RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780814|ref|YP_003065227.1| DNA gyrase subunit B
[Candidatus Liberibacter asiaticus str. psy62]
(803 letters)
>1ei1_A DNA gyrase B, GYRB; ATPase domain, dimer, isomerase; HET: DNA ANP;
2.30A {Escherichia coli} SCOP: d.14.1.3 d.122.1.2
Length = 391
Score = 535 bits (1379), Expect = e-152
Identities = 223/394 (56%), Positives = 298/394 (75%), Gaps = 4/394 (1%)
Query: 7 NSSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITV 66
++S D+ SI++LKGLDAV+KRP MYIGDTD +GLHHM++EV+DNAIDE+L G+ I V
Sbjct: 1 SNSSDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIV 60
Query: 67 TLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVS 126
T++ D S +V D+GRGIPT +H EEG+SAAEVIMT LHAGGKF+ SYKVSGGLHGVGVS
Sbjct: 61 TIHADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVS 120
Query: 127 VVNALSSWLKLRIKREGNIYEMSFINGILDNPLVVTGSAGNDTGTEVTFLPSSDIFS-VQ 185
VVNALS L+L I+REG I+ + +G+ PL VTG TGT V F PS + F+ V
Sbjct: 121 VVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETE-KTGTMVRFWPSLETFTNVT 179
Query: 186 DFNYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQ 245
+F Y+ L RLRELSFL+S V I L DKR + +E Y+GGI+AFV YL+++K P+
Sbjct: 180 EFEYEILAKRLRELSFLDSGVSIRLRDKR--DGKEDHFHYEGGIKAFVEYLNKNKTPIHP 237
Query: 246 SPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVE 305
+ +D I +++A++WNDG+ EN+ CFTNNIPQ+DGGTHL+G R+A+TR + +Y++
Sbjct: 238 NIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMD 297
Query: 306 KSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDGLS 365
K SKK K S GDD REG +V+S+K+PDP+FSSQTK+KLVSSEV+S VE +N+ L+
Sbjct: 298 KEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLA 357
Query: 366 AWLEEHPLEAKIIVKKVLDASMVRDAARRARDLT 399
+L E+P +AKI+V K++DA+ R+AARRAR++T
Sbjct: 358 EYLLENPTDAKIVVGKIIDAARAREAARRAREMT 391
>3nuh_B DNA gyrase subunit B; topoisomerase, supercoiling, specialization,
isomera; HET: DNA; 3.10A {Escherichia coli}
Length = 420
Score = 466 bits (1199), Expect = e-131
Identities = 189/420 (45%), Positives = 261/420 (62%), Gaps = 8/420 (1%)
Query: 392 ARRARDLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQAIL 451
+ AR++TRRKG LD+A LPGKLADC ERDP SEL+LVEGDSAGGSAKQGR+R+NQAIL
Sbjct: 1 SNAAREMTRRKGALDLAGLPGKLADCQERDPALSELYLVEGDSAGGSAKQGRNRKNQAIL 60
Query: 452 PLRGKILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGA 511
PL+GKILNVE+ARFDKMLSSQE+ TLITALG GIG+D ++ +KLRYH IIIMTDADVDG+
Sbjct: 61 PLKGKILNVEKARFDKMLSSQEVATLITALGCGIGRDEYNPDKLRYHSIIIMTDADVDGS 120
Query: 512 HIRTLLLTFFFRQMPSLIHNGFLYIIKPPLYGITRGKSLQYVKDEESLEDYLINQSLSEE 571
HIRTLLLTFF+RQMP ++ G +YI +PPLY + +GK QY+KD+E+++ Y I+ +L
Sbjct: 121 HIRTLLLTFFYRQMPEIVERGHVYIAQPPLYKVKKGKQEQYIKDDEAMDQYQISIALDGA 180
Query: 572 IELFCDSKGVISKNDLRNFIDDALKIDKLIKDFYPNHDKTFIEQAVISGVFNCE--SDQE 629
S ++ L + + K+I + K +++ + SD++
Sbjct: 181 TLHTNASAPALAGEALEKLVSEYNATQKMINRMERRYPKAMLKELIYQPTLTEADLSDEQ 240
Query: 630 INVSLASKLANRLNFIAEKSEKSWHGSINNSD-----ILVKRIARGVQEQFVLEGSSIFS 684
+ L + LN + + N++ +V+ GV + L+ I
Sbjct: 241 TVTRWVNALVSELNDKEQHGSQWKFDVHTNAEQNLFEPIVRVRTHGVDTDYPLDHEFITG 300
Query: 685 FGSKYKRIFSNRIEENYLTILSLICNGDKIKITGPCSLLDTIFSIGRKGISMQRYKGLGE 744
+ ++ + + + LD + R+G+S+QRYKGLGE
Sbjct: 301 GEYRRICTLGEKLRGLLEEDAFIERGERRQPVASFEQALDWLVKESRRGLSIQRYKGLGE 360
Query: 745 MNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRREFIQENSLPSA-LDI 803
MN QLWETT++P++R +LRV + DA AD LF+ LMGD VEPRR FI+EN+L +A +DI
Sbjct: 361 MNPEQLWETTMDPESRRMLRVTVKDAIAADQLFTTLMGDAVEPRRAFIEENALKAANIDI 420
>1kij_A DNA gyrase subunit B; topoisomerase, gyrase B-coumarin complex;
HET: DNA NOV; 2.30A {Thermus thermophilus} SCOP:
d.14.1.3 d.122.1.2
Length = 390
Score = 440 bits (1132), Expect = e-124
Identities = 171/391 (43%), Positives = 242/391 (61%), Gaps = 4/391 (1%)
Query: 9 SYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTL 68
SYDA +I++LKGL+ V+ RP+MYIG T G HH+ E+LDNA+DE+L GYA I V L
Sbjct: 2 SYDASAIRVLKGLEGVRHRPAMYIGGTG-VEGYHHLFKEILDNAVDEALAGYATEILVRL 60
Query: 69 NMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVV 128
N DGS TV DNGRGIP DL EEG A EVI LH+GGKF Q +YKVSGGLHGVG SVV
Sbjct: 61 NEDGSLTVEDNGRGIPVDLMPEEGKPAVEVIYNTLHSGGKFEQGAYKVSGGLHGVGASVV 120
Query: 129 NALSSWLKLRIKREGNIYEMSFINGILDNPLVVTGSAGND-TGTEVTFLPSSDIFSVQDF 187
NALS W + + REG + ++F G + PL V G A TGT VTF P +IF F
Sbjct: 121 NALSEWTVVEVFREGKHHRIAFSRGEVTEPLRVVGEAPRGKTGTRVTFKPDPEIFGNLRF 180
Query: 188 NYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQSP 247
+ ++ RLRE+++L + +++ D++ + KGG+ +F L + L + P
Sbjct: 181 DPSKIRARLREVAYLVAGLKLVFQDRQHGKE--EVFLDKGGVASFAKALAEGEDLLYEKP 238
Query: 248 IRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEKS 307
I+G+ + +++ GY+ +L + N IP +DGGTHL+ +SA +R + Y +K+
Sbjct: 239 FLIRGTHGEVEVEVGFLHTQGYNAEILTYANMIPTRDGGTHLTAFKSAYSRALNQYAKKA 298
Query: 308 FGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDGLSAW 367
+K+ GDD EG +V+S+K+P+P+F QTK KL++ E + V V + L
Sbjct: 299 GLNKEKGPQPTGDDLLEGLYAVVSVKLPNPQFEGQTKGKLLNPEAGTAVGQVVYERLLEI 358
Query: 368 LEEHPLEAKIIVKKVLDASMVRDAARRARDL 398
LEE+P AK + +K L A+ R+AAR+AR+L
Sbjct: 359 LEENPRIAKAVYEKALRAAQAREAARKAREL 389
>1s16_A Topoisomerase IV subunit B; two-domain protein complexed with
ADPNP; HET: ANP; 2.10A {Escherichia coli} SCOP: d.14.1.3
d.122.1.2
Length = 390
Score = 367 bits (942), Expect = e-102
Identities = 136/398 (34%), Positives = 217/398 (54%), Gaps = 11/398 (2%)
Query: 7 NSSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITV 66
+Y+AD+I++L GL+ V++RP MY T +H+ EV+DN++DE+L G+A + V
Sbjct: 2 TQTYNADAIEVLTGLEPVRRRPGMYTDTT----RPNHLGQEVIDNSVDEALAGHAKRVDV 57
Query: 67 TLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVS 126
L+ D S V D+GRG+P D+H EEG+ A E+I+ RLHAGGKF+ K+Y+ SGGLHGVG+S
Sbjct: 58 ILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGIS 117
Query: 127 VVNALSSWLKLRIKREGNIYEMSFINGILDNP-LVVTGSAGNDTGTEVTFLPSSDIFSVQ 185
VVNALS +++ ++R+G +Y ++F NG VV +TGT V F P F
Sbjct: 118 VVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSP 177
Query: 186 DFNYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQ 245
F+ L H L+ + L V+I+ D+ + + Y+ G+ +++ L +
Sbjct: 178 RFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQR--WCYQDGLNDYLAEAVNGLPTLPE 235
Query: 246 SPIRIQGSRDNISIDLAMRWND-GYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYV 304
P + D ++D A+ W G + N IP GGTH++GLR L + +
Sbjct: 236 KPFIGNFAGDTEAVDWALLWLPEGGELLTESYVNLIPTMQGGTHVNGLRQGLLDAMREFC 295
Query: 305 EKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVNDGL 364
E + +D + VLS+KM DP+F+ QTKE+L S + + V V D
Sbjct: 296 EYR-NILPRGVKLSAEDIWDRCAYVLSVKMQDPQFAGQTKERLSSRQCAAFVSGVVKDAF 354
Query: 365 SAWLEEHPLEAKIIVKKVLDASMVRDAARRARDLTRRK 402
WL ++ A+++ + + ++ R R A+ + R+K
Sbjct: 355 ILWLNQNVQAAELLAEMAISSAQRR--MRAAKKVVRKK 390
>1pvg_A DNA topoisomerase II; GHKL ATPase domain; HET: DNA ANP; 1.80A
{Saccharomyces cerevisiae} SCOP: d.14.1.3 d.122.1.2 PDB:
1qzr_A*
Length = 418
Score = 322 bits (825), Expect = 3e-88
Identities = 81/421 (19%), Positives = 156/421 (37%), Gaps = 51/421 (12%)
Query: 1 MSDNIQNSSYDADSIQILKGLDAVKKRPSMYIGDTDGES--------------------- 39
M +D Q + L+ + KRP YIG + +
Sbjct: 3 MVTMSTEPVSASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTIV 62
Query: 40 -GLHHMIYEVLDNAIDESLEGYA-DIITVTLN-MDGSCTVSDNGRGIPTDLHKEEGISAA 96
GL + E+L NA D + + I V ++ + + V ++G+GIP ++H +E I
Sbjct: 63 PGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPIEIHNKENIYIP 122
Query: 97 EVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKL--RIKREGNIYEMSFIN-G 153
E+I L ++ KV+GG +G G + N S+ L G Y + N
Sbjct: 123 EMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFILETADLNVGQKYVQKWENNM 182
Query: 154 ILDNPLVVTGSAGNDTGTEVTFLPSSDIFSVQDFNYDTLQHRLRELSFLNSSVQISLIDK 213
+ +P +T + T+VTF P F +++ + D L R + +N SV+ +
Sbjct: 183 SICHPPKITSYKKGPSYTKVTFKPDLTRFGMKELDNDILGVMRRRVYDINGSVRDINVYL 242
Query: 214 RSPEPREITM-----FYKGGIEAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWNDG 268
+ Y +E + I R N ++A +D
Sbjct: 243 NGKSLKIRNFKNYVELYLKSLEKKRQLDNGEDGAAKSDIPTILYERINNRWEVAFAVSDI 302
Query: 269 YHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTS 328
+ + F N+I GGTH++ + + ++I+ + V +
Sbjct: 303 SFQQI-SFVNSIATTMGGTHVNYITDQIVKKISEILXXXXXXS-----VKSFQIKNNMFI 356
Query: 329 VLSIKMPDPRFSSQTKEKLVS-------------SEVRSVVESFVNDGLSAWLEEHPLEA 375
++ + +P F+SQTKE+L + + ++++ + + + + A
Sbjct: 357 FINCLIENPAFTSQTKEQLTTRVKDFGSRCEIPLEYINKIMKTDLATRMFEIADANEENA 416
Query: 376 K 376
Sbjct: 417 L 417
>3cwv_A DNA gyrase, B subunit, truncated; structural genomics, unknown
function, ATP-binding, isomerase, nucleotide-binding,
topoisomerase; HET: DNA; 1.95A {Myxococcus xanthus dk
1622}
Length = 369
Score = 295 bits (755), Expect = 3e-80
Identities = 80/373 (21%), Positives = 147/373 (39%), Gaps = 29/373 (7%)
Query: 20 GLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTLNMDGSCTVSDN 79
++ V+KRP MY GD E GLHH++Y +LD A +E+ G + + + DGS +
Sbjct: 11 IVENVRKRPGMYCGDVG-EYGLHHLVYFLLDVAYEEARRGECRDVVLEVGGDGSIALFCT 69
Query: 80 GRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRI 139
R + + + R+ G F + G + V ALSS ++ I
Sbjct: 70 SRTVTAE------------NLVRVATGAGFLGRPPGD-GWGWDSMLVVSLALSSRYQVDI 116
Query: 140 KREGNIYEMSFINGILDNPLVVTGS-----AGNDTGTEVTFLPSSDIFSVQDFNYDTLQH 194
+G + + +G + G V F+P + IF V F+ L
Sbjct: 117 WADGRQWRVMGEHGHPQGEGAAVTPMEPMPVSAERGVRVHFVPDATIFEVLAFDRARLSR 176
Query: 195 RLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQSPIRIQGSR 254
R EL+ L +++S D + E GG+ + L + L P+ +
Sbjct: 177 RCNELAALAPGLRVSFADLQRGERTL--WHLPGGVAQWAHVLTEARPQLHPEPVVFDFTW 234
Query: 255 DNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFGSKKDK 314
D + + A++W + +L F N + G H+ G+ AL + ++ G+
Sbjct: 235 DGLRVQCALQWCEDEDSTLLSFANAVRTVRHGAHVKGVTQALRGALAKLSGETRGAFP-- 292
Query: 315 RSVIGDDCREGFTSVLSIKMPDP--RFSSQTKEKLVSSEVRSVVESFVNDGLSAWLEEHP 372
+G T+++++ P F+ TKE L + + + L EHP
Sbjct: 293 ----WARVAQGLTAIVAVSGPRRQMAFAGPTKELLAIPGLEEAIRKQLQPLFIELLREHP 348
Query: 373 LEAKIIVKKVLDA 385
+ ++ ++ +
Sbjct: 349 VTPALLARRTSGS 361
>2xkj_E Topoisomerase IV; type IIA topoisomerase; 2.20A {Acinetobacter
baumannii} PDB: 2xkk_A*
Length = 767
Score = 280 bits (717), Expect = 1e-75
Identities = 83/177 (46%), Positives = 111/177 (62%), Gaps = 2/177 (1%)
Query: 390 DAARRARDLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQA 449
+A RK ++ +LPGKLADC + ++SELF+VEGDSAGGSAKQ R + QA
Sbjct: 9 GRRLKAAKKVERKKIVSGPALPGKLADCVGQTREESELFIVEGDSAGGSAKQARDKNFQA 68
Query: 450 ILPLRGKILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVD 509
I+P+RGKILN D++L+SQE+ + A+G G D D+++LRY KI I+ DAD D
Sbjct: 69 IMPIRGKILNTWEVSSDEVLASQEVHDIAIAIGVDPGSD--DLSELRYGKICILADADSD 126
Query: 510 GAHIRTLLLTFFFRQMPSLIHNGFLYIIKPPLYGITRGKSLQYVKDEESLEDYLINQ 566
G HI TLL F + P+L+ G LY+ PPL+ I GK + Y D+E LE L N
Sbjct: 127 GLHIATLLCALFVKHFPALVEEGHLYVAMPPLFRIDIGKDVHYALDDEELETILKNV 183
Score = 59.7 bits (144), Expect = 2e-09
Identities = 25/75 (33%), Positives = 44/75 (58%), Gaps = 1/75 (1%)
Query: 730 GRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRL-MGDEVEPR 788
G K + R+KGLGEMNA QL ETT++P+TR L+++ + DA L +L R
Sbjct: 185 GNKNPQITRFKGLGEMNAIQLRETTMDPNTRRLVQLDLDDAHLTAGLLDKLLAKKRAADR 244
Query: 789 REFIQENSLPSALDI 803
++++++ + + +
Sbjct: 245 KQWLEQKGNLADITV 259
>3fv5_A DNA topoisomerase 4 subunit B; topoisomerase IV B subunit complex,
antibiotic resistance, ATP-binding, nucleotide-binding;
HET: DNA 1EU; 1.80A {Escherichia coli} PDB: 1s14_A*
Length = 201
Score = 255 bits (653), Expect = 3e-68
Identities = 88/207 (42%), Positives = 128/207 (61%), Gaps = 7/207 (3%)
Query: 20 GLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTLNMDGSCTVSDN 79
GL+ V++RP MY T +H+ EV+DN++DE+L G+A + V L+ D S V D+
Sbjct: 1 GLEPVRRRPGMYTDTT----RPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDD 56
Query: 80 GRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRI 139
GRG+P D+H EEG+ A E+I+ RLHAGGKF+ K+Y+ SGGLHGVG+SVVNALS +++ +
Sbjct: 57 GRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLHGVGISVVNALSKRVEVNV 116
Query: 140 KREGNIYEMSFINGILDNPLVVTGSAGN-DTGTEVTFLPSSDIFSVQDFNYDTLQHRLRE 198
+R+G +Y ++F NG L V G+ G +TGT V F P F F+ L H L+
Sbjct: 117 RRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKA 176
Query: 199 LSFLNSSVQISLIDKRSPEPREITMFY 225
+ L V+I+ D+ + E Y
Sbjct: 177 KAVLCPGVEITFKDEINNT--EQRWCY 201
>3g7e_A DNA gyrase subunit B; isomerase; HET: DNA B46; 2.20A {Escherichia
coli} PDB: 1kzn_A* 1aj6_A*
Length = 203
Score = 250 bits (640), Expect = 9e-67
Identities = 122/199 (61%), Positives = 147/199 (73%), Gaps = 2/199 (1%)
Query: 20 GLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTLNMDGSCTVSDN 79
GLDAV+KRP MYIGDTD +GLHHM++EV+DNAIDE+L G+ I VT++ D S +V D+
Sbjct: 1 GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDD 60
Query: 80 GRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRI 139
GRGIPT +H EEG+SAAEVIMT LHAGGKF+ SYKVSGGLHGVGVSVVNALS L+L I
Sbjct: 61 GRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVI 120
Query: 140 KREGNIYEMSFINGILDNPLVVTGSAGNDTGTEVTFLPSSDI-FSVQDFNYDTLQHRLRE 198
+REG I+ + +G+ PL VTG TGT V F PS + +V +F Y+ L RLRE
Sbjct: 121 QREGKIHRQIYEHGVPQAPLAVTGETEK-TGTMVRFWPSLETFTNVTEFEYEILAKRLRE 179
Query: 199 LSFLNSSVQISLIDKRSPE 217
LSFLNS V I L DKR +
Sbjct: 180 LSFLNSGVSIRLRDKRDGK 198
>3l4j_A DNA topoisomerase 2; topoisomerase, protein-DNA complex, covalently
linked comple supercoiling; HET: DNA PTR TSP; 2.48A
{Saccharomyces cerevisiae} PDB: 3l4k_A* 1bjt_A 1bgw_A
2rgr_A*
Length = 757
Score = 248 bits (633), Expect = 4e-66
Identities = 54/163 (33%), Positives = 81/163 (49%), Gaps = 8/163 (4%)
Query: 407 IASLPGKLADCSE---RDPKKSELFLVEGDSAGGSAKQGRS---RENQAILPLRGKILNV 460
I + P KL D ++ ++ K L L EGDSA A G + R+ PLRGK+LNV
Sbjct: 3 ITNYP-KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNV 61
Query: 461 ERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTF 520
A D++L + EI + +G + D LRY ++IMTD D DG+HI+ L++ F
Sbjct: 62 REASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLIINF 121
Query: 521 FFRQMPSLIH-NGFLYIIKPPLYGITRGKSLQYVKDEESLEDY 562
P L+ GFL P+ ++ K + ++ DY
Sbjct: 122 LESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDY 164
Score = 41.3 bits (96), Expect = 9e-04
Identities = 14/73 (19%), Positives = 30/73 (41%), Gaps = 1/73 (1%)
Query: 730 GRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRR 789
+ + YKGLG A ++ E N D + + + D + + + R+
Sbjct: 173 HKFTWKQKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQG-NDKDYIDLAFSKKKADDRK 231
Query: 790 EFIQENSLPSALD 802
E++++ + LD
Sbjct: 232 EWLRQYEPGTVLD 244
>2xcs_B DNA gyrase subunit B, DNA gyrase subunit A; isomerase, type IIA
topoisomerase; HET: DNA 5UA RXV; 2.10A {Staphylococcus
aureus} PDB: 2xcr_B* 2xcq_A* 2xco_A*
Length = 692
Score = 242 bits (619), Expect = 2e-64
Identities = 95/148 (64%), Positives = 114/148 (77%), Gaps = 1/148 (0%)
Query: 405 LDIASLPGKLADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERAR 464
+D+ASLPGKLADCS + P++ E+FLVEGDSAGGS K GR QAILPLRGKILNVE+AR
Sbjct: 1 MDVASLPGKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVEKAR 60
Query: 465 FDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQ 524
D++L++ EI +ITA GTGIG D FD+ K RYHKI+IMTDADVDGAHIRTLLLTFF+R
Sbjct: 61 LDRILNNNEIRQMITAFGTGIGGD-FDLAKARYHKIVIMTDADVDGAHIRTLLLTFFYRF 119
Query: 525 MPSLIHNGFLYIIKPPLYGITRGKSLQY 552
M LI G++YI +PP G+
Sbjct: 120 MRPLIEAGYVYIAQPPTGYKGLGEMNAD 147
Score = 57.6 bits (139), Expect = 1e-08
Identities = 40/66 (60%), Positives = 52/66 (78%)
Query: 737 QRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRREFIQENS 796
YKGLGEMNA QLWETT+NP+ R+LL+VK+ DA +AD F LMGD VE RR+FI++N+
Sbjct: 136 TGYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEADQTFEMLMGDVVENRRQFIEDNA 195
Query: 797 LPSALD 802
+ + LD
Sbjct: 196 VYANLD 201
>1bjt_A Topoisomerase II; quaternary change, DNA-binding, DNA topology;
2.50A {Saccharomyces cerevisiae} SCOP: e.11.1.1 PDB:
1bgw_A 2rgr_A*
Length = 793
Score = 236 bits (603), Expect = 1e-62
Identities = 59/204 (28%), Positives = 91/204 (44%), Gaps = 14/204 (6%)
Query: 390 DAARRARDLTRRKGVLDIASLPGKLADCSE---RDPKKSELFLVEGDSAGGSAKQGRS-- 444
+ A + D TR+ + + KL D ++ ++ K L L EGDSA A G +
Sbjct: 1 ENALKKSDGTRKSRITNYP----KLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVV 56
Query: 445 -RENQAILPLRGKILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIM 503
R+ PLRGK+LNV A D++L + EI + +G + D LRY ++IM
Sbjct: 57 GRDYYGCYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIM 116
Query: 504 TDADVDGAHIRTLLLTFFFRQMPSLI-HNGFLYIIKPPLYGITRGKSLQYVKDEESLEDY 562
TD D DG+HI+ L++ F L+ GFL P+ ++ K + ++ DY
Sbjct: 117 TDQDHDGSHIKGLIINFLESSFLGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDY 176
Query: 563 LINQSLSEEIELFCDSKGVISKND 586
+ EE K K
Sbjct: 177 EKWR---EEESHKFTWKQKYYKGL 197
Score = 30.2 bits (67), Expect = 2.0
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 2/57 (3%)
Query: 736 MQRYKGLGEMNASQLWETTLNPDTR--SLLRVKITDASQADDLFSRLMGDEVEPRRE 790
+ YKGLG A ++ E N D ++ D D FS+ D+ +
Sbjct: 191 QKYYKGLGTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLR 247
>2q2e_B Type 2 DNA topoisomerase 6 subunit B; DNA-binding, SPO11, ATPase;
4.00A {Methanosarcina mazei}
Length = 621
Score = 229 bits (585), Expect = 2e-60
Identities = 67/548 (12%), Positives = 149/548 (27%), Gaps = 60/548 (10%)
Query: 12 ADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDE-SLEGYADIITVTLNM 70
A + + + +K + D+ S L + E +DNA+D G I V +
Sbjct: 10 AKKQKSISVAEFFEKNRQILGFDSAPRS-LITTVKEAVDNALDACEEAGILPDILVQVER 68
Query: 71 DG----SCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVS 126
G + + DNG GI + + +L G +F+ + K S G G+G+S
Sbjct: 69 TGPDYVTVIIEDNGPGIVREQI--------PKVFAKLLYGSRFH--ALKQSRGQQGIGIS 118
Query: 127 VVNALSSW-------LKLRIKREGNIYEMSFINGILDN-PLVVTGSAGNDTGTEVTFLPS 178
+ + + + + N P ++ + T +
Sbjct: 119 AAVLYAQMTAGRHTKILSKTSPTAPAHYYELMINTSTNEPDILVDEVRDWFRPHGTQIEL 178
Query: 179 SDIFSVQDFNYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYLDR 238
+ ++ L+ + +N +I+LID E E +
Sbjct: 179 EMRAAYVKGRRQSIYEYLKATAIVNPHARITLIDPDGNEEV---------FERATDKMPE 229
Query: 239 HKKPLMQSPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSALTR 298
+ ++ P I+ L + + + F K G + A
Sbjct: 230 PAEEILPHPEGIELG------TLMKMLHYTERQKLAPFLRYSFCKIGLLTAEEICKA--- 280
Query: 299 QITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVES 358
+ D ++ + R+ + +K+ P + + + +E
Sbjct: 281 -------AGLDPEIDPHALGRHEARKLIEAFEKVKIMAP--PTDCLSPIGEDLIYRGLEK 331
Query: 359 FVNDGLSAWLEEHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASLPGKLADCS 418
A P V + ++ + + L + +
Sbjct: 332 ETTVDFIATSTRKPAVYSGNPFVVEVGMAYGGNLPKEEKISIMRFANRVPLLYQQGGCVT 391
Query: 419 ERDPKKSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGTLI 478
+ + + GG G + + + + + I I
Sbjct: 392 THAVEDIKWKQYGLNQPGGGIPVGPVILLIHVASINVPFTSESKDA---IADIPVIKEEI 448
Query: 479 TALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIK 538
+ + Y + I T +L ++ ++ I
Sbjct: 449 DLAIKEVARK-----LKHYLSKQSNLKKRREKEIIITKVLPKLAAKVAHVLEKDVPD-IN 502
Query: 539 PPLYGITR 546
P + I
Sbjct: 503 PVVAKIMG 510
Score = 79.1 bits (194), Expect = 3e-15
Identities = 10/63 (15%), Positives = 23/63 (36%), Gaps = 3/63 (4%)
Query: 730 GRKGISMQRYKGLGEMNASQL--WETTLNPDTRSLLRVKITDASQADDL-FSRLMGDEVE 786
K + + M W+ + + + +L KI AS+ + +L+ + +E
Sbjct: 549 PCKVSGAKPEPKVVTMGNDYDYVWDISASAGSSKVLSYKIESASEEELQKLPQLIVEGIE 608
Query: 787 PRR 789
Sbjct: 609 EEL 611
>3m4i_A DNA gyrase subunit B; GYRB, toprim, type II topoisomerase,
tuberculosi quinolone binding site, DNA binding site,
ATP-binding; HET: DNA; 1.95A {Mycobacterium
tuberculosis} PDB: 3ig0_A* 2zjt_A*
Length = 242
Score = 220 bits (561), Expect = 1e-57
Identities = 91/234 (38%), Positives = 132/234 (56%), Gaps = 10/234 (4%)
Query: 414 LADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQE 473
+ D + DP+KSEL++VEGDSAGGSAK GR QAILPLRGKI+NVE+AR D++L + E
Sbjct: 9 VDDDDKTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTE 68
Query: 474 IGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGF 533
+ +ITALGTGI + FDI KLRYHKI++M DADVDG HI TLLLT FR M LI NG
Sbjct: 69 VQAIITALGTGIHDE-FDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGH 127
Query: 534 LYIIKPPLYGITRGKSLQYVKDEESLEDYLINQSLSEEIELFCDSKGVISKNDLRNFIDD 593
+++ +PPLY + +S + D L+ K + ++ ++ +
Sbjct: 128 VFLAQPPLYKLKWQRSDPEFAYSDRERDGLLE-------AGLKAGKKINKEDGIQRYKGL 180
Query: 594 ALKIDKLIKDFYPNHDKTFIEQAVISGVFNCESDQEINVSLASKLANRLNFIAE 647
K + + + + Q + +D+ ++ + + R +FI
Sbjct: 181 GEMDAKELWETTMDPSVRVLRQVTLDD--AAAADELFSILMGEDVDARRSFITR 232
Score = 99.3 bits (247), Expect = 3e-21
Identities = 38/74 (51%), Positives = 52/74 (70%), Gaps = 1/74 (1%)
Query: 731 RKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRRE 790
K +QRYKGLGEM+A +LWETT++P R L +V + DA+ AD+LFS LMG++V+ RR
Sbjct: 169 NKEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRS 228
Query: 791 FIQENSLP-SALDI 803
FI N+ LD+
Sbjct: 229 FITRNAKDVRFLDV 242
>1zxm_A TOPO IIA ATPase, DNA topoisomerase II, alpha isozyme; GHKL
nucleotide-binding fold; HET: DNA ANP; 1.87A {Homo
sapiens} PDB: 1zxn_A*
Length = 400
Score = 212 bits (541), Expect = 2e-55
Identities = 68/411 (16%), Positives = 153/411 (37%), Gaps = 56/411 (13%)
Query: 13 DSIQILKGLDAVKKRPSMYIGDTDGES---------------------GLHHMIYEVLDN 51
Q L+ + RP YIG + + GL+ + E+L N
Sbjct: 4 RIYQKKTQLEHILLRPDTYIGSVELVTQQMWVYDEDVGINYREVTFVPGLYKIFDEILVN 63
Query: 52 AIDESLEG-YADIITVTLNMD-GSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKF 109
A D I VT++ + ++ +NG+GIP HK E + +I +L +
Sbjct: 64 AADNKQRDPKMSCIRVTIDPENNLISIWNNGKGIPVVEHKVEKMYVPALIFGQLLTSSNY 123
Query: 110 NQKSYKVSGGLHGVGVSVVNALSSWLKLR--IKREGNIYEMSFINGILDNPLVVTGSAGN 167
+ KV+GG +G G + N S+ + + +++ ++++ + +
Sbjct: 124 DDDEKKVTGGRNGYGAKLCNIFSTKFTVETASREYKKMFKQTWMDNMGRAGEMELKPFNG 183
Query: 168 DTGTEVTFLPSSDIFSVQDFNYDTLQHRL---RELSFLNSSVQISLIDKRSPEPREITMF 224
+ T +TF P F +Q + D + + +++ V++ L +
Sbjct: 184 EDYTCITFQPDLSKFKMQSLDKDIVALMVRRAYDIAGSTKDVKVFLNGNK---------L 234
Query: 225 YKGGIEAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKD 284
G ++V + K + +++ + N ++ + ++ + + F N+I
Sbjct: 235 PVKGFRSYVDMYLKDKLDETGNSLKVIHEQVNHRWEVCLTMSEKGFQQI-SFVNSIATSK 293
Query: 285 GGTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTK 344
GG H+ + + ++ V+K K +V + ++ + +P F SQTK
Sbjct: 294 GGRHVDYVADQIVTKLVDVVKKKN---KGGVAVKAHQVKNHMWIFVNALIENPTFDSQTK 350
Query: 345 EKLVS-------------SEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKV 382
E + +++ + + + + W++ + KK
Sbjct: 351 ENMTLQPKSFGSTCQLSEKFIKAAIGCGIVESILNWVKFK--AQVQLNKKC 399
>3g75_A DNA gyrase subunit B; antibiotic resistance, isomerase; HET: DNA
B48; 2.30A {Staphylococcus aureus} PDB: 3g7b_A*
Length = 184
Score = 207 bits (529), Expect = 6e-54
Identities = 86/209 (41%), Positives = 121/209 (57%), Gaps = 27/209 (12%)
Query: 20 GLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYADIITVTLNMDGSCTVSDN 79
GL+AV+KRP MYIG T E GLHH+++E++DN+IDE+L GYA+ I V + D V+DN
Sbjct: 1 GLEAVRKRPGMYIGSTS-ERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDN 59
Query: 80 GRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRI 139
GRGIP D+ ++ G A EVI+T SVVNALS L++ +
Sbjct: 60 GRGIPVDIQEKMGRPAVEVILT-----------------------SSVVNALSQDLEVYV 96
Query: 140 KREGNIYEMSFINGILDNPLVVTGSAGNDTGTEVTFLPSSDIF-SVQDFNYDTLQHRLRE 198
R IY ++ G+ L G+ + TGT + F +IF +NY+TLQ R+RE
Sbjct: 97 HRNETIYHQAYKKGVPQFDLKEVGTT-DKTGTVIRFKADGEIFTETTVYNYETLQQRIRE 155
Query: 199 LSFLNSSVQISLIDKRSPE-PREITMFYK 226
L+FLN +QI+L D+R E RE + Y+
Sbjct: 156 LAFLNKGIQITLRDERDEENVREDSYHYE 184
>3k9f_C DNA topoisomerase 4 subunit B; quinolone, topoisomerase,
protein-DNA cleavage complex; HET: DNA LFX; 2.90A
{Streptococcus pneumoniae} PDB: 3fof_C* 3foe_C*
Length = 268
Score = 199 bits (508), Expect = 1e-51
Identities = 91/239 (38%), Positives = 129/239 (53%), Gaps = 20/239 (8%)
Query: 396 RDLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQAILPLRG 455
D K D L GKL ++P K+EL+LVEGDSAGGSAKQGR R+ QAILPLRG
Sbjct: 19 DDDKHMKNKKDKGLLSGKLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRG 78
Query: 456 KILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRT 515
K++N +A+ +L ++EI T+I +G G+G D F I Y KIIIMTDAD DGAHI+T
Sbjct: 79 KVINTAKAKMADILKNEEINTMIYTIGAGVGAD-FSIEDANYDKIIIMTDADTDGAHIQT 137
Query: 516 LLLTFFFRQMPSLIHNGFLYIIKPPLYGITRGKSLQYVKDEESLED-------------- 561
LLLTFF+R M L+ G +YI PPLY +++GK + +
Sbjct: 138 LLLTFFYRYMRPLVEAGHVYIALPPLYKMSKGKGKKEEVAYAWTDGELEELRKQFGKGAT 197
Query: 562 YLINQSLSE--EIELFCDSKGVISKNDLRNFIDDALKIDKLIKDFY---PNHDKTFIEQ 615
+ L E +L+ + ++ +R I+D + ++ + + +IE
Sbjct: 198 LQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIED 256
Score = 102 bits (255), Expect = 3e-22
Identities = 40/66 (60%), Positives = 55/66 (83%)
Query: 730 GRKGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRR 789
KG ++QRYKGLGEMNA QLWETT+NP+TR+L+RV I D ++A+ + LMGD+VEPRR
Sbjct: 192 FGKGATLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRR 251
Query: 790 EFIQEN 795
++I++N
Sbjct: 252 KWIEDN 257
>2zjt_A DNA gyrase subunit B; GYRB-CTD, toprim, tail, DNA topoisomerase II,
G- segment, T-segment, ATP-binding, nucleotide-binding;
HET: DNA; 2.80A {Mycobacterium tuberculosis}
Length = 247
Score = 197 bits (501), Expect = 9e-51
Identities = 100/248 (40%), Positives = 139/248 (56%), Gaps = 31/248 (12%)
Query: 414 LADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQE 473
+ + DP+KSEL++VEGDSAGGSAK GR QAILPLRGKI+NVE+AR D++L + E
Sbjct: 1 MTPYAFTDPRKSELYVVEGDSAGGSAKSGRDSMFQAILPLRGKIINVEKARIDRVLKNTE 60
Query: 474 IGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGF 533
+ +ITALGTGI D FDI KLRYHKI++M DADVDG HI TLLLT FR M LI NG
Sbjct: 61 VQAIITALGTGIH-DEFDIGKLRYHKIVLMADADVDGQHISTLLLTLLFRFMRPLIENGH 119
Query: 534 LYIIKPPLYGITRGKSLQYVKDEESLEDYLINQSLSEEIELFCD-----SKGVISKN--- 585
+++ +PPLY + +S + D L+ L ++ + KG+ +
Sbjct: 120 VFLAQPPLYKLKWQRSDPEFAYSDRERDGLLEAGLKAGKKINKEDGIQRYKGLGEMDAKE 179
Query: 586 --------DLRNF----IDDALKIDKLIKDFY---PNHDKTFIEQAVISGVFNCESDQEI 630
+R +DDA D+L + ++FI + N + + +
Sbjct: 180 LWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSFITR-------NAKDVRFL 232
Query: 631 NVSLASKL 638
+V LA+ L
Sbjct: 233 DVKLAAAL 240
Score = 97.4 bits (242), Expect = 1e-20
Identities = 38/73 (52%), Positives = 52/73 (71%), Gaps = 1/73 (1%)
Query: 732 KGISMQRYKGLGEMNASQLWETTLNPDTRSLLRVKITDASQADDLFSRLMGDEVEPRREF 791
K +QRYKGLGEM+A +LWETT++P R L +V + DA+ AD+LFS LMG++V+ RR F
Sbjct: 162 KEDGIQRYKGLGEMDAKELWETTMDPSVRVLRQVTLDDAAAADELFSILMGEDVDARRSF 221
Query: 792 IQENSLP-SALDI 803
I N+ LD+
Sbjct: 222 ITRNAKDVRFLDV 234
>2zbk_B Type 2 DNA topoisomerase 6 subunit B; DNA binding protein,
decatenation, ATPase, drug design, DNA-binding,
magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus
shibatae}
Length = 530
Score = 136 bits (343), Expect = 2e-32
Identities = 61/569 (10%), Positives = 135/569 (23%), Gaps = 80/569 (14%)
Query: 12 ADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDE-SLEGYADIITVTLNM 70
+ L + K+ P + + L+ + E+++N++D + G I +T+++
Sbjct: 4 KEKFTSLSPAEFFKRNPELAGFPNPARA-LYQTVRELIENSLDATDVHGILPNIKITIDL 62
Query: 71 DG------SCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVG 124
V DNG GIP R+ K+ + + G++G+G
Sbjct: 63 IDDARQIYKVNVVDNGIGIPPQ--------EVPNAFGRVLYSSKYVNRQ---TRGMYGLG 111
Query: 125 VSVVNALSS-------WLKLRIKREGNIYEMSFINGILDNPLVVTGSAGNDTGTEVTFLP 177
V S ++ IY I N ++ +
Sbjct: 112 VKAAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTS 171
Query: 178 SSDIFSVQDF-NYDTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVSYL 236
+ + ++ + + D
Sbjct: 172 VAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEG--------------NVTYYPR 217
Query: 237 DRHKKPLMQSPIRIQGSRDNISIDLAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSAL 296
+K P ++ + + N + F N Q G
Sbjct: 218 LTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIKEFLVNEFQSIG----------- 266
Query: 297 TRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVV 356
+E + K + ++ ++ D F S + + L +
Sbjct: 267 DTTADKILELAGLKPNKKVKNLTEEEIT---RLVETFKKDEDFRSPSADSLSVIGEDLIE 323
Query: 357 ESFVNDGLSAWLEEHPLEAKIIVKKVLDASMVRDAARRARDLTRRKGVLDIASLPGKLAD 416
+ + K GV S+P
Sbjct: 324 LGLKKIFNPDFAASITRKPKAYQGHPFI---------------VEAGVAFGGSIPVGEEP 368
Query: 417 CSERDPKKSELFLVEGDSAGGSAKQGRSRENQAILPLRGKILNVERARFDKMLSSQEIGT 476
R K L E + + I + +++ + K+
Sbjct: 369 IVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMVHLCSTKIPYKSAGKE 428
Query: 477 LITALGTGIGQDSFDINKLRYHKIIIMTDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYI 536
I N + K +M A ++ ++ +
Sbjct: 429 SIAE----------VENIEKEIKNALMEVARKLKQYLSEKRKEQEAKKKLLAYLKYIPEV 478
Query: 537 IKPPLYGITRGKSLQYVKDEESLEDYLIN 565
+ + G K + + + L
Sbjct: 479 SRSLATFLASGNKELVSKYQNEISEGLFK 507
>1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix
two-turns helix; 2.00A {Sulfolobus shibatae} SCOP:
a.156.1.3 d.14.1.3 d.122.1.2 PDB: 1mx0_A* 1z5b_A*
1z5a_A* 1z59_A* 1z5c_A* 2hkj_A*
Length = 471
Score = 67.3 bits (164), Expect = 1e-11
Identities = 25/193 (12%), Positives = 57/193 (29%), Gaps = 20/193 (10%)
Query: 32 IGDTDGESGLHHMIYEVLDNAIDESLE-GYADIITVTLNMDG------SCTVSDNGRGIP 84
G + L+ + E+++N++D + G I +T+++ V DNG GIP
Sbjct: 24 AGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLIDDARQIYKVNVVDNGIGIP 83
Query: 85 TDLHKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRIK---- 140
R+ K+ + + GL + + + + I+
Sbjct: 84 PQEVPN--------AFGRVLYSSKYVNRQTRGMYGLGVKAAVLYSQMHQDKPIEIETSPV 135
Query: 141 REGNIYEMSFINGILDNPLVVTGSAGNDTGTEVTFLPSSDIFSVQDFNYDT-LQHRLREL 199
IY I N ++ + + + + ++
Sbjct: 136 NSKRIYTFKLKIDINKNEPIIVERGSVENTRGFHGTSVAISIPGDWPKAKSRIYEYIKRT 195
Query: 200 SFLNSSVQISLID 212
+ + D
Sbjct: 196 YIITPYAEFIFKD 208
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 56.1 bits (135), Expect = 3e-08
Identities = 100/697 (14%), Positives = 176/697 (25%), Gaps = 319/697 (45%)
Query: 31 YIGD--TDGESGLHHMIYEVLDNAIDES-LEGYADIITVTLNMDGSCTVSDNGRGIPTDL 87
Y+ + G + + + LEG DI + + T L
Sbjct: 67 YVSSLVEPSKVGQFDQVLNLCLTEFENCYLEG-NDIHALAAKLLQE---------NDTTL 116
Query: 88 HKEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRIKREGN--I 145
K E+I + A + K S +AL R EGN +
Sbjct: 117 VK-----TKELIKNYITARIMAKRPFDKKS----------NSAL-----FRAVGEGNAQL 156
Query: 146 YEMSFINGILDNPLVVTGSAGNDTGTEVTFLPSSDIFSVQDFNYDTLQHRLRELSFLNSS 205
+ G GN T+ F EL
Sbjct: 157 V-------------AIFGGQGN---TDDYF---------------------EEL------ 173
Query: 206 VQISLIDKRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQSP-----IRIQGSRDNISID 260
R++ Y + + + L+++ + QG ++
Sbjct: 174 -------------RDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQG------LN 214
Query: 261 LAMRWNDGYHENVLCFTNNIPQKDGGTHLSGLRSA--------LTRQITSYVEKSFGSKK 312
+ + W + +N P KD +L S + Q+ YV
Sbjct: 215 I-LEWLEN--------PSNTPDKD---YLL---SIPISCPLIGVI-QLAHYV-------- 250
Query: 313 DKRSVIGDDCREGFTSVLSIKMPDP-----RFS-----SQTKEKLVSSEVRSVV---ESF 359
V + +L P SQ LV++ + ESF
Sbjct: 251 ----VT---AK-----LLGF---TPGELRSYLKGATGHSQ---GLVTAVAIAETDSWESF 292
Query: 360 VNDGLSA-----W--LEEH---PLEAKIIVKKVLDASMVRDAARRA----------RDLT 399
A + + + P L S++ D+ +LT
Sbjct: 293 FVSVRKAITVLFFIGVRCYEAYP-------NTSLPPSILEDSLENNEGVPSPMLSISNLT 345
Query: 400 RRKGVLDI-----ASLPGKLADCSERDPKKSELFLVEGDSA---GGSAKQGRSRENQAIL 451
++ V D + LP K+ E+ LV G G + S
Sbjct: 346 -QEQVQDYVNKTNSHLP--------AG-KQVEISLVNGAKNLVVSGPPQ---S------- 385
Query: 452 PLRGKILNVERARFDKMLSSQEIGTLITALGTGIGQDSFDINKLRYHKIIIMTDADVDGA 511
L G LN+ LR K + +D +
Sbjct: 386 -LYG--LNL---------------------------------TLR--K--AKAPSGLDQS 405
Query: 512 HIRTLLLTFFFRQMPSLIHNGFLYIIKP---P-LYGITRGKSLQYVKDEESLEDYLINQS 567
I F + N FL + P L + + + + N
Sbjct: 406 RIP-------FSERKLKFSNRFLPVASPFHSHLLVPAS-----DLINKDLVKNNVSFNAK 453
Query: 568 -LSEEIELFCDSKGVISKNDLRNFIDDALKIDKLIK---------------------DFY 605
+ +I ++ G +DLR ++++ DF
Sbjct: 454 DI--QIPVYDTFDG----SDLRVLSGSI--SERIVDCIIRLPVKWETTTQFKATHILDFG 505
Query: 606 P------------NHDKTFIEQAVISGVFNCESDQEI 630
P N D T + + +++G + D +
Sbjct: 506 PGGASGLGVLTHRNKDGTGV-RVIVAGTLDINPDDDY 541
Score = 53.8 bits (129), Expect = 1e-07
Identities = 100/729 (13%), Positives = 183/729 (25%), Gaps = 339/729 (46%)
Query: 158 PLVVT-GSAGNDTGTEVTFL-PSSDIFSVQDFNYDTLQHRLRELSFLNSSVQISLIDKRS 215
PL ++ GS E L P++ F +L+E F L
Sbjct: 8 PLTLSHGS------LEHVLLVPTASFFIAS---------QLQE-QFNKI-----L----- 41
Query: 216 PEPREITMFYKGGIEAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWNDGYHENVLC 275
PEP E F + + P +P +L ++ L
Sbjct: 42 PEP----------TEGFAADDE----P--TTPA-----------ELVGKF--------LG 66
Query: 276 FTNNIPQKDG-GTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLSIKM 334
+ +++ + G L LT E +
Sbjct: 67 YVSSLVEPSKVGQFDQVLNLCLT-----EFENCY-------------------------- 95
Query: 335 PDPRFSSQTKEKLVSSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLDASMVRD--AA 392
L +++ ++ + + + L K+++ ++ A
Sbjct: 96 ------------LEGNDIHALAAKLLQE------NDTTLVKT---KELI-----KNYITA 129
Query: 393 RRARDLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSAGGSAKQGRSRENQAILP 452
R K L ++L + GG QG
Sbjct: 130 RIMAKRPFDKKS------NSALFRAVGEG--NAQLVAI----FGG---QG---------- 164
Query: 453 LRGKILNVERARFDKMLSSQE--------IGTLITALGT---GIGQDSFDINKLRYHKII 501
N + F+++ ++ +G LI + + + D K+ +
Sbjct: 165 ------NTDDY-FEEL---RDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLN 214
Query: 502 IM---TDADVDGAHIRTLLLTFFFRQMPSLIHNGFLYIIK-P---PLYGITRGKSLQYVK 554
I+ + P Y++ P PL G+
Sbjct: 215 ILEWLENPS----------------NTPDK-----DYLLSIPISCPLIGVI--------- 244
Query: 555 DEESLEDYLI-----NQSLSEEIELFC----DSKGVI------SKNDLRNFIDDALKIDK 599
L Y++ + E S+G++ + +F K
Sbjct: 245 ---QLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAIT 301
Query: 600 LIKDFYPNHDKTFIEQAVISGVFNCESDQEI-NVSLASKLANRLNFIAEKSEKSWHG--- 655
++ F FI G + N SL I E S ++ G
Sbjct: 302 VL--F-------FI------G---VRCYEAYPNTSLPPS-------ILEDSLENNEGVPS 336
Query: 656 ---SINNSDILVKRIARGV-QEQFVLEGSSIFSFGSKYKRI-FSNRI--EENYLTILSLI 708
SI + QEQ ++ + +N + I SL+
Sbjct: 337 PMLSI-----------SNLTQEQ--VQ-----------DYVNKTNSHLPAGKQVEI-SLV 371
Query: 709 CNG-DKIKITGP-------CSLLDTI------------FSIGRK-GISMQ---------- 737
NG + ++GP L FS RK S +
Sbjct: 372 -NGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFS-ERKLKFSNRFLPVASPFHS 429
Query: 738 RYKGLGEMNASQLWETTLNPDTRSL----LRVKITDASQADDLFSRLMGDEVEPRREFIQ 793
L + AS L L + S +++ + D DL R
Sbjct: 430 HL--L--VPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDL------------RVL-S 472
Query: 794 ENSLPSALD 802
+ +D
Sbjct: 473 GSISERIVD 481
Score = 49.2 bits (117), Expect = 4e-06
Identities = 61/403 (15%), Positives = 113/403 (28%), Gaps = 177/403 (43%)
Query: 1 MSDNIQNSSYDADSIQIL--KGLDAVK------KRP----------SM----------YI 32
++ + + + +GL+ ++ P S Y+
Sbjct: 191 SAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYV 250
Query: 33 ------GDTDGE--------SGLHH--------MI---------YEVLDNAID------- 54
G T GE +G H I + + AI
Sbjct: 251 VTAKLLGFTPGELRSYLKGATG--HSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGV 308
Query: 55 ESLEGYADI-ITVTLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKS 113
E Y + + ++ D S +N G+P+ + ++ +V Q
Sbjct: 309 RCYEAYPNTSLPPSILED-SL---ENNEGVPSPMLSISNLTQEQV------------QD- 351
Query: 114 YKVSGGLHGVGVSVVNALSSWLKLRIKREGNIYEMSFINGILDNPLVVTGSAGNDTGTEV 173
+ V+ N+ + + +S +NG N LVV+G
Sbjct: 352 -------Y---VNKTNS-------HLPAGKQVE-ISLVNG-AKN-LVVSG---------- 381
Query: 174 TFLPSSDIFSVQDFNYDTLQHRLREL---SFLNSSVQISLIDKRSPEPREITM-FYKGGI 229
P S+ N LR+ S L+ S +I +R + + F +
Sbjct: 382 --PPQ----SLYGLN-----LTLRKAKAPSGLDQS-RIPF-SERKL---KFSNRFLP--V 423
Query: 230 EA-FVS-YL----DRHKKPLMQSPIRIQGSRDNISIDLAM---RWNDG-----YHENVL- 274
+ F S L D K L+++ + D+ + DG ++
Sbjct: 424 ASPFHSHLLVPASDLINKDLVKNNVSFNAK------DIQIPVYDTFDGSDLRVLSGSISE 477
Query: 275 ----CFTN---NIPQ--KDGGTHL--------SGLRSALTRQI 300
C + TH+ SGL LT +
Sbjct: 478 RIVDCIIRLPVKWETTTQFKATHILDFGPGGASGL-GVLTHRN 519
Score = 38.4 bits (89), Expect = 0.007
Identities = 18/92 (19%), Positives = 26/92 (28%), Gaps = 40/92 (43%)
Query: 746 NASQLWETTLNPDTRSLLRVKITDASQADD-------LFSRLMG---DEVEPR------- 788
ASQL E + L + T+ ADD L + +G VEP
Sbjct: 29 IASQLQEQFN----KIL--PEPTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQ 82
Query: 789 ----------REFIQEN-------SLPSALDI 803
+++ N L D
Sbjct: 83 VLNLCLTEFENCYLEGNDIHALAAKLLQENDT 114
Score = 28.8 bits (64), Expect = 4.7
Identities = 21/105 (20%), Positives = 41/105 (39%), Gaps = 24/105 (22%)
Query: 144 NIYEMSFINGILDNPLVVTGSAGNDTGTEV-------TF-------LPSSDIFSVQDFNY 189
+ Y S ++ +++NP+ +T G + G + F L + IF ++ N
Sbjct: 1655 DTYGFSILDIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVDGKLKTEKIF--KEINE 1712
Query: 190 DTLQHRLRELSFLNSSVQISLIDKRSPEPREITMFYKGGIEAFVS 234
+ + R L S+ Q + +P +T+ K E S
Sbjct: 1713 HSTSYTFRSEKGLLSATQFT-------QP-ALTLMEKAAFEDLKS 1749
>3h4l_A DNA mismatch repair protein PMS1; ATP binding, DNA repair, DNA
damage, nucleus, phosphop DNA binding protein, protein
binding; HET: DNA ANP; 2.50A {Saccharomyces cerevisiae}
Length = 367
Score = 49.3 bits (117), Expect = 3e-06
Identities = 25/173 (14%), Positives = 60/173 (34%), Gaps = 17/173 (9%)
Query: 47 EVLDNAIDESLEGYADIITVTLNMDG--SCTVSDNGRGIPTDLHKEEGISAAEVIMTRLH 104
E++DN+ID + A+ I + G S SDNG GI ++ +
Sbjct: 32 ELVDNSIDAN----ANQIEIIFKDYGLESIECSDNGDGIDPSNYE------FLALKHYTS 81
Query: 105 AGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRIKREGNIYEMSFI-NGILDNPLVVTG 163
KF + + G G +S + ++ + ++ + G + + +
Sbjct: 82 KIAKFQDVAKVQTLGFRGEALSSLCGIAKLSVITTTSPPKADKLEYDMVGHITSKTTTSR 141
Query: 164 SAGNDTGTEVTFLP----SSDIFSVQDFNYDTLQHRLRELSFLNSSVQISLID 212
+ G F + + ++ + +N++++ S+ +
Sbjct: 142 NKGTTVLVSQLFHNLPVRQKEFSKTFKRQFTKCLTVIQGYAIINAAIKFSVWN 194
>1h7s_A PMS1 protein homolog 2; DNA repair, GHL ATPase, mismatch repair,
HNPCC; 1.95A {Homo sapiens} SCOP: d.14.1.3 d.122.1.2
PDB: 1h7u_A* 1ea6_A*
Length = 365
Score = 45.9 bits (108), Expect = 4e-05
Identities = 34/240 (14%), Positives = 71/240 (29%), Gaps = 18/240 (7%)
Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDG--SCTVSDNGRGIPTDLHKEEGISAAEV 98
L + E+++N++D A I + L G VSDNG G+ + + +
Sbjct: 35 LSTAVKELVENSLDAG----ATNIDLKLKDYGVDLIEVSDNGCGVEEENFE---GLTLKH 87
Query: 99 IMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNALSSWLKLRIKREGNIYEMSFI--NGILD 156
+++ Q G G +S + ALS + NG +
Sbjct: 88 HTSKIQEFADLTQVETF---GFRGEALSSLCALSDVTISTCHASAKVGTRLMFDHNGKII 144
Query: 157 NPLVVTGSAGNDTGTEVTFLPSSDIFSVQDFNYDT----LQHRLRELSFLNSSVQISLID 212
G + F N + L +++ +++S +
Sbjct: 145 QKTPYPRPRGTTVSVQQLFSTLPVRHKEFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTN 204
Query: 213 KRSPEPREITMFYKGGIEAFVSYLDRHKKPLMQSPIRIQGSRDNISIDLAMRWNDGYHEN 272
+ R+ + G + + +QS I + S+ + +
Sbjct: 205 QLGQGKRQPVVCTGGSPSIKENIGSVFGQKQLQSLIPFVQLPPSDSVCEEYGLSCSDALH 264
>3na3_A DNA mismatch repair protein MLH1; MUTL protein homolog 1, DNA damag
repair, structural genomics consortium, SGC, protein
bindin; HET: DNA ATP; 2.50A {Homo sapiens}
Length = 348
Score = 38.1 bits (88), Expect = 0.008
Identities = 14/90 (15%), Positives = 30/90 (33%), Gaps = 12/90 (13%)
Query: 47 EVLDNAIDESLEGYADIITVTLNMDG--SCTVSDNGRGIPTDLHKEEGISAAEVIMTRLH 104
E+++N +D + I V + G + DNG GI +
Sbjct: 35 EMIENCLDAK----STSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFT------TS 84
Query: 105 AGGKFNQKSYKVSGGLHGVGVSVVNALSSW 134
F + + G G ++ ++ ++
Sbjct: 85 KLQSFEDLASISTYGFRGEALASISHVAHV 114
>2q8g_A [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1; GHKL
ATPase/kinase family, pyruvate dehydrogenase complex,
mitochondrial kinase; HET: AZX; 1.90A {Homo sapiens}
PDB: 2q8f_A* 2q8h_A
Length = 407
Score = 37.0 bits (85), Expect = 0.015
Identities = 21/141 (14%), Positives = 49/141 (34%), Gaps = 21/141 (14%)
Query: 1 MSDNIQNSSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGY 60
++ +++ + +P + S L+HM++E+ NA+ ++E +
Sbjct: 207 ARRLCDLYYINSPELELEELNAKSPGQPIQVVYV---PSHLYHMVFELFKNAMRATMEHH 263
Query: 61 ADI-----ITVTLNMDGSC---TVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQ- 111
A+ I V + + +SD G G+P + +++ +
Sbjct: 264 ANRGVYPPIQVHVTLGNEDLTVKMSDRGGGVPLRKIDR--------LFNYMYSTAPRPRV 315
Query: 112 -KSYKVSGGLHGVGVSVVNAL 131
S V G G+ +
Sbjct: 316 ETSRAVPLAGFGYGLPISRLY 336
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 36.8 bits (84), Expect = 0.020
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 22/58 (37%)
Query: 554 KDEESLEDYLINQSLSEEIELFCDSKGVISKNDLRNFIDDALKIDKLIKDFY--PNHD 609
K ++ LE++ NQ SE++E KN + N I D K FY P+ D
Sbjct: 115 KAKKDLEEW--NQRQSEQVE----------KNKINNRIAD--------KAFYQQPDAD 152
>1y8o_A [pyruvate dehydrogenase [lipoamide]] kinase isozyme 3; pyruvate
dehydrogenase kinase 3, lipoyl-bearing domain; HET: LPA
ADP; 2.48A {Homo sapiens} SCOP: a.29.5.1 d.122.1.4 PDB:
1y8n_A* 1y8p_A* 2pnr_A* 2q8i_A*
Length = 419
Score = 34.7 bits (79), Expect = 0.074
Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 9/55 (16%)
Query: 41 LHHMIYEVLDNAIDESLEGYAD------IITVTLNMDGSC---TVSDNGRGIPTD 86
L HM++E+ N++ ++E Y D + + + +SD G G+P
Sbjct: 254 LFHMLFELFKNSMRATVELYEDRKEGYPAVKTLVTLGKEDLSIKISDLGGGVPLR 308
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl
reductase, beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 34.0 bits (77), Expect = 0.13
Identities = 119/557 (21%), Positives = 202/557 (36%), Gaps = 154/557 (27%)
Query: 118 GGLHGVGVSVVNALSSWLKLRIKRE---GNIYEMSFINGILD--NPLVVTGSAGNDT--G 170
G G G+ V+AL K R K E +I + SFIN + N L+++ S T G
Sbjct: 1045 GNCSGSGMGGVSALRGMFKDRFKDEPVQNDILQESFINTMSAWVNMLLISSSGPIKTPVG 1104
Query: 171 TEVTFLPSSDIFSVQDF-----------NYDTLQHRLRELSFLNSSVQISLIDK----RS 215
T + S DI V+ YD Q F N + +++ R+
Sbjct: 1105 ACATSVESVDI-GVETILSGKARICIVGGYDDFQEE-GSFEFGNMKATSNTLEEFEHGRT 1162
Query: 216 PE--PREITMFYKGGIEAFVSYLDRHKKPLMQSPIRIQGSRDNISI--DLAMRWNDGYHE 271
P R T G +EA QG+ I + DLA++
Sbjct: 1163 PAEMSRPATTTRNGFMEA-------------------QGAGIQIIMQADLALKM------ 1197
Query: 272 NVLCFTNNIPQKDGGTHLSGLRSALTRQITSYVEKSFGSKKDKRSVIGDDCREGFTSVLS 331
G + G+ A+ T + +S + I RE +SV
Sbjct: 1198 --------------GVPIYGI-VAMAATATDKIGRSVPAPGKG---ILTTAREHHSSV-- 1237
Query: 332 IKMPDPRFSSQ-TKEKLVSSEVRSVVESFVNDGLSAW---LEEHPLEAK--IIVKKVLD- 384
K P + + K +LV+ E + ++ +V + L A EE P E + ++++ +
Sbjct: 1238 -KYASPNLNMKYRKRQLVTREAQ--IKDWVENELEALKLEAEEIPSEDQNEFLLERTREI 1294
Query: 385 ----ASMVRDAARR-ARDLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSAG--- 436
S +R A ++ D +R IA L G LA + + D G
Sbjct: 1295 HNEAESQLRAAQQQWGNDFYKRDP--RIAPLRGALAT-----------YGLTIDDLGVAS 1341
Query: 437 --GSAKQGRSRENQAILPLRGKILNVERAR-----FDKMLSSQEIGT--------LITAL 481
G++ + + A + K L F K L+ G + L
Sbjct: 1342 FHGTSTKANDKNESATINEMMKHLGRSEGNPVIGVFQKFLTGHPKGAAGAWMMNGALQIL 1401
Query: 482 GTGI---GQDSFDINKL--RYHKIIIMTDA-DVDGAHIRTLLLTFF-FRQMPSLIHNGFL 534
+GI +++ +++K+ ++ ++ + DG +R + +T F F Q G
Sbjct: 1402 NSGIIPGNRNADNVDKILEQFEYVLYPSKTLKTDG--VRAVSITSFGFGQ-----KGGQA 1454
Query: 535 YIIKPP-LYG-ITRGKSLQYVKD----EESLEDYLINQSLSEEIELFCDSKGVISKNDLR 588
++ P LYG IT + +YV E+S + N + +LF +SK
Sbjct: 1455 IVVHPDYLYGAITEDRYNEYVAKVSAREKSAYKFFHNGMIYN--KLF------VSK---- 1502
Query: 589 NFIDDALKIDKLIKDFY 605
+ A D+L +D Y
Sbjct: 1503 ---EHAPYTDELEEDVY 1516
>2e0a_A Pyruvate dehydrogenase kinase isozyme 4; PDK4, ATP-binding,
structural genomics, NPPSFA; HET: ANP; 1.86A {Homo
sapiens} PDB: 2zdx_A* 2zdy_A* 2zkj_A* 3d2r_A*
Length = 394
Score = 33.5 bits (76), Expect = 0.21
Identities = 18/92 (19%), Positives = 35/92 (38%), Gaps = 16/92 (17%)
Query: 41 LHHMIYEVLDNAIDESLEGYAD-----IITVTLNMDGS---CTVSDNGRGIPTDLHKEEG 92
LHHM++E+ NA+ ++E + I V + + +SD G G+P +
Sbjct: 231 LHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRIIDR-- 288
Query: 93 ISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVG 124
+ + ++ + L G G
Sbjct: 289 ------LFSYTYSTAPTPVMDNSRNAPLAGFG 314
>2btz_A Pyruvate dehydrogenase kinase isoenzyme 2; GHKL motif regulation,
transferase; 2.2A {Homo sapiens} PDB: 2bu2_A* 2bu5_A*
2bu6_A* 2bu7_A* 2bu8_A* 3crk_A* 1jm6_A* 3crl_A*
Length = 394
Score = 33.1 bits (75), Expect = 0.25
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 11/84 (13%)
Query: 11 DADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGYAD-----IIT 65
+ ++I + A K+P + S L+HM++E+ NA+ ++E + I
Sbjct: 205 ASPDLEIQEINAANSKQPIHMVYV---PSHLYHMLFELFKNAMRATVESHESSLILPPIK 261
Query: 66 VTLNMDGS---CTVSDNGRGIPTD 86
V + + +SD G G+P
Sbjct: 262 VMVALGEEDLSIKMSDRGGGVPLR 285
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 33.1 bits (74), Expect = 0.26
Identities = 13/43 (30%), Positives = 16/43 (37%), Gaps = 15/43 (34%)
Query: 16 QILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLE 58
Q LK L A K +Y D D L AI ++E
Sbjct: 20 QALKKLQASLK---LY-AD-DSAPAL----------AIKATME 47
>1keh_A Precursor of cephalosporin acylase; glutaryl-7-ACA, hydrolase;
2.50A {Brevundimonas diminuta} SCOP: d.153.1.2 PDB:
1oqz_A
Length = 689
Score = 32.9 bits (74), Expect = 0.27
Identities = 14/53 (26%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 349 SSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVLD---ASMVRDAARRARDL 398
S + R+ +++F G++A+ +++P + V++VL A +V A R L
Sbjct: 97 SPDFRANLDAFA-AGINAYAQQNPDDISPEVRQVLPVSGADVVAHAHRLMNFL 148
>1ixm_A SPO0B, protein (sporulation response regulatory protein);
phosphotransferase, two component system; 2.60A
{Bacillus subtilis} SCOP: d.123.1.1 PDB: 2ftk_A* 1f51_A
Length = 192
Score = 32.0 bits (71), Expect = 0.50
Identities = 6/51 (11%), Positives = 15/51 (29%), Gaps = 5/51 (9%)
Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDGSC-----TVSDNGRGIPTD 86
L ++ ++ + +TV+L D + +G
Sbjct: 110 LAKLMRKLFHLFDQAVSRESENHLTVSLQTDHPDRQLILYLDFHGAFADPS 160
>1b63_A MUTL; DNA mismatch repair, ATPase; HET: ANP; 1.90A {Escherichia
coli} SCOP: d.14.1.3 d.122.1.2 PDB: 1nhh_A* 1nhi_A*
1bkn_A 1nhj_A* 1b62_A*
Length = 333
Score = 31.7 bits (71), Expect = 0.67
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 6/42 (14%)
Query: 47 EVLDNAIDESLEGYADIITVTLNMDG--SCTVSDNGRGIPTD 86
E+++N++D A I + + G + DNG GI D
Sbjct: 31 ELVENSLDAG----ATRIDIDIERGGAKLIRIRDNGCGIKKD 68
>1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG,
8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET:
DRZ ANG; 1.90A {Homo sapiens} SCOP: a.96.1.3 d.129.1.2
PDB: 1m3h_A* 1n39_A* 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A*
1fn7_A* 1n3a_A* 1n3c_A* 1ebm_A* 1ko9_A 2noe_A* 2noh_A*
2nol_A* 1yqk_A 2noz_A* 2nof_A* 1yqr_A* 1yql_A* 1yqm_A*
...
Length = 317
Score = 30.8 bits (69), Expect = 1.0
Identities = 24/215 (11%), Positives = 57/215 (26%), Gaps = 15/215 (6%)
Query: 542 YGITRGKSLQYVKDEESLEDYLINQSLSEEIELFCDSKGVISK-----NDLRNFIDDALK 596
G+ + + EE L + S+ D + K L
Sbjct: 48 SGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGS 107
Query: 597 IDKLIKDFYPNHDKTFI-EQAVISGVFNCESDQEINVSLASKLANRLNFIAEKSEKSWHG 655
+D ++ + Q I +F+ N++ + + RL
Sbjct: 108 VDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDD 167
Query: 656 SINNSDILVKRIARGVQEQFVLEGSSIFSFGSKYKRIFSNRIEENYLTILSLICNGDKIK 715
+ ++ +A E + + G Y+ + + L + +++
Sbjct: 168 VTYHGFPSLQALAGPEVEAHLRKL------GLGYRARYVSASARAILEEQGGLAWLQQLR 221
Query: 716 ITGPCSLLDT---IFSIGRKGISMQRYKGLGEMNA 747
+ + +G K L + A
Sbjct: 222 ESSYEEAHKALCILPGVGTKVADCICLMALDKPQA 256
>1f0k_A MURG, UDP-N-acetylglucosamine-N-acetylmuramyl- (pentapeptide)
pyrophosphoryl-undecaprenol...; rossmann fold,
transferase; 1.90A {Escherichia coli} SCOP: c.87.1.2
PDB: 1nlm_A*
Length = 364
Score = 31.1 bits (69), Expect = 1.1
Identities = 9/61 (14%), Positives = 20/61 (32%), Gaps = 2/61 (3%)
Query: 357 ESFVNDGLSAWLEEHPLEAKIIVKKV--LDASMVRDAARRARDLTRRKGVLDIASLPGKL 414
G + +E+ L + + + A RAR + +A+ ++
Sbjct: 294 LPLEKAGAAKIIEQPQLSVDAVANTLAGWSRETLLTMAERARAASIPDATERVANEVSRV 353
Query: 415 A 415
A
Sbjct: 354 A 354
>3d36_A Sporulation kinase B; GHKL ATPase, four helix bundle, class I
two-component histidine kinase, phosphoprotein; HET:
ADP; 2.03A {Geobacillus stearothermophilus}
Length = 244
Score = 31.0 bits (70), Expect = 1.2
Identities = 9/47 (19%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDG-SCTVSDNGRGIPTD 86
+ V+ NAI+ G + V+++ ++D G G+ +
Sbjct: 124 FRQCLLNVMKNAIEAMPNGGTLQVYVSIDNGRVLIRIADTGVGMTKE 170
>1kbi_A Cytochrome B2, L-LCR; flavocytochrome B2, electron transfer,
oxidoreductase; HET: HEM FMN; 2.30A {Saccharomyces
cerevisiae} SCOP: c.1.4.1 d.120.1.1 PDB: 1fcb_A* 1lco_A*
1ldc_A* 1sze_A* 2oz0_A* 1szf_A* 1szg_A* 1ltd_A* 1kbj_A*
1qcw_A*
Length = 511
Score = 30.9 bits (69), Expect = 1.3
Identities = 36/216 (16%), Positives = 70/216 (32%), Gaps = 44/216 (20%)
Query: 336 DPRFSSQTKEKLVSSEVRS---------VVESFVNDGLSAWLEEHPLEAKIIVK---KVL 383
+P+ K+K+ +EV V+ +V D L+ +L HP +I K
Sbjct: 1 EPKLDM-NKQKISPAEVAKHNKPDDCWVVINGYVYD-LTRFLPNHPGGQDVIKFNAGK-- 56
Query: 384 DASMV------RDAARRARDLTRRKGVLDIASLPGKLADCSERDPKKSELFLVEGDSAGG 437
D + + + + ++ G L + P + K +
Sbjct: 57 DVTAIFEPLHAPNVIDKYIAPEKKLGPLQGSMPPELVCPPYAPGETKED----------- 105
Query: 438 SAKQGRSRENQAILPLRGKILNVE--RARFDKMLSSQEIGTLITALGTGIGQDSFDINKL 495
R + +++LP I+N+ + L+ Q + + + N
Sbjct: 106 ---IARKEQLKSLLPPLDNIINLYDFEYLASQTLTKQAWAYYSSGANDEV---THRENHN 159
Query: 496 RYHKIIIMTDA--DVDGAHIRTLLLTFFFRQMPSLI 529
YH+I DV I T +L +P +
Sbjct: 160 AYHRIFFKPKILVDVRKVDISTDMLGSHVD-VPFYV 194
>2ajr_A Sugar kinase, PFKB family; TM0828, possible 1-phosphofructokinase
(EC 2.7.1.56), structural genomics, joint center for
structural genomics; HET: MSE; 2.46A {Thermotoga
maritima} SCOP: c.72.1.1
Length = 331
Score = 30.3 bits (67), Expect = 1.6
Identities = 18/69 (26%), Positives = 27/69 (39%), Gaps = 16/69 (23%)
Query: 63 IITVTLN--MDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGK-FNQKSYKVSGG 119
++TVTLN +D + D ++ T++ GGK N VS
Sbjct: 14 VLTVTLNPALDREIFIE--------DFQVNRLYRINDLSKTQMSPGGKGIN-----VSIA 60
Query: 120 LHGVGVSVV 128
L +GV V
Sbjct: 61 LSKLGVPSV 69
>1fm2_A Glutaryl 7-aminocephalosporanic acid acylase; cephalosporin
acylase, antibiotics, penicillin acylase, N- terminal
hydrolase; 2.00A {Brevundimonas diminuta} SCOP:
d.153.1.2 PDB: 1ghd_A 3jtq_A 3jtr_A 2adv_A 2ae3_A 2ae5_A
2ae4_A 1or0_A 1jw0_A 1jvz_A 1gk1_A 1gk0_A
Length = 169
Score = 30.3 bits (68), Expect = 1.7
Identities = 9/35 (25%), Positives = 23/35 (65%), Gaps = 1/35 (2%)
Query: 349 SSEVRSVVESFVNDGLSAWLEEHPLEAKIIVKKVL 383
S + R+ +++F G++A+ +++P + V++VL
Sbjct: 97 SPDFRANLDAFA-AGINAYAQQNPDDISPEVRQVL 130
>1h72_C HK, homoserine kinase; transferase, threonine biosynthesis; HET:
ANP; 1.8A {Methanococcus jannaschii} SCOP: d.14.1.5
d.58.26.1 PDB: 1fwl_A 1fwk_A* 1h73_A* 1h74_A*
Length = 296
Score = 30.4 bits (67), Expect = 1.8
Identities = 16/74 (21%), Positives = 28/74 (37%)
Query: 57 LEGYADIITVTLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIMTRLHAGGKFNQKSYKV 116
L+ D+I V D + + + IPTD K A+ ++ + G K
Sbjct: 25 LKEPYDVIEVEAIDDKEIIIEVDDKNIPTDPDKNVAGIVAKKMIDDFNIGKGVKITIKKG 84
Query: 117 SGGLHGVGVSVVNA 130
G+G S ++
Sbjct: 85 VKAGSGLGSSAASS 98
>1ysr_A Sensor-type histidine kinase PRRB; ATP-binding domain, structural
genomics, mycobacterium tuberculosis structural
proteomics project; 1.78A {Mycobacterium tuberculosis}
SCOP: d.122.1.3 PDB: 1ys3_A
Length = 150
Score = 30.2 bits (68), Expect = 2.0
Identities = 16/86 (18%), Positives = 33/86 (38%), Gaps = 3/86 (3%)
Query: 1 MSDNIQNSSYDADSIQILKGLDAVKKRPSMYIGDTDGESGLHHMIYEVLDNAIDESLEGY 60
++D + +++DA I + V + +G +GL + + NA+
Sbjct: 10 ITDLLDRAAHDAARIYPDLDVSLVPSPTCIIVGL---PAGLRLAVDNAIANAVKHGGATL 66
Query: 61 ADIITVTLNMDGSCTVSDNGRGIPTD 86
+ V+ + DNG G+P
Sbjct: 67 VQLSAVSSRAGVEIAIDDNGSGVPEG 92
>3a0r_A Sensor protein; four helix bundle, PAS fold, kinase,
phosphoprotein, transferase, two-component regulatory
system; 3.80A {Thermotoga maritima}
Length = 349
Score = 30.0 bits (67), Expect = 2.3
Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDG-SCTVSDNGRGIPTDLHK 89
+ ++ ++ NAI+ + E IT +V ++G IP +L +
Sbjct: 245 IKQVLINLVQNAIEATGENGKIKITSEDMYTKVRVSVWNSGPPIPEELKE 294
>1gkz_A [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase;
transferase, mitochondrial protein kinase, potassium;
HET: ADP; 2.2A {Rattus norvegicus} SCOP: a.29.5.1
d.122.1.4 PDB: 1gjv_A 1gkx_A*
Length = 388
Score = 29.8 bits (66), Expect = 2.4
Identities = 19/110 (17%), Positives = 35/110 (31%), Gaps = 21/110 (19%)
Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDGSC---------TVSDNGRGIPTDLH--- 88
L +++ E+L NA+ ++E + D ++ + +SD G GI
Sbjct: 239 LDYILPELLKNAMRATMESHLDTPYNVPDVVITIANNDVDLIIRISDRGGGIAHKDLDRV 298
Query: 89 -------KEEGISAAEVIMTRLHAGGKFNQKSYKVSGGLHGVGVSVVNAL 131
E + H +S + G G G+ A
Sbjct: 299 MDYHFTTAEASTQDPRISPLFGHLDMHSGGQSGPMHG--FGFGLPTSRAY 346
>2zxr_A Single-stranded DNA specific exonuclease RECJ; DNA repair,
hydrolase; 2.15A {Thermus thermophilus} PDB: 2zxo_A
2zxp_A 1ir6_A
Length = 666
Score = 29.7 bits (66), Expect = 2.5
Identities = 28/107 (26%), Positives = 39/107 (36%), Gaps = 30/107 (28%)
Query: 10 YDADSI----QILKGLDAVKKRPSMYIGD--TDGESGLHHMIYEVLDNAIDESLEGYADI 63
YDAD + +++GL A+ +I +G Y VL + E LE
Sbjct: 81 YDADGLTGTAILVRGLAALGADVHPFIPHRLEEG--------YGVLMERVPEHLEASDLF 132
Query: 64 ITVTLNMDGSCTVSDNGRG--IPTDLHKEEGISAAEVIMTRLHAGGK 108
+TV D G E G+ EVI+T H GK
Sbjct: 133 LTV-----------DCGITNHAELRELLENGV---EVIVTDHHTPGK 165
>1id0_A PHOQ histidine kinase; PHOQ/PHOP, signal transduction,
transferase; HET: ANP; 1.60A {Escherichia coli} SCOP:
d.122.1.3 PDB: 3cgz_A 3cgy_A
Length = 152
Score = 29.3 bits (66), Expect = 3.1
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 7/49 (14%)
Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDGSC---TVSDNGRGIPTD 86
++ VLDNA LE + ++ V D+G GIP
Sbjct: 45 FVEVMGNVLDNACKYCLEF----VEISARQTDEHLYIVVEDDGPGIPLS 89
>3lig_A Fructosyltransferase; five bladed beta-propeller fold, hydrolase;
1.80A {Aspergillus japonicus} PDB: 3ldk_A* 3lem_A*
3ldr_A 3lih_A* 3lf7_A 3lfi_A*
Length = 634
Score = 29.4 bits (65), Expect = 3.4
Identities = 4/11 (36%), Positives = 6/11 (54%)
Query: 353 RSVVESFVNDG 363
+VVE + N
Sbjct: 579 NAVVEVYANGR 589
>1bxd_A ENVZ(290-450), protein (osmolarity sensor protein (ENVZ));
histidine kinase, osmosensor, His-Asp phosphorelay
system, signal transduction; HET: ANP; NMR {Escherichia
coli} SCOP: d.122.1.3
Length = 161
Score = 29.5 bits (66), Expect = 3.4
Identities = 15/91 (16%), Positives = 31/91 (34%), Gaps = 15/91 (16%)
Query: 41 LHHMIYEVLDNAIDESLEGYADIITVTLNMDGSCTVSDNGRGIPTDLHKEEGISAAEVIM 100
+ + ++ NA G+ + + T V D+G GI + K
Sbjct: 48 IKRAVANMVVNAARYG-NGWIKVSSGTEPNRAWFQVEDDGPGIAPEQRK----------- 95
Query: 101 TRLHAGGKFNQKSYKVSGGLHGVGVSVVNAL 131
H F + + G+G+++V +
Sbjct: 96 ---HLFQPFVRGDSARTISGTGLGLAIVQRI 123
>2a33_A Hypothetical protein; structural genomics, protein structure
initiative, center for eukaryotic structural genomics,
CESG, AT2G37210; 1.95A {Arabidopsis thaliana} SCOP:
c.129.1.1 PDB: 2q4o_A
Length = 215
Score = 28.9 bits (64), Expect = 4.5
Identities = 7/34 (20%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 579 KGVISKNDLRNFI--DDALKIDKLIKDFYPNHDK 610
+G IS + A ++ K ++++ P H++
Sbjct: 164 EGFISPTAREIIVSAPTAKELVKKLEEYAPCHER 197
>3kf3_A Invertase; GH32, glycoprotein, glycosidase, hydrolase; HET: FRU
NAG; 1.90A {Schwanniomyces occidentalis} PDB: 3kf5_A*
Length = 509
Score = 28.3 bits (62), Expect = 6.7
Identities = 11/61 (18%), Positives = 23/61 (37%), Gaps = 6/61 (9%)
Query: 303 YVEKSFGSKKDKRSVIGDDCREGFTSVLSIKMPDPRFSSQTKEKLVSSEVRSVVESFVND 362
Y+++ + + R D + L FS +V ++++E + ND
Sbjct: 413 YIDRHIPNVEFPRKQFFTDKLAAYLEPLDYDQDLRVFSLYG---IVD---KNIIELYFND 466
Query: 363 G 363
G
Sbjct: 467 G 467
>1o60_A 2-dehydro-3-deoxyphosphooctonate aldolase; structural genomics,
transferase; 1.80A {Haemophilus influenzae} SCOP:
c.1.10.4 PDB: 3e9a_A
Length = 292
Score = 28.2 bits (62), Expect = 7.2
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 576 CDSKGVISKNDLRNFIDDALKIDKLIKDF 604
CD + + L F+ ID L+K F
Sbjct: 249 CDGPSALPLSALEGFVSQMKAIDDLVKSF 277
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.317 0.135 0.383
Gapped
Lambda K H
0.267 0.0546 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 6,700,655
Number of extensions: 320193
Number of successful extensions: 979
Number of sequences better than 10.0: 1
Number of HSP's gapped: 919
Number of HSP's successfully gapped: 76
Length of query: 803
Length of database: 5,693,230
Length adjustment: 100
Effective length of query: 703
Effective length of database: 3,268,830
Effective search space: 2297987490
Effective search space used: 2297987490
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 (27.7 bits)