = 60/74 (81%), Gaps = 1/74 (1%)
Query: 731 RKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRRE 790
+KG +QRYKGLGEMN QLWETT++P+TR LL+V I DA +AD++FS LMGD+VEPRR
Sbjct: 562 KKGYEIQRYKGLGEMNPDQLWETTMDPETRRLLQVTIEDADEADEIFSTLMGDKVEPRRN 621
Query: 791 FIQENSL-PSALDI 803
FI+EN+L LDI
Sbjct: 622 FIEENALFVENLDI 635
>gnl|CDD|35576 KOG0355, KOG0355, KOG0355, DNA topoisomerase type II [Chromatin
structure and dynamics].
Length = 842
Score = 262 bits (670), Expect = 3e-70
Identities = 144/603 (23%), Positives = 250/603 (41%), Gaps = 48/603 (7%)
Query: 18 LKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTLNM-DGSCTV 76
L + ++KR + GL+ + E+L NA D+ + + I VT++ +V
Sbjct: 34 LMWVYDMEKRKMVQR---TYVPGLYKIFDEILVNAADKQRDPKMNTIKVTIDKEKNEISV 90
Query: 77 SDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGG--LHGVGVSVVNALSSW 134
+NG+GIP +HK E + E+I L ++ KV+GG +G + + +
Sbjct: 91 YNNGKGIPVTIHKVEKVYVPELIFGNLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFT 150
Query: 135 LKLRIKREGNIYEMSFING-ILDNPLVVTGSAGNDTGTEVTFLPSSDIFSVQDFNYDTLQ 193
++ + ++ ++IN D + S D T++TF P + F +++ + D +
Sbjct: 151 VETADREYKMAFKQTWINNMTRDEEPKIVPSTDED-YTKITFSPDLEKFKMKELDDDIVA 209
Query: 194 HRLRELSFLNS---SVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRH-KKPLMQSPIR 249
R L SV++ L K P ++ F Y+ + + + ++
Sbjct: 210 LMARRAYDLAGSVKSVKVELNGKNIP------------VKGFYDYVKMYLEVLWLNDDLK 257
Query: 250 IQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFG 309
N ++A+ +D + V F N+I GGTH+ + + ++ V+K
Sbjct: 258 PLHEVLNFRWEVALALSDVGFQQV-SFVNSIATTKGGTHVDYVVDQIVAKLIDVVKKKKV 316
Query: 310 SKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDGLSAWLE 369
K SV + ++ + +P F SQTKE+L R + +++ + +E
Sbjct: 317 KKD--ISVKPFQVKNHLWVFVNCLIENPTFESQTKERLTLRPKRFGSDCELSEKFTKAIE 374
Query: 370 EHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASLPGKLADCSERDPKKSELFL 429
+ I+ K L+ A +R + +R KG+ + SE K L L
Sbjct: 375 LKGVVESIL-SKSLNKYKDDLAKKRGKLTSRSKGIPKLEDANDAGTKTSE----KCTLIL 429
Query: 430 VEGDSA---GGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTGIG 486
EGDSA S R+ + PLRGK+LNV A ++L + EI +I LG
Sbjct: 430 TEGDSAKSLAVSGLSVVGRDYYGVFPLRGKLLNVREASHKQILKNAEINAIIKILGLQYK 489
Query: 487 QDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKPPLYGITR 546
+ FD+ LRY K++IMTD D DG+HI+ LL+ F PSL+ FL P+ T+
Sbjct: 490 KKYFDVESLRYGKLMIMTDQDHDGSHIKGLLINFIHHFWPSLLQIPFLEEFITPIVKATK 549
Query: 547 GKSLQYVKDEESLEDYLINQSLSEEIELFCDSKGVISKNDLRNFIDDALKIDKLIKDFYP 606
GK E + N S + L K+++
Sbjct: 550 GKQEVSFYSLPEYEKWKKNTD-------NWKSWKIKYYKGLGTSTSKEA------KEYFS 596
Query: 607 NHD 609
+ D
Sbjct: 597 DLD 599
Score = 34.9 bits (80), Expect = 0.091
Identities = 9/64 (14%), Positives = 18/64 (28%)
Query: 730 GRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRR 789
K ++ YKGLG + + E + D +L + +
Sbjct: 571 NWKSWKIKYYKGLGTSTSKEAKEYFSDLDRHRILFKYDGGIDDEAIDMAFSKKKIDARKE 630
Query: 790 EFIQ 793
+
Sbjct: 631 WLRK 634
>gnl|CDD|173786 cd03366, TOPRIM_TopoIIA_GyrB, TOPRIM_TopoIIA_GyrB:
topoisomerase-primase (TOPRIM) nucleotidyl
transferase/hydrolase domain of the type found in
proteins of the type IIA family of DNA topoisomerases
similar to the Escherichia coli GyrB subunit. TopoIIA
enzymes cut both strands of the duplex DNA to remove
(relax) both positive and negative supercoils in DNA.
These enzymes covalently attach to the 5' ends of the
cut DNA, separate the free ends of the cleaved strands,
pass another region of the duplex through this gap, then
rejoin the ends. These proteins also catenate/
decatenate duplex rings. DNA gyrase is more effective
at relaxing supercoils than decatentating DNA. DNA
gyrase in addition inserts negative supercoils in the
presence of ATP. The TOPRIM domain has two conserved
motifs, one of which centers at a conserved glutamate
and the other one at two conserved aspartates (DxD). The
conserved glutamate may act as a general base in strand
joining and as a general acid in strand cleavage by
topisomerases. The DXD motif may co-ordinate Mg2+, a
cofactor required for full catalytic function.
Length = 114
Score = 228 bits (584), Expect = 4e-60
Identities = 90/115 (78%), Positives = 100/115 (86%), Gaps = 1/115 (0%)
Query: 425 SELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTG 484
SEL++VEGDSAGGSAKQGR R QAILPLRGKILNVE+AR DK+L ++EI LITALGTG
Sbjct: 1 SELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILNVEKARLDKILKNEEIRALITALGTG 60
Query: 485 IGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKP 539
IG+D FD+ KLRYHKIIIMTDADVDGAHIRTLLLTFFFR M LI NG +YI +P
Sbjct: 61 IGED-FDLEKLRYHKIIIMTDADVDGAHIRTLLLTFFFRYMRPLIENGHVYIAQP 114
>gnl|CDD|48467 cd00822, TopoII_Trans_DNA_gyrase, TopoIIA_Trans_DNA_gyrase:
Transducer domain, having a ribosomal S5 domain 2-like
fold, of the type found in proteins of the type IIA
family of DNA topoisomerases similar to the B subunits
of E. coli DNA gyrase and E. coli Topoisomerase IV which
are heterodimers composed of two subunits. The type
IIA enzymes are the predominant form of topoisomerase
and are found in some bacteriophages, viruses and
archaea, and in all bacteria and eukaryotes. All type
IIA topoisomerases are related to each other at amino
acid sequence level, though their oligomeric
organization sometimes differs. TopoIIA enzymes cut
both strands of the duplex DNA to remove (relax) both
positive and negative supercoils in DNA. These enzymes
covalently attach to the 5' ends of the cut DNA,
separate the free ends of the cleaved strands, pass
another region of the duplex through this gap, then
rejoin the ends. TopoIIA enzymes also catenate/
decatenate duplex rings. E.coli DNA gyrase is a
heterodimer composed of two subunits. E. coli DNA gyrase
B subunit 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..
Length = 172
Score = 220 bits (561), Expect = 2e-57
Identities = 86/172 (50%), Positives = 125/172 (72%)
Query: 227 GGIEAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGG 286
GG++ FV L++ K+PL + PI I+G +D + +++A++W D Y EN+L F NNIP +GG
Sbjct: 1 GGLKDFVEELNKDKEPLHEEPIYIEGEKDGVEVEVALQWTDSYSENILSFVNNIPTPEGG 60
Query: 287 THLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEK 346
TH +G R+ALTR I Y +K+ KK + GDD REG T+V+S+K+P+P+F QTK+K
Sbjct: 61 THETGFRAALTRAINDYAKKNNLLKKKDVKLTGDDIREGLTAVISVKVPEPQFEGQTKDK 120
Query: 347 LVSSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLDASMVRDAARRARDL 398
L +SEVRS+VES V + L WLEE+P EAK I++K + A+ R+AAR+AR+L
Sbjct: 121 LGNSEVRSIVESAVREALEEWLEENPEEAKKILEKAILAAKAREAARKAREL 172
>gnl|CDD|173780 cd01030, TOPRIM_TopoIIA_like, TOPRIM_TopoIIA_like:
topoisomerase-primase (TOPRIM) nucleotidyl
transferase/hydrolase domain of the type found in
proteins of the type IIA family of DNA topoisomerases
similar to Saccharomyces cerevisiae Topoisomerase II.
TopoIIA enzymes cut both strands of the duplex DNA to
remove (relax) both positive and negative supercoils in
DNA. These enzymes covalently attach to the 5' ends of
the cut DNA, separate the free ends of the cleaved
strands, pass another region of the duplex through this
gap, then rejoin the ends. These proteins also catenate/
decatenate duplex rings. The TOPRIM domain has two
conserved motifs, one of which centers at a conserved
glutamate and the other one at two conserved aspartates
(DxD). The conserved glutamate may act as a general base
in strand joining and as a general acid in strand
cleavage by topisomerases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 115
Score = 217 bits (556), Expect = 9e-57
Identities = 81/115 (70%), Positives = 94/115 (81%)
Query: 425 SELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTG 484
EL LVEGDSAGGSAKQGR R QA+ PLRGKILNVE+A K+L ++EI +I ALG G
Sbjct: 1 CELILVEGDSAGGSAKQGRDRVFQAVFPLRGKILNVEKASLKKILKNEEIQNIIKALGLG 60
Query: 485 IGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIKP 539
IG+D FD++KLRY KIIIMTDADVDG+HIRTLLLTFF+R PSL+ NGFLYI +
Sbjct: 61 IGKDDFDLDKLRYGKIIIMTDADVDGSHIRTLLLTFFYRFWPSLLENGFLYIAQT 115
>gnl|CDD|143961 pfam00204, DNA_gyraseB, DNA gyrase B. This family represents the
second domain of DNA gyrase B which has a ribosomal S5
domain 2-like fold. This family is structurally related
to PF01119.
Length = 173
Score = 195 bits (499), Expect = 3e-50
Identities = 82/174 (47%), Positives = 118/174 (67%), Gaps = 4/174 (2%)
Query: 228 GIEAFVSYLDRHKKPLMQSPIRIQGSR---DNISIDLAMRWNDGYHENVLCFTNNIPQKD 284
G++ +V L++ K PL I +G D I +++A++WND Y EN++ F NNIP D
Sbjct: 1 GLKDYVKELNKDKTPLHPEVIYFEGEEAFDDRIEVEVALQWNDSYSENIVSFVNNIPTPD 60
Query: 285 GGTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTK 344
GGTH+ G R+ALTR + Y +K G K K + GDD REG T+V+S+K+P+P+F QTK
Sbjct: 61 GGTHVDGFRAALTRALNEYAKKK-GLLKKKDKITGDDIREGLTAVVSVKIPNPQFEGQTK 119
Query: 345 EKLVSSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLDASMVRDAARRARDL 398
EKL +SEVRS VES V++ + +LE++P AK I++K L A+ R AAR+AR+L
Sbjct: 120 EKLGNSEVRSAVESVVSEKFAKFLEKNPEIAKKILEKALAAAKARLAARKAREL 173
>gnl|CDD|144542 pfam00986, DNA_gyraseB_C, DNA gyrase B subunit, carboxyl terminus.
The amino terminus of eukaryotic and prokaryotic DNA
topoisomerase II are similar, but they have a different
carboxyl terminus. The amino-terminal portion of the DNA
gyrase B protein is thought to catalyse the
ATP-dependent super-coiling of DNA. See pfam00204. The
carboxyl-terminal end supports the complexation with the
DNA gyrase A protein and the ATP-independent relaxation.
This family also contains Topoisomerase IV. This is a
bacterial enzyme that is closely related to DNA gyrase,.
Length = 65
Score = 124 bits (315), Expect = 7e-29
Identities = 41/64 (64%), Positives = 53/64 (82%)
Query: 730 GRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRR 789
G K + +QR+KGLGEMN QLWETT++P+TR LL+V I DA +AD++FS LMG +VEPRR
Sbjct: 2 GNKKVEIQRFKGLGEMNPEQLWETTMDPETRRLLQVTIEDAEEADEMFSTLMGKDVEPRR 61
Query: 790 EFIQ 793
EFI+
Sbjct: 62 EFIE 65
>gnl|CDD|173785 cd03365, TOPRIM_TopoIIA, TOPRIM_TopoIIA: topoisomerase-primase
(TOPRIM) nucleotidyl transferase/hydrolase domain of the
type found in proteins of the type IIA family of DNA
topoisomerases similar to Saccharomyces cerevisiae
Topoisomerase II. TopoIIA enzymes cut both strands of
the duplex DNA to remove (relax) both positive and
negative supercoils in DNA. These enzymes covalently
attach to the 5' ends of the cut DNA, separate the free
ends of the cleaved strands, pass another region of the
duplex through this gap, then rejoin the ends. These
proteins also catenate/ decatenate duplex rings. The
TOPRIM domain has two conserved motifs, one of which
centers at a conserved glutamate and the other one at
two conserved aspartates (DxD). This glutamate and two
aspartates, cluster together to form a highly acid
surface patch. The conserved glutamate may act as a
general base in strand joining and as a general acid in
strand cleavage by topisomerases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 120
Score = 103 bits (258), Expect = 2e-22
Identities = 46/113 (40%), Positives = 63/113 (55%), Gaps = 5/113 (4%)
Query: 427 LFLVEGDSAGGSAKQGRS---RENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGT 483
L L EGDSA A G S R+ + PLRGK+LNV A +++ + EI + LG
Sbjct: 3 LILTEGDSAKALAVAGLSVVGRDYYGVFPLRGKLLNVREASHKQIMENAEIQNIKKILGL 62
Query: 484 GIGQDSF-DINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLI-HNGFL 534
G+ + LRY +++IMTD D DG+HI+ LL+ F PSL+ GFL
Sbjct: 63 QHGKSDYESTKSLRYGRLMIMTDQDHDGSHIKGLLINFIHSFWPSLLKIPGFL 115
>gnl|CDD|145582 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 = 67.7 bits (166), Expect = 1e-11
Identities = 34/111 (30%), Positives = 45/111 (40%), Gaps = 18/111 (16%)
Query: 38 ESGLHHMIYEVLDNAIDESLEGYADIITVTLNMDG---SCTVSDNGRGIPTDLHKEEGIS 94
E L ++ +LDNAI + G I VTL DG TV DNG GIP
Sbjct: 3 EDRLRQVLSNLLDNAIKHAPAG--GEIEVTLERDGGRLRITVEDNGIGIP---------- 50
Query: 95 AAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRIKREGNI 145
E + + ++ S KV G G+G+S+V L I E
Sbjct: 51 -PEDLPKIFEPFFRTDKDSRKVGG--TGLGLSIVRKLVELHGGTITVESEP 98
>gnl|CDD|73195 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 = 57.3 bits (138), Expect = 2e-08
Identities = 29/125 (23%), Positives = 53/125 (42%), Gaps = 25/125 (20%)
Query: 229 IEAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWND---GYHENVLCFTNNIPQKDG 285
++ ++ + K + I ++G D ++ A+ + D + F N P ++G
Sbjct: 1 LKDRLAEILGDK--VADKLIYVEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREG 58
Query: 286 GTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPD--PRFS-SQ 342
GTH+ +R A TR + GDD R +VLS+K+P +
Sbjct: 59 GTHVKAVREAYTRAL-----------------NGDDVRRYPVAVLSLKIPPSLVDVNVHP 101
Query: 343 TKEKL 347
TKE++
Sbjct: 102 TKEEV 106
>gnl|CDD|28956 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 = 54.2 bits (130), Expect = 1e-07
Identities = 29/102 (28%), Positives = 43/102 (42%), Gaps = 18/102 (17%)
Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDG---SCTVSDNGRGIPTDLHKEEGISAAE 97
L ++ +L NAI + EG IT+++ DG V DNG GIP + +
Sbjct: 1 LQQVLLNLLSNAIKHTPEG-GGRITISVERDGDHLEIRVEDNGPGIPEEDLE-------- 51
Query: 98 VIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRI 139
+F+ S GG G+G+S+V L RI
Sbjct: 52 ------RIFERFSDGSRSRKGGGTGLGLSIVKKLVELHGGRI 87
>gnl|CDD|173773 cd00188, TOPRIM, Topoisomerase-primase domain. This is a
nucleotidyl transferase/hydrolase domain found in type
IA, type IIA and type IIB topoisomerases, bacterial
DnaG-type primases, small primase-like proteins from
bacteria and archaea, OLD family nucleases from
bacterial and archaea, and bacterial DNA repair proteins
of the RecR/M family. This domain has two conserved
motifs, one of which centers at a conserved glutamate
and the other one at two conserved aspartates (DxD).
This glutamate and two aspartates, cluster together to
form a highly acid surface patch. The conserved
glutamate may act as a general base in nucleotide
polymerization by primases and in strand joining in
topoisomerases and, as a general acid in strand cleavage
by topisomerases and nucleases. The DXD motif may
co-ordinate Mg2+, a cofactor required for full catalytic
function.
Length = 83
Score = 45.9 bits (109), Expect = 5e-05
Identities = 23/109 (21%), Positives = 34/109 (31%), Gaps = 26/109 (23%)
Query: 425 SELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTG 484
+L +VEG S + Q A++ L G LN R ++L
Sbjct: 1 KKLIIVEGPSDALALAQAGGY-GGAVVALGGHALNKTRELLKRLLG-------------- 45
Query: 485 IGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGF 533
++II TDAD +G I LL +
Sbjct: 46 -----------EAKEVIIATDADREGEAIALRLLELLKSLGKKVRRLLL 83
>gnl|CDD|48469 cd03481, TopoIIA_Trans_ScTopoIIA, TopoIIA_Trans_ScTopoIIA:
Transducer domain, having a ribosomal S5 domain 2-like
fold, of the type found in proteins of the type IIA
family of DNA topoisomerases similar to Saccharomyces
cerevisiae Topo IIA. S. cerevisiae Topo IIA is a
homodimer encoded by a single gene. The type IIA enzymes
are the predominant form of topoisomerase and are found
in some bacteriophages, viruses and archaea, and in all
bacteria and eukaryotes. All type IIA topoisomerases
are related to each other at amino acid sequence level,
though their oligomeric organization sometimes differs.
TopoIIA enzymes cut both strands of the duplex DNA to
remove (relax) both positive and negative supercoils in
DNA. These enzymes covalently attach to the 5' ends of
the cut DNA, separate the free ends of the cleaved
strands, pass another region of the duplex through this
gap, then rejoin the ends. TopoIIA enzymes also
catenate/ decatenate duplex rings. 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..
Length = 153
Score = 39.8 bits (93), Expect = 0.003
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 276 FTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMP 335
F N+I GGTH+ + + +++ V+K K +V + ++ +
Sbjct: 49 FVNSIATTKGGTHVDYVADQIVKKLDEVVKK---KNKGGINVKPFQVKNHLWIFVNCLIE 105
Query: 336 DPRFSSQTKEKLVS 349
+P F SQTKE L +
Sbjct: 106 NPSFDSQTKETLTT 119
>gnl|CDD|145089 pfam01751, Toprim, Toprim domain. This is a conserved region from
DNA primase. This corresponds to the Toprim domain
common to DnaG primases, topoisomerases, OLD family
nucleases and RecR proteins. Both DnaG motifs IV and V
are present in the alignment, the DxD (V) motif may be
involved in Mg2+ binding and mutations to the conserved
glutamate (IV) completely abolish DnaG type primase
activity. DNA primase EC:2.7.7.6 is a
nucleotidyltransferase it synthesizes the
oligoribonucleotide primers required for DNA replication
on the lagging strand of the replication fork; it can
also prime the leading stand and has been implicated in
cell division. This family also includes the atypical
archaeal A subunit from type II DNA topoisomerases. Type
II DNA topoisomerases catalyse the relaxation of DNA
supercoiling by causing transient double strand breaks.
Length = 89
Score = 39.2 bits (92), Expect = 0.004
Identities = 19/105 (18%), Positives = 32/105 (30%), Gaps = 25/105 (23%)
Query: 425 SELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTG 484
L +VEG S + + + + L G + D + ++E
Sbjct: 1 KVLIIVEGPSDAIALAKAGGYKGNVV-ALLGHLS-------DVIPLTKEQ---------- 42
Query: 485 IGQDSFDINKLRYHK--IIIMTDADVDGAHIRTLLLTFFFRQMPS 527
+ K K +I+ TD D +G I LL
Sbjct: 43 -----LKLLKKLAKKDEVILATDPDREGEAIAWKLLELLKPLGKK 82
>gnl|CDD|109760 pfam00716, Peptidase_S21, Assemblin (Peptidase family S21).
Length = 326
Score = 32.4 bits (74), Expect = 0.48
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 10/72 (13%)
Query: 337 PRFSSQTKEKLVSSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLDASMVRDAARRAR 396
S +E L+S +++ G SAW P + +++ K +DA +RD R
Sbjct: 140 RDLSPAEREALLSLAKQAL-------GDSAWEPSFPSDTYVLLAKAVDAMFIRD---RLP 189
Query: 397 DLTRRKGVLDIA 408
L + V I
Sbjct: 190 KLKTDRRVAGIK 201
>gnl|CDD|36006 KOG0787, KOG0787, KOG0787, Dehydrogenase kinase [Signal
transduction mechanisms].
Length = 414
Score = 32.2 bits (73), Expect = 0.51
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 14/70 (20%)
Query: 26 KRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYAD--------IITVTLN-MDGSCTV 76
++Y+ S L++M++E+ NA+ ++E + D +TV D +
Sbjct: 251 LSFTVYV-----PSHLYYMLFELFKNAMRATVEHHGDDGDELPPIKVTVAKGDEDLLIKI 305
Query: 77 SDNGRGIPTD 86
SD G G+P
Sbjct: 306 SDRGGGVPHR 315
>gnl|CDD|33640 COG3850, NarQ, Signal transduction histidine kinase,
nitrate/nitrite-specific [Signal transduction
mechanisms].
Length = 574
Score = 29.9 bits (67), Expect = 2.6
Identities = 16/76 (21%), Positives = 27/76 (35%), Gaps = 5/76 (6%)
Query: 43 HMIY---EVLDNAIDESLEGYADIITVTLNMDGSCTVSDNGRGIPTDLHKEE--GISAAE 97
H++ E L NAI + + + + TV DNG GI G++
Sbjct: 481 HLLQIVREALSNAIKHAQASEIKVTVSQNDGQVTLTVEDNGVGIDEAAEPSGHYGLNIMR 540
Query: 98 VIMTRLHAGGKFNQKS 113
RL + ++
Sbjct: 541 ERAQRLGGQLRIRRRE 556
>gnl|CDD|30987 COG0642, BaeS, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 336
Score = 29.8 bits (65), Expect = 3.0
Identities = 17/68 (25%), Positives = 28/68 (41%), Gaps = 1/68 (1%)
Query: 19 KGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTLNMDGSCTVSD 78
KG++ P + D L ++ +L NAI + G I + + +V D
Sbjct: 208 KGIELAVDLPELPYVLGD-PERLRQVLVNLLSNAIKYTPGGEITISVRQDDEQVTISVED 266
Query: 79 NGRGIPTD 86
G GIP +
Sbjct: 267 TGPGIPEE 274
>gnl|CDD|33099 COG3290, CitA, Signal transduction histidine kinase regulating
citrate/malate metabolism [Signal transduction
mechanisms].
Length = 537
Score = 29.4 bits (66), Expect = 3.8
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 48 VLDNAIDESLEGYAD-IITVTLNMDGS---CTVSDNGRGIPTDL 87
++DNA++ L + I ++L+ G V+D G GIP ++
Sbjct: 435 LIDNALEALLAPEENKEIELSLSDRGDELVIEVADTGPGIPPEV 478
>gnl|CDD|173777 cd01027, TOPRIM_RNase_M5_like, TOPRIM_ RNase M5_like: The
topoisomerase-primase (TOPRIM) nucleotidyl
transferase/hydrolase domain found in Ribonuclease M5:
(RNase M5) and other small primase-like proteins from
bacteria and archaea. RNase M5 catalyzes the maturation
of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM
domain has two conserved motifs, one of which centers at
a conserved glutamate and the other one at two conserved
aspartates (DxD). The conserved glutamate may act as a
general base in nucleotide polymerization by primases.
The DXD motif may co-ordinate Mg2+, a cofactor required
for full catalytic function.
Length = 81
Score = 29.5 bits (67), Expect = 4.0
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 478 ITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLL 517
I G+ I +++ ++ K Y +II+TD D G IR L
Sbjct: 26 IETNGSIINKETIELIKKAYRGVIILTDPDRKGEKIRKKL 65
>gnl|CDD|31579 COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA replication,
recombination, and repair].
Length = 538
Score = 29.5 bits (66), Expect = 4.0
Identities = 30/109 (27%), Positives = 46/109 (42%), Gaps = 16/109 (14%)
Query: 25 KKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLE-GYADIITVTLNMDG----SCTVSDN 79
+K M +G L ++E++ N++D E G I V + G V DN
Sbjct: 22 RKNKEM-LGFDGPIRSLTTTVHELVTNSLDACEEAGILPDIKVEIERIGKDHYKVIVEDN 80
Query: 80 GRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVV 128
G GIP EE I + ++ G KF++ S G G+G+S
Sbjct: 81 GPGIP-----EEQIPK---VFGKMLYGSKFHRN--IQSRGQQGIGISAA 119
>gnl|CDD|173934 cd08175, G1PDH, Glycerol-1-phosphate dehydrogenase (G1PDH)
catalyzes the reversible reduction of dihydroxyacetone
phosphate (DHAP) to glycerol-1-phosphate (G1P) in an
NADH-dependent manner. Glycerol-1-phosphate
dehydrogenase (G1PDH) plays a role in the synthesis of
phosphoglycerolipids in Gram-positive bacterial species.
It catalyzes the reversibly reduction of
dihydroxyacetone phosphate (DHAP) to
glycerol-1-phosphate (G1P) in a NADH-dependent manner.
Its activity requires a Ni++ ion. In Bacillus subtilis,
it has been described as AraM gene in L-arabinose (ara)
operon. AraM protein forms homodimer. This family is
bacteria specific.
Length = 348
Score = 29.5 bits (67), Expect = 4.2
Identities = 7/26 (26%), Positives = 15/26 (57%)
Query: 383 LDASMVRDAARRARDLTRRKGVLDIA 408
+D + R + A+++ R +LD+A
Sbjct: 317 IDKELFRKSLILAKEIRDRYTLLDLA 342
>gnl|CDD|37391 KOG2180, KOG2180, KOG2180, Late Golgi protein sorting complex,
subunit Vps53 [Intracellular trafficking, secretion, and
vesicular transport].
Length = 793
Score = 29.2 bits (65), Expect = 4.3
Identities = 13/96 (13%), Positives = 32/96 (33%), Gaps = 2/96 (2%)
Query: 289 LSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLV 348
+ L+ +L QI + +F + + V+ P R + +
Sbjct: 181 IDKLKKSLLSQIFQDFKAAFSGGETHEEALLLQKLSDACLVVDALEPSVR--EELIKWFC 238
Query: 349 SSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLD 384
S ++ + F + +A L++ + + D
Sbjct: 239 SQQLEEYEQIFRENEEAASLDKLDRRYAWFKRLLRD 274
>gnl|CDD|146633 pfam04100, Vps53_N, Vps53-like, N-terminal. Vps53 complexes with
Vps52 and Vps54 to form a multi- subunit complex
involved in regulating membrane trafficking events.
Length = 375
Score = 29.0 bits (65), Expect = 4.8
Identities = 18/96 (18%), Positives = 38/96 (39%), Gaps = 2/96 (2%)
Query: 289 LSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLV 348
+S L+ +L QI + +FGS+ + R+ + V P R + +
Sbjct: 166 ISKLKGSLLSQIFQDFKSAFGSQGEHRTGLLLQKLSDACLVADALDPSVR--EELIKWFC 223
Query: 349 SSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLD 384
S ++ + F + +AWL++ + + D
Sbjct: 224 SQQLEEYEQIFRENEEAAWLDKIDRRYAWFKRLLRD 259
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.317 0.135 0.383
Gapped
Lambda K H
0.267 0.0649 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 9,319,454
Number of extensions: 501084
Number of successful extensions: 1207
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1187
Number of HSP's successfully gapped: 36
Length of query: 803
Length of database: 6,263,737
Length adjustment: 102
Effective length of query: 701
Effective length of database: 4,059,619
Effective search space: 2845792919
Effective search space used: 2845792919
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: 61 (27.4 bits)