RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11240
(363 letters)
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 289 bits (741), Expect = 3e-88
Identities = 111/178 (62%), Positives = 134/178 (75%), Gaps = 12/178 (6%)
Query: 11 GLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWMEECRR 70
GLGTST KE KEYFSN+++HRI F Y D+DD I +AFSKK V++RK W+T +
Sbjct: 594 GLGTSTDKEGKEYFSNIDKHRIRFVYVDDSDDDSIDLAFSKKRVEDRKEWITNY------ 647
Query: 71 RKEMGIGEDYLYTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCL 130
+ G D+ + K +TY++FVNKELILFS DNERSIPSL DGLKPG RK+LF C
Sbjct: 648 --KGGTYVDH----SKKKLTYSDFVNKELILFSIADNERSIPSLVDGLKPGQRKILFACF 701
Query: 131 KRNDRREVKVAQLAGSVAEHSAYHHGEQSLMSTIINLAQNFVGSNNINLLQPIGQFGT 188
KRN + E+KVAQL+G V+EHSAYHHGEQSL TI+ +AQNFVGSNNINLL P GQFG+
Sbjct: 702 KRNLKNEIKVAQLSGYVSEHSAYHHGEQSLQQTIVGMAQNFVGSNNINLLYPCGQFGS 759
Score = 141 bits (358), Expect = 6e-37
Identities = 60/146 (41%), Positives = 87/146 (59%), Gaps = 4/146 (2%)
Query: 219 DYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTT 278
DY++Y T TV F V ++ L + E +G+ KVFKL++T++ ++M FD G + K+
Sbjct: 919 DYRDYSTANTVHFTVKLNDGVLEQWEEEGIEKVFKLKSTISTTNMVLFDENGKIKKYSDA 978
Query: 279 NQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIA 338
ILKEFY VRL+ Y KRK+YL G L E +L+N+ RFI +G+L I N KKK+++
Sbjct: 979 LDILKEFYLVRLDLYKKRKEYLLGKLERELARLSNKVRFIKHVINGELVITNAKKKDLVK 1038
Query: 339 ELIKRKYDSDP----VKSWKMKQNKE 360
EL K Y KS K+ +E
Sbjct: 1039 ELKKLGYVRFKDIIKKKSEKITAEEE 1064
>gnl|CDD|215593 PLN03128, PLN03128, DNA topoisomerase 2; Provisional.
Length = 1135
Score = 260 bits (665), Expect = 3e-78
Identities = 106/181 (58%), Positives = 124/181 (68%), Gaps = 12/181 (6%)
Query: 11 GLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWMEECRR 70
GLGTSTS+EAKEYFSN++ H+ F + D D I MAFSKK V++RK WL
Sbjct: 587 GLGTSTSEEAKEYFSNLDIHKKEFLWQSDEDGDLIDMAFSKKRVEDRKIWLN-------- 638
Query: 71 RKEMGIGEDYLYTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCL 130
+T I+Y++F+NKELILFS D RSIPS+ DGLKP RKVLF C
Sbjct: 639 ----NYEPGTFLDQTGNGISYSDFINKELILFSQADLARSIPSMVDGLKPSQRKVLFACF 694
Query: 131 KRNDRREVKVAQLAGSVAEHSAYHHGEQSLMSTIINLAQNFVGSNNINLLQPIGQFGTFL 190
KRN + E+KVAQL+G VAEHSAYHHGE SL STII +AQ+FVGSNNINLL P GQFGT L
Sbjct: 695 KRNLKSEIKVAQLSGYVAEHSAYHHGEASLASTIIGMAQDFVGSNNINLLTPSGQFGTRL 754
Query: 191 F 191
Sbjct: 755 Q 755
Score = 146 bits (370), Expect = 1e-38
Identities = 61/140 (43%), Positives = 92/140 (65%)
Query: 219 DYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTT 278
D+KE HTDTTV F VT+S +K+ +A +GL K FKL TT++ S+M FD+ G + K+D+
Sbjct: 918 DFKENHTDTTVHFTVTLSEEKMARALAEGLEKKFKLSTTISTSNMHLFDKDGKIKKYDSP 977
Query: 279 NQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIA 338
IL+EF+ +RL+ Y KRK+ L L E KL N+ARFI+ G++ + NRK+ E++A
Sbjct: 978 EDILEEFFHLRLDLYVKRKEVLLENLEYELKKLDNKARFILAVVKGEIVVNNRKRAELLA 1037
Query: 339 ELIKRKYDSDPVKSWKMKQN 358
EL ++ +D P + + N
Sbjct: 1038 ELEEKGFDKFPKTAKISETN 1057
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 238 bits (609), Expect = 2e-70
Identities = 103/178 (57%), Positives = 125/178 (70%), Gaps = 12/178 (6%)
Query: 11 GLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTWLTTWMEECRR 70
GLGTST+KE KEYF N+ +H+ F + + D I +AFSKK ++ RK WL +
Sbjct: 612 GLGTSTAKEGKEYFKNLGKHKKDFVWEDEQDGDAIELAFSKKKIEARKNWLRQY------ 665
Query: 71 RKEMGIGEDYLYTKTTKAITYTEFVNKELILFSNMDNERSIPSLCDGLKPGSRKVLFTCL 130
E G D +T K + Y++FVNKELILFS D +RSIPS+ DGLKPG RK+LF
Sbjct: 666 --EPGTHLD----QTQKDVKYSDFVNKELILFSMADLQRSIPSMVDGLKPGQRKILFCSF 719
Query: 131 KRNDRREVKVAQLAGSVAEHSAYHHGEQSLMSTIINLAQNFVGSNNINLLQPIGQFGT 188
KRN +E KVAQL+G V+EHSAYHHGEQSL STII +AQ+FVGSNNINLL P GQFGT
Sbjct: 720 KRNFVKEAKVAQLSGYVSEHSAYHHGEQSLASTIIGMAQDFVGSNNINLLLPNGQFGT 777
Score = 137 bits (346), Expect = 2e-35
Identities = 61/134 (45%), Positives = 88/134 (65%)
Query: 219 DYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTT 278
D K Y+ DTTV F V +S + + A+ +GL K FKL TT++ S+M FD GV+ K+DT
Sbjct: 945 DVKAYNDDTTVHFEVILSEENMLAAKQEGLLKKFKLTTTISTSNMHLFDSKGVIKKYDTP 1004
Query: 279 NQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEMIA 338
QIL+EF+ +RLEYY KRK+ L L E LKL N+ RFI+ DG++ + NRKK +++
Sbjct: 1005 EQILEEFFHLRLEYYEKRKEVLLKNLEFELLKLENKVRFILAVVDGEIIVNNRKKADLVE 1064
Query: 339 ELIKRKYDSDPVKS 352
EL ++ + P K+
Sbjct: 1065 ELRQKGFTPFPKKA 1078
>gnl|CDD|214660 smart00434, TOP4c, DNA Topoisomerase IV. Bacterial DNA
topoisomerase IV, GyrA, ParC.
Length = 444
Score = 150 bits (380), Expect = 2e-41
Identities = 41/103 (39%), Positives = 55/103 (53%), Gaps = 5/103 (4%)
Query: 89 ITYTEFVNKELILFSNM-DNERSIPSLCDGLKPGSRKVLFTCLKRNDRR-EVKVAQLAGS 146
I +F+NKE + +S N R+IP + DGLKP R++L+ KR E KV G
Sbjct: 1 IDIEDFINKEYLDYSMSVINGRAIPDVRDGLKPVQRRILYAMFKRGLTPDEPKVKSARGV 60
Query: 147 VAEHSAYH-HGEQSLMSTIINLAQNFVGSNNINLLQPIGQFGT 188
YH HG+ SL TI+ +AQ+F NN LL G FG+
Sbjct: 61 GDVMGKYHPHGDSSLYDTIVRMAQDFS--NNYPLLDGQGNFGS 101
Score = 125 bits (316), Expect = 3e-32
Identities = 38/131 (29%), Positives = 65/131 (49%), Gaps = 3/131 (2%)
Query: 217 SNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFD 276
+ E H T V+ V+ + + + ++GL+K+ KLQTT +I+ + FD G K++
Sbjct: 265 IDVRDESHDRTGVRIVIELKRGAMAEVVLNGLYKLTKLQTTFSINMLALFDN-GRPKKYN 323
Query: 277 TTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEM 336
+ILKEF RLE Y +RK+YL G L + FI ++ + R K++
Sbjct: 324 LK-EILKEFLDHRLEVYTRRKEYLLGKLE-AERLHILEGLFIALSIIDEIIVLIRSSKDL 381
Query: 337 IAELIKRKYDS 347
E ++ +
Sbjct: 382 AKEAKEKLMER 392
>gnl|CDD|238111 cd00187, TOP4c, DNA Topoisomerase, subtype IIA; domain A';
bacterial DNA topoisomerase IV (C subunit, ParC),
bacterial DNA gyrases (A subunit, GyrA),mammalian DNA
toposiomerases II. DNA topoisomerases are essential
enzymes that regulate the conformational changes in DNA
topology by catalysing the concerted breakage and
rejoining of DNA strands during normal cellular growth.
Length = 445
Score = 133 bits (337), Expect = 3e-35
Identities = 40/85 (47%), Positives = 54/85 (63%), Gaps = 6/85 (7%)
Query: 107 NERSIPSLCDGLKPGSRKVLFTCLKRN---DRREVKVAQLAGSVAEHSAYHHGEQSLMST 163
N R++P + DGLKP R++L+ KR D+ E KVA+L G VA + HG+ SL T
Sbjct: 1 NGRALPDVRDGLKPVQRRILYAMFKRGLTPDKPEKKVARLVGDVAGKY-HPHGDSSLYDT 59
Query: 164 IINLAQNFVGSNNINLLQPIGQFGT 188
I+ +AQ+F SNNI LL P G FG+
Sbjct: 60 IVRMAQDF--SNNIPLLDPQGNFGS 82
Score = 114 bits (288), Expect = 2e-28
Identities = 41/132 (31%), Positives = 64/132 (48%), Gaps = 4/132 (3%)
Query: 219 DYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFDTT 278
D ++ ++FV+ + + + ++GL+KV KLQTT I+ M AFD G K
Sbjct: 260 DVRDESDREGIRFVIELKRGAMAEVVLNGLYKVTKLQTTFGIN-MVAFDPNGRPKKL-NL 317
Query: 279 NQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCD--GDLRIENRKKKEM 336
+IL+EF RLE Y +RK+Y G A L + I+ + +R + KK +
Sbjct: 318 KEILQEFLDHRLEVYTRRKEYELGKAEARLHILEGLLKAILNIDEVINLIRSSDEAKKAL 377
Query: 337 IAELIKRKYDSD 348
I EL K +
Sbjct: 378 IEELEKLGFSEI 389
>gnl|CDD|215969 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 427
Score = 120 bits (303), Expect = 1e-30
Identities = 35/84 (41%), Positives = 50/84 (59%), Gaps = 8/84 (9%)
Query: 109 RSIPSLCDGLKPGSRKVLFTCLK---RNDRREVKVAQLAGSVAEHSAYH-HGEQSLMSTI 164
R+IP + DGLKP R++L+ K D++ KVA+L G V YH HG+ S+ +
Sbjct: 1 RAIPDVRDGLKPVQRRILYAMFKLGLNLDKKYKKVARLVGDV--MGKYHPHGDASIYDAL 58
Query: 165 INLAQNFVGSNNINLLQPIGQFGT 188
+ +AQ+FVG NI LL G FG+
Sbjct: 59 VRMAQDFVG--NIPLLDGQGNFGS 80
Score = 98.0 bits (245), Expect = 1e-22
Identities = 38/137 (27%), Positives = 68/137 (49%), Gaps = 11/137 (8%)
Query: 216 ESNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKF 275
+ +D ++ +D V+ V+ + + ++ L+K KLQ++ + +++ FD K+
Sbjct: 248 KGSDIRDE-SDRGVRIVIELKRGANPEVVLNKLYKKTKLQSSFSTNNLVLFDGG---PKY 303
Query: 276 DTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLT------NQARFIVEKCDGDLRIE 329
+ILKEF RLE Y +RK+YL L L N+ F++E G +
Sbjct: 304 LNLKEILKEFLEHRLEVYKRRKEYLLEKLEERLHILEGLLKALNKIDFVIEVIRGSI-DL 362
Query: 330 NRKKKEMIAELIKRKYD 346
+ KKE+I EL + + D
Sbjct: 363 KKAKKELIEELSEIQAD 379
>gnl|CDD|223266 COG0188, GyrA, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), A subunit [DNA replication,
recombination, and repair].
Length = 804
Score = 93.9 bits (234), Expect = 7e-21
Identities = 24/103 (23%), Positives = 49/103 (47%), Gaps = 5/103 (4%)
Query: 89 ITYTEFVNKELILFSNMDN-ERSIPSLCDGLKPGSRKVLFTCLKRNDRREVKVAQLAGSV 147
I + + + + ++ R++P + DGLKP R++L+ + + K + A V
Sbjct: 11 IDIEDEMKRSYLDYAMSVIVGRALPDVRDGLKPVQRRILYAMFELGLTPDKKYKKSARIV 70
Query: 148 AE--HSAYHHGEQSLMSTIINLAQNFVGSNNINLLQPIGQFGT 188
+ + HG+ S+ ++ +AQ+F S L+ G FG+
Sbjct: 71 GDVMGKYHPHGDSSIYDALVRMAQDF--SLRYPLVDGQGNFGS 111
Score = 43.4 bits (103), Expect = 1e-04
Identities = 24/130 (18%), Positives = 46/130 (35%), Gaps = 4/130 (3%)
Query: 217 SNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTLAISSMCAFDRYGVLTKFD 276
S+ E ++ V+ + D + + ++ L K+ LQT+ ++ K
Sbjct: 289 SDIRDE-SDREGIRIVIELKRDAVAEVVLNNLFKLTDLQTSF---NVNMLALVNGRPKVL 344
Query: 277 TTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIENRKKKEM 336
+IL EF RLE +R +Y L ++ + I K K
Sbjct: 345 NLKEILSEFLEHRLEVVTRRTEYELNKAEERLHILEGLLIALLNIDEVIEIIRESKDKPE 404
Query: 337 IAELIKRKYD 346
E + ++
Sbjct: 405 AKEELMARFG 414
>gnl|CDD|222896 PHA02592, 52, DNA topisomerase II medium subunit; Provisional.
Length = 439
Score = 84.3 bits (209), Expect = 6e-18
Identities = 40/108 (37%), Positives = 58/108 (53%), Gaps = 7/108 (6%)
Query: 87 KAITYTEFVNKELILFSNMD-NERSIPSLCDGLKPGSRKVLFTCLK--RNDRREV-KVAQ 142
K + VN E + ++ ER+IP+L DGLKP R V+ L+ + ++ + KVA
Sbjct: 4 KERSLKSIVNNEALEYAMYTVEERAIPNLIDGLKPVQRFVIHRALEYAKGNKEKFDKVAA 63
Query: 143 LAGSVAEHSAYHHGEQSLMSTIINLAQNFVGSNNINLLQPIGQFGTFL 190
+AG VA+ YHHGE S +A + +NNI LL G FG+ L
Sbjct: 64 IAGGVADLG-YHHGETSAQDAGALMANTW--NNNIPLLDGQGNFGSRL 108
Score = 40.8 bits (96), Expect = 9e-04
Identities = 27/142 (19%), Positives = 57/142 (40%), Gaps = 17/142 (11%)
Query: 199 SGAVVNALDFGSGGWRFESNDYKEYHTDTTVKFVVTMSPDKLHKAEMDGLHKVFKLQTTL 258
G +V+ D G+RF+ VT+ ++ +A + + K F L +
Sbjct: 254 KGKIVSYDDCTEDGFRFK----------------VTLKREENEEATHEKIMKDFGLIERV 297
Query: 259 AISSMCAFDRYGVLTKFDTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFI 318
+ ++ + G L ++ ++++F +R Y KR Y +A FI
Sbjct: 298 S-QNITVINENGKLKVYENAEDLIRDFVEIRKTYVQKRIQYEIKETEEAFDLALAKAEFI 356
Query: 319 VEKCDGDLRIENRKKKEMIAEL 340
G++ ++ + + E+ EL
Sbjct: 357 KRVIAGEIVLQGKTRSELTEEL 378
>gnl|CDD|214659 smart00433, TOP2c, TopoisomeraseII. Eukaryotic DNA topoisomerase
II, GyrB, ParE.
Length = 594
Score = 72.6 bits (179), Expect = 6e-14
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 1/56 (1%)
Query: 11 GLGTSTSKEAKEYFSNMERHRILFKYSGDNDDA-HIRMAFSKKLVDERKTWLTTWM 65
GLG + + E + ER +LF D D+A I A V+ RK W+
Sbjct: 538 GLGEMNADQLWETTMDPERRTLLFVTLDDADEADLIFSALMGDKVEPRKEWIEENA 593
>gnl|CDD|236598 PRK09631, PRK09631, DNA topoisomerase IV subunit A; Provisional.
Length = 635
Score = 51.6 bits (124), Expect = 3e-07
Identities = 23/62 (37%), Positives = 37/62 (59%), Gaps = 4/62 (6%)
Query: 108 ERSIPSLCDGLKPGSRKVLFTCLKRNDRREVKVAQLAGSVAEHSAYH-HGEQSLMSTIIN 166
+R+IP + DGLKP R++L + + +D + KVA + G YH HG+ S+ ++N
Sbjct: 22 DRAIPDVIDGLKPVQRRILHSLFEMHDGKFHKVANVVG---NTMKYHPHGDASIYEALVN 78
Query: 167 LA 168
LA
Sbjct: 79 LA 80
>gnl|CDD|170022 PRK09630, PRK09630, DNA topoisomerase IV subunit A; Provisional.
Length = 479
Score = 45.7 bits (108), Expect = 3e-05
Identities = 30/84 (35%), Positives = 47/84 (55%), Gaps = 10/84 (11%)
Query: 108 ERSIPSLCDGLKPGSRKVLFTCLKRNDRREVKVAQLAG-SVAEHSAYHHGEQSLMSTIIN 166
ER+IP + DGLKP R++L+T + +D + KVA +AG ++A H HG+ ++ ++
Sbjct: 22 ERAIPHILDGLKPVQRRLLWTLFRMDDGKMHKVANIAGRTMALHP---HGDAPIVEALVV 78
Query: 167 LAQNFVGSNNINLLQPIGQFGTFL 190
LA N L+ G FG L
Sbjct: 79 LA------NKGYLIDTQGNFGNPL 96
>gnl|CDD|233256 TIGR01063, gyrA, DNA gyrase, A subunit. This model describes the
common type II DNA topoisomerase (DNA gyrase). Two
apparently independently arising families, one in the
Proteobacteria and one in Gram-positive lineages, are
both designated toposisomerase IV [DNA metabolism, DNA
replication, recombination, and repair].
Length = 800
Score = 45.0 bits (107), Expect = 5e-05
Identities = 27/84 (32%), Positives = 46/84 (54%), Gaps = 8/84 (9%)
Query: 109 RSIPSLCDGLKPGSRKVLFTCLK---RNDRREVKVAQLAGSVAEHSAYH-HGEQSLMSTI 164
R++P + DGLKP R++L+ + D+ K A++ G V YH HG+ ++ T+
Sbjct: 25 RALPDVRDGLKPVHRRILYAMYELGLTPDKPYKKSARIVGDVM--GKYHPHGDSAIYDTL 82
Query: 165 INLAQNFVGSNNINLLQPIGQFGT 188
+ +AQ+F S L+ G FG+
Sbjct: 83 VRMAQDF--SLRYPLVDGQGNFGS 104
>gnl|CDD|237192 PRK12758, PRK12758, DNA topoisomerase IV subunit A; Provisional.
Length = 869
Score = 41.9 bits (99), Expect = 4e-04
Identities = 23/63 (36%), Positives = 36/63 (57%), Gaps = 4/63 (6%)
Query: 108 ERSIPSLCDGLKPGSRKVLFTCLKRNDRREVKVAQLAGSVAEHSAYH-HGEQSLMSTIIN 166
ER++P + DGLKP R++L + + +D R KVA + G YH HG+ S+ ++
Sbjct: 41 ERAVPHIEDGLKPVQRRILHSMKEMDDGRYNKVANVVGHTM---QYHPHGDASIGDALVQ 97
Query: 167 LAQ 169
L Q
Sbjct: 98 LGQ 100
>gnl|CDD|237576 PRK13979, PRK13979, DNA topoisomerase IV subunit A; Provisional.
Length = 957
Score = 35.5 bits (82), Expect = 0.045
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 6/68 (8%)
Query: 108 ERSIPSLCDGLKPGSRKVLFTCLKRN---DRREVKVAQLAGSVAEHSAYH-HGEQSLMST 163
+R++P + DGLKP R++L+ D+ K A++ G + YH HG+ S+
Sbjct: 36 DRALPDVRDGLKPVHRRILYGAYMLKAFPDKPYYKSARIVGDIL--GKYHPHGDSSVYDA 93
Query: 164 IINLAQNF 171
++ LAQ+F
Sbjct: 94 MVILAQDF 101
>gnl|CDD|233255 TIGR01061, parC_Gpos, DNA topoisomerase IV, A subunit,
Gram-positive. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation of
chromosome segregation. Not every bacterium has both a
topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 738
Score = 34.4 bits (79), Expect = 0.088
Identities = 24/85 (28%), Positives = 46/85 (54%), Gaps = 8/85 (9%)
Query: 108 ERSIPSLCDGLKPGSRKVLFTCLKRN---DRREVKVAQLAGSVAEHSAYH-HGEQSLMST 163
+R++P + DGLKP R++L+ + D+ K A+ G + YH HG+ S+
Sbjct: 24 DRALPDIRDGLKPVQRRILYAMFQDGNTFDKPYKKSARTVGEIM--GKYHPHGDSSIYDA 81
Query: 164 IINLAQNFVGSNNINLLQPIGQFGT 188
++ ++Q++ NN L++ G G+
Sbjct: 82 MVRMSQDW--KNNWTLVEMHGNNGS 104
>gnl|CDD|130134 TIGR01062, parC_Gneg, DNA topoisomerase IV, A subunit,
proteobacterial. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation of
chromosome segregation. Not every bacterium has both a
topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 735
Score = 34.5 bits (79), Expect = 0.10
Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 6/68 (8%)
Query: 108 ERSIPSLCDGLKPGSRKVLFTCLK---RNDRREVKVAQLAGSVAEHSAYH-HGEQSLMST 163
+R++P + DGLKP R++++ + + + K A+ G V YH HG+ +
Sbjct: 24 DRALPFIGDGLKPVQRRIVYAMSELGLNANAKYKKSARTVGDVL--GKYHPHGDSACYEA 81
Query: 164 IINLAQNF 171
++ +AQ F
Sbjct: 82 MVLMAQPF 89
>gnl|CDD|223265 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 33.6 bits (78), Expect = 0.18
Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 5/54 (9%)
Query: 11 GLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKL---VDERKTWL 61
GLG + E + E R+L D D+A FS + V+ R+ ++
Sbjct: 572 GLGEMNPDQLWETTMDPETRRLLQVTIEDADEA--DEIFSTLMGDKVEPRRNFI 623
>gnl|CDD|235503 PRK05561, PRK05561, DNA topoisomerase IV subunit A; Validated.
Length = 742
Score = 33.5 bits (78), Expect = 0.20
Identities = 22/68 (32%), Positives = 39/68 (57%), Gaps = 6/68 (8%)
Query: 108 ERSIPSLCDGLKPGSRKVLFTCLK---RNDRREVKVAQLAGSVAEHSAYH-HGEQSLMST 163
+R++P + DGLKP R++L+ + D + K A++ G V YH HG+ S+
Sbjct: 33 DRALPDVRDGLKPVQRRILYAMSELGLTPDAKFKKSARVVGDVL--GKYHPHGDSSIYDA 90
Query: 164 IINLAQNF 171
++ +AQ+F
Sbjct: 91 MVRMAQDF 98
>gnl|CDD|132234 TIGR03190, benz_CoA_bzdN, benzoyl-CoA reductase, bzd-type, N
subunit. Members of this family are the N subunit of
one of two related types of four-subunit ATP-dependent
benzoyl-CoA reductase. This enzyme system catalyzes the
dearomatization of benzoyl-CoA, a common intermediate in
pathways for the degradation for a number of different
aromatic compounds, such as phenol and toluene.
Length = 377
Score = 29.2 bits (65), Expect = 3.6
Identities = 27/82 (32%), Positives = 40/82 (48%), Gaps = 13/82 (15%)
Query: 272 LTKFDTTNQILKEFYAV-----RL--EYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDG 324
LT + T+ +L++ AV RL E + RK+ V G EAL + A+FI
Sbjct: 150 LTGKEITDDMLRDALAVCDENRRLLRELFDYRKEADPKVTGVEALYASLTAQFI------ 203
Query: 325 DLRIENRKKKEMIAELIKRKYD 346
D R N K+++A L RK +
Sbjct: 204 DKREHNEMLKKVLAALPSRKVE 225
>gnl|CDD|226389 COG3871, COG3871, Uncharacterized stress protein (general stress
protein 26) [General function prediction only].
Length = 145
Score = 28.1 bits (63), Expect = 4.1
Identities = 14/76 (18%), Positives = 32/76 (42%)
Query: 1 MNTIHDVMIAGLGTSTSKEAKEYFSNMERHRILFKYSGDNDDAHIRMAFSKKLVDERKTW 60
M HD + T+K++++ + ++ + D+ DA + ++ + +LV++R
Sbjct: 36 MTFNHDGPKGTIWFFTNKDSRKVEEIKKNPKVCVLFGYDDHDAFVEVSGTAELVEDRAKI 95
Query: 61 LTTWMEECRRRKEMGI 76
W E G
Sbjct: 96 DELWTSVLEAWFEQGK 111
>gnl|CDD|129323 TIGR00219, mreC, rod shape-determining protein MreC. MreC (murein
formation C) is involved in the rod shape determination
in E. coli, and more generally in cell shape
determination of bacteria whether or not they are
rod-shaped. Cells defective in MreC are round. Species
with MreC include many of the Proteobacteria,
Gram-positives, and spirochetes [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 283
Score = 28.7 bits (64), Expect = 4.8
Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 8/77 (10%)
Query: 270 GVLTKFDTTNQILKEFYAVRLEYYAKRKDYLEGVLGAEALKLTNQARFIVEKCDGDLRIE 329
G+ N + E Y +R E K + + + LK N + E + L +
Sbjct: 60 GISENLKDVNNLEYENYKLRQELLKKNQQLE---ILTQNLKQENVR--LRELLNSPLSSD 114
Query: 330 NRKKKEMIAELIKRKYD 346
K + AE+I YD
Sbjct: 115 EYK---ISAEVIYLNYD 128
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
0.319 0.133 0.387
Gapped
Lambda K H
0.267 0.0798 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,249,309
Number of extensions: 1743752
Number of successful extensions: 1429
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1401
Number of HSP's successfully gapped: 36
Length of query: 363
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 265
Effective length of database: 6,590,910
Effective search space: 1746591150
Effective search space used: 1746591150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.8 bits)