RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7792
(138 letters)
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 103 bits (259), Expect = 6e-27
Identities = 42/84 (50%), Positives = 62/84 (73%), Gaps = 1/84 (1%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
M+ATDVAS+GLD +++K+VIN+D P+ +E+YVHRIGRTGR+G G + TF+ + +
Sbjct: 431 MIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLT-PDKYRLA 489
Query: 61 LDLKHLLLEARQRIPPFLAELESE 84
DL +L EA+Q +PP L +L +E
Sbjct: 490 RDLVKVLREAKQPVPPELEKLSNE 513
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription /
Translation, ribosomal structure and biogenesis].
Length = 513
Score = 101 bits (253), Expect = 5e-26
Identities = 37/93 (39%), Positives = 56/93 (60%), Gaps = 3/93 (3%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+VATDVA++GLD ++ HVINYD+P D E+YVHRIGRTGR+G+ G+A +F+ + + L
Sbjct: 327 LVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKL 386
Query: 61 LDLKHLL---LEARQRIPPFLAELESETEKFLD 90
++ L L + +P E +
Sbjct: 387 KRIEKRLERKLPSAVLLPLDEPEDAKLLKTTRP 419
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 85.0 bits (211), Expect = 2e-20
Identities = 29/50 (58%), Positives = 39/50 (78%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTF 50
+VATDVA++GL + HV NYD+PDD E+YVHRIGRTGR+G +G + +
Sbjct: 309 LVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 84.5 bits (210), Expect = 4e-20
Identities = 28/52 (53%), Positives = 40/52 (76%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFIN 52
+VATDVA++GLD + ++ VINY++ D E +VHRIGRTGR+G GLA + +
Sbjct: 296 LVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVA 347
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 83.5 bits (207), Expect = 8e-20
Identities = 27/51 (52%), Positives = 41/51 (80%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFI 51
+VATDVA++G+D +++ HVIN+DMP + Y+HRIGRTGR+G+ G A + +
Sbjct: 299 LVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLV 349
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 75.0 bits (185), Expect = 2e-18
Identities = 23/50 (46%), Positives = 33/50 (66%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTF 50
+VATDV ++G+D + VINYD+P +Y+ RIGR GR+G+ G A
Sbjct: 82 LVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety
of helicases and helicase related proteins. It may be
that this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 71.8 bits (177), Expect = 1e-17
Identities = 22/42 (52%), Positives = 32/42 (76%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG 42
+VATDVA +G+D ++ VINYD+P + +Y+ RIGR GR+G
Sbjct: 37 LVATDVAGRGIDLPDVNLVINYDLPWNPASYIQRIGRAGRAG 78
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 77.2 bits (190), Expect = 1e-17
Identities = 35/61 (57%), Positives = 45/61 (73%), Gaps = 2/61 (3%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
++ATDVA++GLD E I V+NYD+P D E+YVHRIGRTGR+G+ G A F+ N E L
Sbjct: 299 LIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVE--NRERRL 356
Query: 61 L 61
L
Sbjct: 357 L 357
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 76.8 bits (189), Expect = 2e-17
Identities = 38/76 (50%), Positives = 55/76 (72%), Gaps = 6/76 (7%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+VATD+A++GLD EE+ HV+NY++P+ E+YVHRIGRTGR+ TG A + + DE L
Sbjct: 299 LVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLV--CVDEHKL 356
Query: 61 L-DLKHLLLEARQRIP 75
L D++ LL ++ IP
Sbjct: 357 LRDIEKLL---KKEIP 369
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 72.3 bits (177), Expect = 9e-16
Identities = 29/61 (47%), Positives = 45/61 (73%), Gaps = 2/61 (3%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+VATDVA +G+ + I HVIN+ +P+D ++YVHRIGRTGR+G +G++ +F D++
Sbjct: 389 LVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFA--GEDDAFQ 446
Query: 61 L 61
L
Sbjct: 447 L 447
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 66.9 bits (164), Expect = 1e-15
Identities = 22/42 (52%), Positives = 29/42 (69%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG 42
+VATDVA +GLD + VI YD+P +Y+ RIGR GR+G
Sbjct: 41 LVATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 68.4 bits (167), Expect = 2e-14
Identities = 38/83 (45%), Positives = 51/83 (61%), Gaps = 6/83 (7%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+VATDVA++GL + +K+V NYD+P D E+YVHRIGRT R G+ G A +F E
Sbjct: 311 LVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFAC----ERYA 366
Query: 61 LDLKHLLLEARQRIP--PFLAEL 81
+ L + Q+IP P AEL
Sbjct: 367 MSLPDIEAYIEQKIPVEPVTAEL 389
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 66.0 bits (161), Expect = 1e-13
Identities = 25/57 (43%), Positives = 41/57 (71%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDE 57
++ TD+ ++G+D +++ VINYD+P ENY+HRIGR+GR G+ G+A F+ + E
Sbjct: 321 LITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIE 377
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 64.0 bits (156), Expect = 7e-13
Identities = 29/79 (36%), Positives = 48/79 (60%), Gaps = 1/79 (1%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVL 60
+VAT V +G+D ++ VI +DMP+ ++ Y+H+IGR R G+ G A F+N+ + ++
Sbjct: 422 IVATGVLGRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEED-RNLF 480
Query: 61 LDLKHLLLEARQRIPPFLA 79
+L LL + IP LA
Sbjct: 481 PELVALLKSSGAAIPRELA 499
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 44.6 bits (106), Expect = 3e-06
Identities = 28/121 (23%), Positives = 46/121 (38%), Gaps = 23/121 (19%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTF---------- 50
MVAT+ G+D +++ VI+YD+P +E+Y GR GR G A
Sbjct: 284 MVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQR 343
Query: 51 --INKSNDESVLLDLKHLLLEARQRIPPFLAELESET---EKFLDLGGDER--GCAYCGG 103
I +S + ++ +A E++T L G++ C C
Sbjct: 344 YLIEQSKPDEEQKQ------IELAKLRQMIAYCETQTCRRLVLLKYFGEDEPEPCGNCDN 397
Query: 104 L 104
Sbjct: 398 C 398
>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ. The
ATP-dependent DNA helicase RecQ of E. coli is about 600
residues long. This model represents bacterial proteins
with a high degree of similarity in domain architecture
and in primary sequence to E. coli RecQ. The model
excludes eukaryotic and archaeal proteins with RecQ-like
regions, as well as more distantly related bacterial
helicases related to RecQ [DNA metabolism, DNA
replication, recombination, and repair].
Length = 591
Score = 43.1 bits (102), Expect = 1e-05
Identities = 19/42 (45%), Positives = 27/42 (64%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG 42
MVAT+ G+D ++ VI+YDMP ++E+Y GR GR G
Sbjct: 278 MVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDG 319
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. All
proteins in this family for which functions are known
are 3'-5' DNA-DNA helicases. These proteins are used for
recombination, recombinational repair, and possibly
maintenance of chromosome stability. 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 = 470
Score = 41.3 bits (97), Expect = 4e-05
Identities = 15/41 (36%), Positives = 24/41 (58%)
Query: 2 VATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG 42
VAT G++ +++ VI+Y +P +E+Y GR GR G
Sbjct: 281 VATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDG 321
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 35.8 bits (83), Expect = 0.003
Identities = 18/42 (42%), Positives = 26/42 (61%), Gaps = 2/42 (4%)
Query: 1 MVATDVASKGLDFEEIKHVINYD-MPDDVENYVHRIGRTGRS 41
+VAT V +GLD E+ VI Y+ +P ++ + R GRTGR
Sbjct: 429 LVATSVGEEGLDIPEVDLVIFYEPVPSEIR-SIQRKGRTGRK 469
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 32.4 bits (74), Expect = 0.062
Identities = 14/41 (34%), Positives = 25/41 (60%)
Query: 2 VATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSG 42
VAT G++ ++ V+++D+P ++E+Y GR GR G
Sbjct: 291 VATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDG 331
>gnl|CDD|222730 pfam14392, zf-CCHC_4, Zinc knuckle. The zinc knuckle is a zinc
binding motif composed of the the following CX2CX4HX4C
where X can be any amino acid. This particular family is
found in plant proteins.
Length = 49
Score = 28.0 bits (63), Expect = 0.28
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 98 CAYCGGLGHRITACPK 113
C +CG LGH CPK
Sbjct: 34 CFHCGRLGHSDKECPK 49
>gnl|CDD|197667 smart00343, ZnF_C2HC, zinc finger.
Length = 17
Score = 27.4 bits (62), Expect = 0.34
Identities = 7/17 (41%), Positives = 7/17 (41%)
Query: 97 GCAYCGGLGHRITACPK 113
C CG GH CP
Sbjct: 1 KCYNCGKEGHIARDCPS 17
>gnl|CDD|182854 PRK10941, PRK10941, hypothetical protein; Provisional.
Length = 269
Score = 29.2 bits (66), Expect = 0.51
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 57 ESVLLDLKHLLLEARQRIPPFLAELESETEKFLDL 91
+ V +L+ L+ AR+ I L + + EK + L
Sbjct: 32 QDVYDELERLVSLAREEISQLL-PQDEQLEKLIAL 65
>gnl|CDD|237029 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
Length = 556
Score = 29.4 bits (67), Expect = 0.53
Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 12/47 (25%)
Query: 13 FEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESV 59
+EE +N ++ D N V+R+ +FI K V
Sbjct: 375 WEEFVRRVNSELADKYGNLVNRV------------LSFIEKYFGGIV 409
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 29.5 bits (67), Expect = 0.56
Identities = 17/43 (39%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 2 VATDVASKGLDFEEIKHVINYD-MPDDVENYVHRIGRTGRSGK 43
V+T VA +GLD + VI Y+ +P ++ + + R GRTGR +
Sbjct: 428 VSTSVAEEGLDIPSVDLVIFYEPVPSEIRS-IQRKGRTGRQEE 469
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 29.5 bits (66), Expect = 0.64
Identities = 13/41 (31%), Positives = 23/41 (56%)
Query: 3 ATDVASKGLDFEEIKHVINYDMPDDVENYVHRIGRTGRSGK 43
AT G++ +++ VI++ +P +E Y GR GR G+
Sbjct: 736 ATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQ 776
>gnl|CDD|189387 pfam00098, zf-CCHC, Zinc knuckle. The zinc knuckle is a zinc
binding motif composed of the the following CX2CX4HX4C
where X can be any amino acid. The motifs are mostly
from retroviral gag proteins (nucleocapsid). Prototype
structure is from HIV. Also contains members involved in
eukaryotic gene regulation, such as C. elegans GLH-1.
Structure is an 18-residue zinc finger.
Length = 18
Score = 26.6 bits (60), Expect = 0.70
Identities = 8/18 (44%), Positives = 9/18 (50%)
Query: 96 RGCAYCGGLGHRITACPK 113
R C CG GH CP+
Sbjct: 1 RKCYNCGKEGHLARDCPE 18
>gnl|CDD|226569 COG4084, COG4084, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 135
Score = 27.9 bits (62), Expect = 1.0
Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 51 INKSNDESVLLDLKHLLLEAR--QR--IPPFLAELESETEKFLDLGGDERGCAYCGGL 104
+ DE++LL + +L + +R + P L + E+ +D+ + C+ GL
Sbjct: 10 ERYAEDENLLLRIMKWILTSYAYRRDVVHPLAELLNIDVEEVIDILSRKLDCSSLYGL 67
>gnl|CDD|173561 PTZ00368, PTZ00368, universal minicircle sequence binding protein
(UMSBP); Provisional.
Length = 148
Score = 27.5 bits (61), Expect = 1.6
Identities = 10/22 (45%), Positives = 10/22 (45%)
Query: 91 LGGDERGCAYCGGLGHRITACP 112
G ER C CG GH CP
Sbjct: 48 GGRGERSCYNCGKTGHLSRECP 69
Score = 26.3 bits (58), Expect = 4.8
Identities = 10/21 (47%), Positives = 10/21 (47%)
Query: 92 GGDERGCAYCGGLGHRITACP 112
G R C CGG GH CP
Sbjct: 100 GAARRACYNCGGEGHISRDCP 120
Score = 25.9 bits (57), Expect = 6.2
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 90 DLGGDERGCAYCGGLGHRITACP 112
G ++ C CG GH CP
Sbjct: 124 KRPGGDKTCYNCGQTGHLSRDCP 146
>gnl|CDD|180286 PRK05848, PRK05848, nicotinate-nucleotide pyrophosphorylase;
Provisional.
Length = 273
Score = 27.7 bits (62), Expect = 2.0
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 62 DLKHLLLEARQRIPPFLAELESETEKF 88
DLK + AR+ I PF A++E E E
Sbjct: 167 DLKEFIQHARKNI-PFTAKIEIECESL 192
>gnl|CDD|223221 COG0143, MetG, Methionyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 558
Score = 27.6 bits (62), Expect = 2.1
Identities = 16/81 (19%), Positives = 25/81 (30%), Gaps = 27/81 (33%)
Query: 11 LDFEEIKHVINYDMPDDVENYVHRIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEA 70
+E+ +N D+ + + N +R FINK D
Sbjct: 372 FSWEDFVERVNADLANKLGNLANRT------------LGFINKYFDG------------- 406
Query: 71 RQRIPPFLAELESETEKFLDL 91
+P A E E+ L L
Sbjct: 407 --VVPAAGAPDLEEDEELLAL 425
>gnl|CDD|171440 PRK12365, PRK12365, ribonucleotide-diphosphate reductase subunit
alpha; Provisional.
Length = 1046
Score = 27.6 bits (61), Expect = 2.5
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 57 ESVLLDLKHLLLEARQRIPPFLAELESETEKFLDLG 92
E + LK + L A + P ++ E S +K++D+G
Sbjct: 923 ERIPDHLKKIFLTAFEIEPEWIIECASRRQKWIDMG 958
>gnl|CDD|130919 TIGR01860, VNFD, nitrogenase vanadium-iron protein, alpha chain.
This model represents the alpha chain of the
vanadium-containing component of the vanadium-iron
nitrogenase compound I. The complex also includes a
second alpha chain, two beta chains and two delta
chains. Compount I interacts with compound II also known
as the iron-protein which transfers electrons to
compound I where the catalysis occurs [Central
intermediary metabolism, Nitrogen fixation].
Length = 461
Score = 27.2 bits (60), Expect = 3.0
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 13/49 (26%)
Query: 67 LLEARQRIPP-----FLAELESETEKFLDLGG--------DERGCAYCG 102
LLE + IP ++ E +T +FL L ERGC+YCG
Sbjct: 4 LLECDEDIPERQKHVYIKEPGEDTTEFLPLSNIATIPGSLSERGCSYCG 52
>gnl|CDD|215168 PLN02299, PLN02299, 1-aminocyclopropane-1-carboxylate oxidase.
Length = 321
Score = 27.0 bits (60), Expect = 3.7
Identities = 26/98 (26%), Positives = 39/98 (39%), Gaps = 19/98 (19%)
Query: 13 FEEIKHVINYDMPDDVENYVHRIGRTGRS-------GKTGL------------ATTFINK 53
FE + H I++++ D+VE + GL +TF +
Sbjct: 37 FELVNHGISHELMDEVEKMTKEHYKKCMEQRFKEMVASKGLEGVQTEVEDLDWESTFFLR 96
Query: 54 SNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLDL 91
ES L D+ L E R+ + F ELE E+ LDL
Sbjct: 97 HLPESNLADIPDLDDEYRKVMKDFALELEKLAEELLDL 134
>gnl|CDD|165553 PHA03296, PHA03296, envelope glycoprotein H; Provisional.
Length = 814
Score = 26.9 bits (59), Expect = 4.2
Identities = 9/29 (31%), Positives = 11/29 (37%)
Query: 76 PFLAELESETEKFLDLGGDERGCAYCGGL 104
PF A + L+L G C CG
Sbjct: 674 PFAARTAKIEDGHLNLHGAAIACILCGHA 702
>gnl|CDD|235941 PRK07118, PRK07118, ferredoxin; Validated.
Length = 280
Score = 26.4 bits (59), Expect = 4.8
Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 91 LGGDERGCAY-CGGLGHRITACP 112
L G +GC+Y C GLG + ACP
Sbjct: 130 LFGGPKGCSYGCLGLGSCVAACP 152
>gnl|CDD|99866 cd06113, citrate_synt_like_1_2, Citrate synthase (CS) catalyzes the
condensation of acetyl coenzyme A (AcCoA) and
oxalacetate (OAA) to form citrate and coenzyme A (CoA),
the first step in the oxidative citric acid cycle (TCA
or Krebs cycle). Peroxisomal CS is involved in the
glyoxylate cycle. This group also includes CS proteins
which functions as a 2-methylcitrate synthase (2MCS).
2MCS catalyzes the condensation of propionyl-CoA (PrCoA)
and OAA to form 2-methylcitrate and CoA during
propionate metabolism. This group contains proteins
which functions exclusively as either a CS or a 2MCS, as
well as those with relaxed specificity which have dual
functions as both a CS and a 2MCS. The overall CS
reaction is thought to proceed through three partial
reactions and involves both closed and open
conformational forms of the enzyme: a) a carbanion or
equivalent is generated from AcCoA by base abstraction
of a proton, b) nucleophilic attack of this carbanion on
OAA to generate citryl-CoA, and c) hydrolysis of
citryl-CoA to produce citrate and CoA. CSs are found in
two structural types: type I (homodimeric) and type II
CSs (homohexameric). Type II CSs are unique to
gram-negative bacteria. Type I CSs are found in eukarya,
gram-positive bacteria, archaea, and in some
gram-negative bacteria. Type I CS is active as a
homodimer, both subunits participating in the active
site. Type II CS is a hexamer of identical subunits
(approximated as a trimer of dimers). Some type II CSs
are strongly and specifically inhibited by NADH through
an allosteric mechanism. This subgroup includes both
gram-positive and gram-negative bacteria.
Length = 406
Score = 26.5 bits (59), Expect = 4.9
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 13 FEEIK-HVINYDMPDDVENYVHRIGRTGRSGKTGL 46
E+IK +V ++ D+V Y+ +I K+GL
Sbjct: 255 LEDIKENVKDWTDEDEVRAYLRKILNKEAFDKSGL 289
>gnl|CDD|219368 pfam07299, FBP, Fibronectin-binding protein (FBP). This family
consists of several bacterial fibronectin-binding
proteins which are thought to be involved in virulence
in Listeria species.
Length = 208
Score = 26.1 bits (58), Expect = 6.5
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 55 NDESVLLDLKHLLLEARQRIPPFLAELESETEKFLD 90
ND +V+ +K L +E +I EL E ++ LD
Sbjct: 25 NDRNVIKAVKALAIE---KILDLFPELSPEQKELLD 57
>gnl|CDD|173050 PRK14586, PRK14586, tRNA pseudouridine synthase ACD; Provisional.
Length = 245
Score = 25.9 bits (57), Expect = 6.9
Identities = 10/35 (28%), Positives = 23/35 (65%), Gaps = 2/35 (5%)
Query: 1 MVATDVASKGLDFEEIKHVINYDMPDDVENYVHRI 35
++A + + + E+IK+ +N ++PDD+ YV ++
Sbjct: 61 VIAFNCPNDRMTEEDIKNAMNANLPDDI--YVKKV 93
>gnl|CDD|217266 pfam02881, SRP54_N, SRP54-type protein, helical bundle domain.
Length = 77
Score = 24.9 bits (55), Expect = 7.0
Identities = 8/37 (21%), Positives = 17/37 (45%)
Query: 34 RIGRTGRSGKTGLATTFINKSNDESVLLDLKHLLLEA 70
+ +T + F+ + + +L +L+ LLEA
Sbjct: 4 GLSKTRSKLGGKIKDLFLGEKKIDELLEELEEALLEA 40
>gnl|CDD|180763 PRK06937, PRK06937, type III secretion system protein; Reviewed.
Length = 204
Score = 25.8 bits (57), Expect = 7.9
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 53 KSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLDLG 92
++ D LL + L+ ARQR AE + E+ LG
Sbjct: 22 RAEDYQSLLSAEELVEAARQRAEEIEAEAQEVYEQQKQLG 61
>gnl|CDD|218229 pfam04722, Ssu72, Ssu72-like protein. The highly conserved and
essential protein Ssu72 has intrinsic phosphatase
activity and plays an essential role in the
transcription cycle. Ssu72 was originally identified in
a yeast genetic screen as enhancer of a defect caused by
a mutation in the transcription initiation factor TFIIB.
It binds to TFIIB and is also involved in mRNA
elongation. Ssu72 is further involved in both poly(A)
dependent and independent termination. It is a subunit
of the yeast cleavage and polyadenylation factor (CPF),
which is part of the machinery for mRNA 3'-end
formation. Ssu72 is also essential for transcription
termination of snRNAs.
Length = 193
Score = 25.6 bits (57), Expect = 8.1
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 2 VATDVASKGLDFEEIKHVINYDMPDDVEN 30
V D+ ++G + HVIN D+ D+ E
Sbjct: 116 VVEDLMNRGSSLNQPVHVINVDIKDNHEE 144
>gnl|CDD|130658 TIGR01597, PYST-B, Plasmodium yoelii subtelomeric family PYST-B.
This model represents a paralogous family of Plasmodium
yoelii genes preferentially located in the subtelomeric
regions of the chromosomes. There are no obvious
homologs to these genes in any other organism.
Length = 255
Score = 26.0 bits (57), Expect = 8.1
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 49 TFINKSNDESVLLDLKHLLLEARQRIPPFLAELESETEKFLD 90
+ I K + + L DL ++ + ++ I ELE E +K LD
Sbjct: 90 SHIKKHKERNTLPDLNNVDKKTKKLINKLQKELE-ELKKELD 130
>gnl|CDD|238936 cd01977, Nitrogenase_VFe_alpha, Nitrogenase_VFe_alpha -like:
Nitrogenase VFe protein, alpha subunit like. This group
contains proteins similar to the alpha subunits of, the
VFe protein of the vanadium-dependent (V-) nitrogenase
and the FeFe protein of the iron only (Fe-) nitrogenase
Nitrogenase catalyzes the ATP-dependent reduction of
dinitrogen (N2) to ammonia. In addition to V- and Fe-
nitrogenases there is a molybdenum (Mo)-dependent
nitrogenase which is the most widespread and best
characterized of these systems. These systems consist
of component 1 (VFe protein, FeFe protein or, MoFe
protein respectively) and, component 2 (Fe protein).
MoFe is an alpha2beta2 tetramer, V-and Fe- nitrogenases
are alpha2beta2delta2 hexamers. The alpha and beta
subunits of VFe and FeFe are similar to the alpha and
beta subunits of MoFe. For MoFe each alphabeta pair
contains one P-cluster (at the alphabeta interface) and,
one molecule of iron molybdenum cofactor (FeMoco)
contained within the alpha subunit. The Fe protein which
has a practically identical structure in all three
systems, it contains a single [4Fe-4S] cluster.
Electrons are transferred from the [4Fe-4S] cluster of
the Fe protein to the P-cluster of the MoFe and in turn
to FeMoCo, the site of substrate reduction. The
V-nitrogenase requires an iron-vanadium cofactor
(FeVco), the iron only-nitrogenase an iron only cofactor
(FeFeco). These cofactors are analogous to the FeMoco.
The V-nitrogenase has P clusters identical to those of
MoFe. In addition to N2, nitrogenase also catalyzes the
reduction of a variety of other substrates such as
acetylene The V-nitrogenase differs from the
Mo-nitrogenase in that it produces free hydrazine, as a
minor product during dinitrogen reduction and, ethane
as a minor product during acetylene reduction.
Length = 415
Score = 25.9 bits (57), Expect = 8.8
Identities = 8/8 (100%), Positives = 8/8 (100%)
Query: 95 ERGCAYCG 102
ERGCAYCG
Sbjct: 6 ERGCAYCG 13
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 26.1 bits (58), Expect = 9.2
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 10 GLDFEEIKHVINYDMPDDVENYVHRIGRTGR 40
G+D +I VI P V ++ RIGR G
Sbjct: 317 GIDIGDIDLVIQLGSPKSVNRFLQRIGRAGH 347
>gnl|CDD|199908 cd10719, DnaJ_zf, Zinc finger domain of DnaJ and HSP40.
Central/middle or CxxCxGxG-motif containing domain of
DnaJ/Hsp40 (heat shock protein 40). DnaJ proteins are
highly conserved and play crucial roles in protein
translation, folding, unfolding, translocation, and
degradation. They act primarily by stimulating the
ATPase activity of Hsp70s, an important chaperonin
family. Hsp40 proteins are characterized by the presence
of an N-terminal J domain, which mediates the
interaction with Hsp70. This central domain contains
four repeats of a CxxCxGxG motif and binds to two Zinc
ions. It has been implicated in substrate binding.
Length = 65
Score = 24.5 bits (54), Expect = 9.4
Identities = 9/17 (52%), Positives = 9/17 (52%), Gaps = 1/17 (5%)
Query: 98 CAYCGGLGHRIT-ACPK 113
C CGG G I CPK
Sbjct: 44 CPTCGGTGKIIKDPCPK 60
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.136 0.392
Gapped
Lambda K H
0.267 0.0806 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,937,410
Number of extensions: 616279
Number of successful extensions: 749
Number of sequences better than 10.0: 1
Number of HSP's gapped: 744
Number of HSP's successfully gapped: 64
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
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: 54 (24.4 bits)