RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13669
(172 letters)
>gnl|CDD|233035 TIGR00585, mutl, DNA mismatch repair protein MutL. All proteins in
this family for which the functions are known are
involved in the process of generalized mismatch repair.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 312
Score = 195 bits (497), Expect = 1e-62
Identities = 68/164 (41%), Positives = 103/164 (62%), Gaps = 1/164 (0%)
Query: 3 VVLNLATAVKELVENSLDAGATSVEVKLKDYGSELVEVTDNGGGVHEDNYEGLTLKHHTS 62
V+ A+ VKELVENSLDAGAT ++V++++ G +L+EV+DNG G+ +++ +H TS
Sbjct: 19 VIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNGSGIDKEDLPLACERHATS 78
Query: 63 KLREFTDLTSVETFGFRGEALSSLCALSSVVIVTRHKLSGVGHWLEFDHHGHIKTKTLVS 122
K++ F DL +ET GFRGEAL+S+ ++S + I T+ + + G I++
Sbjct: 79 KIQSFEDLERIETLGFRGEALASISSVSRLTITTKTSAADGLAYQALLEGGMIESIKPAP 138
Query: 123 RQVGTTVSLHNIFSTLPVRQKEFHRHLKKEFAKMTQVLYGYCLV 166
R VGTTV + ++F LPVR+K KKEF K+ VL Y L+
Sbjct: 139 RPVGTTVEVRDLFYNLPVRRKFLKSP-KKEFRKILDVLQRYALI 181
>gnl|CDD|223400 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA
replication, recombination, and repair].
Length = 638
Score = 165 bits (419), Expect = 2e-48
Identities = 59/158 (37%), Positives = 95/158 (60%), Gaps = 1/158 (0%)
Query: 3 VVLNLATAVKELVENSLDAGATSVEVKLKDYGSELVEVTDNGGGVHEDNYEGLTLKHHTS 62
V+ A+ VKELVENSLDAGAT ++++++ G +L+ V DNG G+ +++ L+H TS
Sbjct: 20 VIERPASVVKELVENSLDAGATRIDIEVEGGGLKLIRVRDNGSGIDKEDLPLALLRHATS 79
Query: 63 KLREFTDLTSVETFGFRGEALSSLCALSSVVIVTRHKLSGVGHWLEFDHHGHIKTKTLVS 122
K+ DL + T GFRGEAL+S+ ++S + I +R + G + + G T +
Sbjct: 80 KIASLEDLFRIRTLGFRGEALASIASVSRLTITSRTAEASEGTQIYAEGGGMEVTVKPAA 139
Query: 123 RQVGTTVSLHNIFSTLPVRQKEFHRHLKKEFAKMTQVL 160
VGTTV + ++F P R+K F + K EF +T+++
Sbjct: 140 HPVGTTVEVRDLFYNTPARRK-FLKSEKTEFGHITELI 176
>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 145 bits (369), Expect = 3e-41
Identities = 58/161 (36%), Positives = 93/161 (57%), Gaps = 8/161 (4%)
Query: 3 VVLNLATAVKELVENSLDAGATSVEVKLKDYGSELVEVTDNGGGVHEDNYEGLTL---KH 59
VV A+ VKELVEN+LDAGAT +++++++ G +L+ V DNG G+ +++ L L +H
Sbjct: 19 VVERPASVVKELVENALDAGATRIDIEIEEGGLKLIRVRDNGCGISKED---LALALARH 75
Query: 60 HTSKLREFTDLTSVETFGFRGEALSSLCALSSVVIVTRHKLSGVGHWLEFDHHGHIKTKT 119
TSK+ DL ++ T GFRGEAL S+ ++S + + +R + G W G I
Sbjct: 76 ATSKIASLDDLEAIRTLGFRGEALPSIASVSRLTLTSRTADAAEG-WQIVYEGGEIVEVK 134
Query: 120 LVSRQVGTTVSLHNIFSTLPVRQKEFHRHLKKEFAKMTQVL 160
+ VGTT+ + ++F P R+K F + K E + V+
Sbjct: 135 PAAHPVGTTIEVRDLFFNTPARRK-FLKSEKTELGHIDDVV 174
>gnl|CDD|222246 pfam13589, HATPase_c_3, Histidine kinase-, DNA gyrase B-, and
HSP90-like ATPase. This family represents,
additionally, the structurally related ATPase domains
of histidine kinase, DNA gyrase B and HSP90.
Length = 134
Score = 58.8 bits (143), Expect = 9e-12
Identities = 28/96 (29%), Positives = 51/96 (53%), Gaps = 5/96 (5%)
Query: 6 NLATAVKELVENSLDAGATSVEVKL-KDYGSELVEVTDNGGGVHEDNY-EGLTLKHHTSK 63
L A+ EL++NS+DA AT+V++ + D G + + + DNGGG+ + L L +SK
Sbjct: 2 TLEDAIAELIDNSIDADATNVKISIDPDRGEDGISIEDNGGGMSYEELRNALKL-GRSSK 60
Query: 64 LREFTDLTSVETFGFRGEALSSLCALSSVVIVTRHK 99
E T++ G + L+SL + + ++ +
Sbjct: 61 EGERDS-TTLGRKGIGMK-LASLSLGRKLTVTSKKE 94
>gnl|CDD|238030 cd00075, HATPase_c, Histidine kinase-like ATPases; This family
includes several ATP-binding proteins for example:
histidine kinase, DNA gyrase B, topoisomerases, heat
shock protein HSP90, phytochrome-like ATPases and DNA
mismatch repair proteins.
Length = 103
Score = 42.2 bits (100), Expect = 9e-06
Identities = 25/131 (19%), Positives = 42/131 (32%), Gaps = 34/131 (25%)
Query: 7 LATAVKELVENSLDAG---ATSVEVKLKDYGSEL-VEVTDNGGGVHEDNYEGLTLKHHTS 62
L + L+ N++ + + ++ G L + V DNG G+ E+
Sbjct: 1 LQQVLLNLLSNAIKHTPEGGGRITISVERDGDHLEIRVEDNGPGIPEE--------DLER 52
Query: 63 KLREFTDLTSVETFGFRGEALSSLCALSSVVIVTRHKLSGVGHWLEFDHHGHIKTKTLVS 122
F+D + G G LS + L H G I + S
Sbjct: 53 IFERFSDGSRSRKGGGTGLGLSIVKKLVE------------------LHGGRI---EVES 91
Query: 123 RQ-VGTTVSLH 132
GTT ++
Sbjct: 92 EPGGGTTFTIT 102
>gnl|CDD|235246 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
Length = 535
Score = 42.6 bits (101), Expect = 4e-05
Identities = 22/54 (40%), Positives = 29/54 (53%), Gaps = 9/54 (16%)
Query: 7 LATAVKELVENSLDAGATS-------VEVKLKDYGSELVEVT--DNGGGVHEDN 51
L T VKELV+NSLDA + +E+K D G + VT DNG G+ +
Sbjct: 37 LYTTVKELVDNSLDACEEAGILPDIKIEIKRVDEGKDHYRVTVEDNGPGIPPEE 90
>gnl|CDD|217081 pfam02518, HATPase_c, Histidine kinase-, DNA gyrase B-, and
HSP90-like ATPase. This family represents the
structurally related ATPase domains of histidine
kinase, DNA gyrase B and HSP90.
Length = 111
Score = 39.6 bits (93), Expect = 8e-05
Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 7 LATAVKELVENSLDAGATS--VEVKLKDYGSEL-VEVTDNGGGVHEDNYEGLTLKHHTSK 63
L + L++N++ +EV L+ G L + V DNG G+ ++ + +
Sbjct: 6 LRQVLSNLLDNAIKHAPAGGEIEVTLERDGGRLRITVEDNGIGIPPEDLPKIFEPFFRTD 65
>gnl|CDD|225827 COG3290, CitA, Signal transduction histidine kinase regulating
citrate/malate metabolism [Signal transduction
mechanisms].
Length = 537
Score = 36.9 bits (86), Expect = 0.003
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 6/64 (9%)
Query: 6 NLATAVKELVENSLDAGAT-----SVEVKLKDYGSELV-EVTDNGGGVHEDNYEGLTLKH 59
+L T + L++N+L+A +E+ L D G ELV EV D G G+ + + + K
Sbjct: 427 DLVTILGNLIDNALEALLAPEENKEIELSLSDRGDELVIEVADTGPGIPPEVRDKIFEKG 486
Query: 60 HTSK 63
++K
Sbjct: 487 VSTK 490
>gnl|CDD|236532 PRK09470, cpxA, two-component sensor protein; Provisional.
Length = 461
Score = 36.4 bits (85), Expect = 0.004
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 7 LATAVKELVENSLDAGATSVEVKLKDYGSEL-VEVTDNGGGVHEDNYE 53
LA+A++ +V N+L T +EV L + V D+G GV E+ E
Sbjct: 354 LASALENIVRNALRYSHTKIEVAFSVDKDGLTITVDDDGPGVPEEERE 401
>gnl|CDD|224307 COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA
replication, recombination, and repair].
Length = 538
Score = 35.5 bits (82), Expect = 0.010
Identities = 19/48 (39%), Positives = 23/48 (47%), Gaps = 7/48 (14%)
Query: 7 LATAVKELVENSLDAGATS-------VEVKLKDYGSELVEVTDNGGGV 47
L T V ELV NSLDA + VE++ V V DNG G+
Sbjct: 37 LTTTVHELVTNSLDACEEAGILPDIKVEIERIGKDHYKVIVEDNGPGI 84
>gnl|CDD|235542 PRK05644, gyrB, DNA gyrase subunit B; Validated.
Length = 638
Score = 35.1 bits (82), Expect = 0.012
Identities = 18/40 (45%), Positives = 25/40 (62%), Gaps = 6/40 (15%)
Query: 11 VKELVENSLD---AG-ATSVEVKLKDYGSELVEVTDNGGG 46
V E+V+NS+D AG +EV + + GS + VTDNG G
Sbjct: 42 VYEIVDNSIDEALAGYCDHIEVTINEDGS--ITVTDNGRG 79
>gnl|CDD|214643 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine
kinase-, DNA gyrase B-, phytochrome-like ATPases.
Length = 111
Score = 32.2 bits (74), Expect = 0.041
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 3/47 (6%)
Query: 7 LATAVKELVENSLDAGATS--VEVKLKDYGSEL-VEVTDNGGGVHED 50
L + L++N++ + V L+ G + + V DNG G+ +
Sbjct: 6 LRQVLSNLLDNAIKYTPEGGRITVTLERDGDHVEITVEDNGPGIPPE 52
>gnl|CDD|223265 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 33.3 bits (77), Expect = 0.046
Identities = 18/40 (45%), Positives = 25/40 (62%), Gaps = 6/40 (15%)
Query: 11 VKELVENSLD---AG-ATSVEVKLKDYGSELVEVTDNGGG 46
V E+V+NS+D AG A ++V L + GS + V DNG G
Sbjct: 41 VWEVVDNSIDEALAGYADRIDVTLHEDGS--ISVEDNGRG 78
>gnl|CDD|235501 PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed.
Length = 631
Score = 33.5 bits (78), Expect = 0.046
Identities = 18/40 (45%), Positives = 24/40 (60%), Gaps = 6/40 (15%)
Query: 11 VKELVENSLD---AG-ATSVEVKLKDYGSELVEVTDNGGG 46
V+E+++NS+D AG +EV L GS V V DNG G
Sbjct: 42 VQEVIDNSVDEALAGHGKRIEVTLHADGS--VSVRDNGRG 79
>gnl|CDD|226434 COG3920, COG3920, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 221
Score = 32.2 bits (74), Expect = 0.087
Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 8/54 (14%)
Query: 1 MAVVLNLATAVKELVENSLDAGATS-----VEVKLK---DYGSELVEVTDNGGG 46
+ L V ELV N+L S + + L D G L+ V D GGG
Sbjct: 117 PDTAVPLGLIVHELVTNALKHAFLSRPGGEIRITLSREGDGGRFLLTVWDEGGG 170
>gnl|CDD|237842 PRK14868, PRK14868, DNA topoisomerase VI subunit B; Provisional.
Length = 795
Score = 32.5 bits (74), Expect = 0.098
Identities = 24/50 (48%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 7 LATAVKELVENSLDAGATSVEVKLKDYGSELVEVTDNGGGVHEDNYEGLT 56
L TAVKE V+N+LD AT L D E+ EV D V EDN G+T
Sbjct: 47 LVTAVKEAVDNALD--ATEEAGILPDIYVEIEEVGDYYRLVVEDNGPGIT 94
>gnl|CDD|233250 TIGR01052, top6b, DNA topoisomerase VI, B subunit. This model
describes DNA topoisomerase VI, an archaeal type II DNA
topoisomerase (DNA gyrase) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 488
Score = 32.1 bits (73), Expect = 0.14
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 7/50 (14%)
Query: 7 LATAVKELVENSLDAGATS-----VEVKLKDYGSE--LVEVTDNGGGVHE 49
L T + ELV NSLDA + ++V+++ G + V V DNG G+ E
Sbjct: 29 LTTVIHELVTNSLDACEEAGILPDIKVEIEKIGKDHYKVTVEDNGPGIPE 78
>gnl|CDD|237841 PRK14867, PRK14867, DNA topoisomerase VI subunit B; Provisional.
Length = 659
Score = 31.7 bits (72), Expect = 0.18
Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 7/49 (14%)
Query: 6 NLATAVKELVENSLDAGATS-----VEVKLKDYGSEL--VEVTDNGGGV 47
++ T + ELV NSLDA + ++V+++ GS+ V V DNG G+
Sbjct: 36 SMTTIIHELVTNSLDACEEAEILPDIKVEIEKLGSDHYKVAVEDNGPGI 84
>gnl|CDD|226951 COG4585, COG4585, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 365
Score = 30.9 bits (70), Expect = 0.32
Identities = 23/80 (28%), Positives = 32/80 (40%), Gaps = 6/80 (7%)
Query: 6 NLATAVKELVENSLD-AGATSVEVKLKDYGSEL-VEVTDNGGGVHEDNY-EGLTLKHHTS 62
L V+E + N++ A AT V V L+ EL +EV DNG G D G L
Sbjct: 279 ALFRIVQEALTNAIRHAQATEVRVTLERTDDELRLEVIDNGVGFDPDKEGGGFGLLGMRE 338
Query: 63 KLREFT---DLTSVETFGFR 79
++ + S G
Sbjct: 339 RVEALGGTLTIDSAPGQGTT 358
>gnl|CDD|130127 TIGR01055, parE_Gneg, DNA topoisomerase IV, B 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. This protein is active as an
alpha(2)beta(2) heterotetramer [DNA metabolism, DNA
replication, recombination, and repair].
Length = 625
Score = 30.3 bits (68), Expect = 0.49
Identities = 30/93 (32%), Positives = 47/93 (50%), Gaps = 18/93 (19%)
Query: 11 VKELVENSLD---AG-ATSVEVKLKDYGSELVEVTDNGGGVHEDNY--EG-------LTL 57
V+E+++NS+D AG A+ + V L + + +EV DNG G+ D + EG LT
Sbjct: 35 VQEVIDNSVDEALAGFASIIMVIL--HQDQSIEVFDNGRGMPVDIHPKEGVSAVEVILTT 92
Query: 58 KHHTSKLREFTDLTSVETFGFRGEALSSLCALS 90
H K F++ + G G +S + ALS
Sbjct: 93 LHAGGK---FSNKNYHFSGGLHGVGISVVNALS 122
>gnl|CDD|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 336
Score = 30.1 bits (67), Expect = 0.51
Identities = 8/47 (17%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 7 LATAVKELVENSLDAG-ATSVEVKLKDYGSEL-VEVTDNGGGVHEDN 51
L + L+ N++ + + ++ ++ + V D G G+ E+
Sbjct: 229 LRQVLVNLLSNAIKYTPGGEITISVRQDDEQVTISVEDTGPGIPEEE 275
>gnl|CDD|236839 PRK11086, PRK11086, sensory histidine kinase DcuS; Provisional.
Length = 542
Score = 27.6 bits (62), Expect = 3.4
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 2 AVVLNLATAVKELVENSLDAGAT----SVEVKLKDYGSEL-VEVTDNGGGVHEDNYEGLT 56
V L T + L+EN+L+A + V L L EV+D+G G+ D + +
Sbjct: 429 DQVHELITILGNLIENALEAVGGEEGGEISVSLHYRNGWLHCEVSDDGPGIAPDEIDAIF 488
Query: 57 LKHHTSK 63
K +++K
Sbjct: 489 DKGYSTK 495
>gnl|CDD|220343 pfam09687, PRESAN, Plasmodium RESA N-terminal. The short,
four-helical domain first identified in the Plasmodium
export proteins PHISTa and PHISTc has been extended to
become this six-helical PRESAN domain identified in the
P. falciparum-specific RESA-type (Ring-infected
erythrocyte surface antigen) proteins in association
with the DnaJ domain. Overall, at least 67 proteins have
been detected in P. falciparum with complete copies of
the PRESAN domain. No versions of this domain were
detected in other apicomplexan genera, suggesting that
the domain was 'invented' after the divergence of the
lineage leading to the genus Plasmodium undergoing a
dramatic proliferation only in P. falciparum. A
secondary structure-prediction derived from the multiple
alignment of the PRESAN family reveals that it is
composed of an all-helical fold with six conserved
helical segments. There is some evidence it might
localise to membranes.
Length = 129
Score = 26.5 bits (59), Expect = 5.7
Identities = 5/22 (22%), Positives = 12/22 (54%)
Query: 143 KEFHRHLKKEFAKMTQVLYGYC 164
+++ KK++ M + L+ Y
Sbjct: 32 NYVNKNEKKKYYNMIEKLWKYF 53
>gnl|CDD|236531 PRK09467, envZ, osmolarity sensor protein; Provisional.
Length = 435
Score = 26.8 bits (60), Expect = 6.5
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 10 AVKELVENSLDAGATSVEVKLKDYGSEL-VEVTDNGGGVHEDNYEGL 55
A+ LV N+ G ++V G +V D+G G+ + + L
Sbjct: 335 ALANLVVNAARYGNGWIKVSSGTEGKRAWFQVEDDGPGIPPEQLKHL 381
>gnl|CDD|236020 PRK07449, PRK07449,
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-
carboxylate synthase; Validated.
Length = 568
Score = 26.3 bits (59), Expect = 9.2
Identities = 6/15 (40%), Positives = 8/15 (53%)
Query: 133 NIFSTLPVRQKEFHR 147
IFS LP ++E
Sbjct: 482 GIFSLLPQPEEEPVF 496
>gnl|CDD|225275 COG2412, COG2412, Uncharacterized conserved protein [Function
unknown].
Length = 101
Score = 25.4 bits (56), Expect = 9.9
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 7 LATAVKELVENSLDAGATSVEVKLKDYGSELVEVTD 42
+A ++L+ + G +EV YG ELVE +
Sbjct: 17 VAACDEDLLGKTFREGGLKIEVSESFYGGELVEEDE 52
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
0.318 0.133 0.381
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,353,976
Number of extensions: 740597
Number of successful extensions: 625
Number of sequences better than 10.0: 1
Number of HSP's gapped: 613
Number of HSP's successfully gapped: 31
Length of query: 172
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 82
Effective length of database: 6,945,742
Effective search space: 569550844
Effective search space used: 569550844
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (24.9 bits)