RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy437
(184 letters)
>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 = 99.8 bits (249), Expect = 6e-25
Identities = 33/88 (37%), Positives = 57/88 (64%), Gaps = 1/88 (1%)
Query: 1 FISSFNRANLKYEILPKK-NVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI 59
F +SF+R NL YE+ K +L++++ I+ ++ G+SGI+YC +RK+ + V A+L I
Sbjct: 192 FCTSFDRPNLYYEVRRKTPKILEDLLRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGI 251
Query: 60 NAISYHAGLADKLRNEVQMKWISNKVHV 87
A +YHAGL R++V K+ +++ V
Sbjct: 252 AAGAYHAGLEISARDDVHHKFQRDEIQV 279
>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 = 87.1 bits (216), Expect = 2e-20
Identities = 35/87 (40%), Positives = 60/87 (68%), Gaps = 1/87 (1%)
Query: 1 FISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERIN 60
FI+SF+R NL++ ++ K N K ++ +K K+ GQSGI+Y +RK+ + +A L + I+
Sbjct: 192 FITSFDRPNLRFSVVKKNNKQKFLLDYLK-KHRGQSGIIYASSRKKVEELAERLESQGIS 250
Query: 61 AISYHAGLADKLRNEVQMKWISNKVHV 87
A++YHAGL++K+R E Q ++ + V V
Sbjct: 251 ALAYHAGLSNKVRAENQEDFLYDDVKV 277
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 86.6 bits (215), Expect = 4e-20
Identities = 30/88 (34%), Positives = 53/88 (60%), Gaps = 1/88 (1%)
Query: 1 FISSFNRANLKYEILPKKNVLKEVISLIKAK-YSGQSGIVYCLTRKECDSVAAALAQERI 59
F SF+R NL +++ K ++ L +SGI+YCLTRK+ + +A L + I
Sbjct: 196 FRGSFDRPNLALKVVEKGEPSDQLAFLATVLPQLSKSGIIYCLTRKKVEELAEWLRKNGI 255
Query: 60 NAISYHAGLADKLRNEVQMKWISNKVHV 87
+A +YHAGL+++ R VQ ++++++ V
Sbjct: 256 SAGAYHAGLSNEERERVQQAFLNDEIKV 283
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 63.6 bits (155), Expect = 4e-12
Identities = 29/76 (38%), Positives = 50/76 (65%), Gaps = 1/76 (1%)
Query: 2 ISSFNRANLKYEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINA 61
ISSF+R N++Y ++ K L +++ ++ + G+SGI+YC +R + + AA L I+A
Sbjct: 205 ISSFDRPNIRYTLVEKFKPLDQLMRYVQEQ-RGKSGIIYCNSRAKVEDTAARLQSRGISA 263
Query: 62 ISYHAGLADKLRNEVQ 77
+YHAGL + +R +VQ
Sbjct: 264 AAYHAGLDNDVRADVQ 279
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 60.7 bits (147), Expect = 4e-11
Identities = 31/88 (35%), Positives = 50/88 (56%), Gaps = 1/88 (1%)
Query: 1 FISSFNRANLKYEILPK-KNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERI 59
F SFNR NL Y ++PK K L+++ IK + + GI+YCL+R +C+ VA L +
Sbjct: 646 FRQSFNRPNLWYSVVPKTKKCLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGH 705
Query: 60 NAISYHAGLADKLRNEVQMKWISNKVHV 87
A YH + R VQ +W +++++
Sbjct: 706 KAAFYHGSMDPAQRAFVQKQWSKDEINI 733
>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 = 46.1 bits (110), Expect = 7e-07
Identities = 18/81 (22%), Positives = 39/81 (48%), Gaps = 2/81 (2%)
Query: 9 NLKYEILPKKNV-LKEVISLIK-AKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHA 66
+K +LP ++ L+ ++ L+K G +++C ++K D +A L + I + H
Sbjct: 1 PIKQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHG 60
Query: 67 GLADKLRNEVQMKWISNKVHV 87
+ + R EV + ++ V
Sbjct: 61 DGSQEEREEVLKDFREGEIVV 81
Score = 27.2 bits (61), Expect = 3.2
Identities = 12/78 (15%), Positives = 29/78 (37%), Gaps = 4/78 (5%)
Query: 62 ISYHAGLADKLRNEVQMKWISNKVHVGHWTVV----SKECDSVAAALAQERINAISYHAG 117
I + + + E ++ + + G ++ K D +A L + I + H
Sbjct: 2 IKQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGD 61
Query: 118 LADKLRNEVQMKWISNKV 135
+ + R EV + ++
Sbjct: 62 GSQEEREEVLKDFREGEI 79
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 39.4 bits (93), Expect = 6e-04
Identities = 21/65 (32%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 12 YEILPKKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADK 71
YE+ P + L + L+ + +S +V+C T+KEC VA AL + +A++ H L +
Sbjct: 222 YEVSPDER-LPALQRLLL-HHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDLEQR 279
Query: 72 LRNEV 76
R++V
Sbjct: 280 DRDQV 284
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 37.1 bits (86), Expect = 0.004
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 29 KAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHV 87
Y GQ+ IV+ +R+ C +A AL + + A YHAGL K R V+ + + ++
Sbjct: 436 SKGYRGQT-IVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAA 493
Score = 27.8 bits (62), Expect = 4.2
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 73 RNEVQMKWISNKVHVGH---WTVVSKECDSVAAALAQERINAISYHAGLADKLRNEVQM 128
+ E + S+K + G +T + C +A AL + + A YHAGL K R V+
Sbjct: 428 KREFSTE--SSKGYRGQTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVER 484
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 27.6 bits (62), Expect = 1.3
Identities = 11/40 (27%), Positives = 20/40 (50%)
Query: 48 DSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHV 87
+ +A L + I H GL+ + R E+ K+ + K+ V
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKV 40
Score = 25.6 bits (57), Expect = 5.5
Identities = 10/40 (25%), Positives = 20/40 (50%)
Query: 98 DSVAAALAQERINAISYHAGLADKLRNEVQMKWISNKVHL 137
+ +A L + I H GL+ + R E+ K+ + K+ +
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKV 40
>gnl|CDD|224016 COG1091, RfbD, dTDP-4-dehydrorhamnose reductase [Cell envelope
biogenesis, outer membrane].
Length = 281
Score = 28.4 bits (64), Expect = 2.1
Identities = 11/46 (23%), Positives = 16/46 (34%), Gaps = 9/46 (19%)
Query: 30 AKYSGQSGIVYCLTRKECD-----SVAAALAQER----INAISYHA 66
+ V R E D +V + + R INA +Y A
Sbjct: 17 RRALPGEFEVIATDRAELDITDPDAVLEVIRETRPDVVINAAAYTA 62
>gnl|CDD|149901 pfam08979, DUF1894, Domain of unknown function (DUF1894).
Members of this family have an important role in
methanogenesis. They assume an alpha-beta globular
structure consisting of six beta-strands and three
alpha-helices forming the secondary structural
topological arrangement of
alpha1-beta1-alpha2-beta2-beta3-beta4-beta5-beta6-
alpha3.
Length = 89
Score = 27.2 bits (61), Expect = 2.1
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 9 NLKYEILPKKNVLKEVISLIKAKY 32
N YEIL K KE I+ Y
Sbjct: 6 NYNYEILLKGATFKECEEYIRKNY 29
>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 = 28.2 bits (63), Expect = 2.4
Identities = 10/60 (16%), Positives = 24/60 (40%), Gaps = 4/60 (6%)
Query: 17 KKNVLKEVISLIKAKYSGQSGIVYCLTRKECDSVAAALAQERINAISYHAGLADKLRNEV 76
K +L +++ IV+ T++ + +A +L + + H L + R+
Sbjct: 260 KLELLLKLLKDEDEGRV----IVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRA 315
>gnl|CDD|219916 pfam08580, KAR9, Yeast cortical protein KAR9. The KAR9 protein in
Saccharomyces cerevisiae is a cytoskeletal protein
required for karyogamy, correct positioning of the
mitotic spindle and for orientation of cytoplasmic
microtubules. KAR9 localises at the shmoo tip in mating
cells and at the tip of the growing bud in anaphase.
Length = 626
Score = 27.1 bits (60), Expect = 6.2
Identities = 16/88 (18%), Positives = 31/88 (35%), Gaps = 16/88 (18%)
Query: 44 RKECDSVAAALAQERIN-AISYHAGLADKLRNEVQMKWISNKVHVGHWTVVSKECDSVAA 102
+K DSV +L + + N H + ++++ K SK
Sbjct: 282 QKMLDSVERSLQKLQNNKTTGMHLDNRTTMTDQIESK--------------SKTISKTFT 327
Query: 103 ALAQERINAISYHAGLADKLRNEVQMKW 130
+ + +I G+A + E+ KW
Sbjct: 328 LIYKALEESILDK-GVASRTNRELAPKW 354
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
0.320 0.134 0.404
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,397,766
Number of extensions: 846418
Number of successful extensions: 700
Number of sequences better than 10.0: 1
Number of HSP's gapped: 695
Number of HSP's successfully gapped: 26
Length of query: 184
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 93
Effective length of database: 6,901,388
Effective search space: 641829084
Effective search space used: 641829084
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: 56 (25.3 bits)