RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7691
(165 letters)
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 112 bits (283), Expect = 9e-30
Identities = 50/94 (53%), Positives = 62/94 (65%), Gaps = 1/94 (1%)
Query: 3 NHAKTQERAARLSESEVEAFRQKKEIT-VKGNNIPCPTQELTEGCFPNAVLQHLKGQGFE 61
N K + LS EV+ R++KEIT + G N+P P FP+ +L+ LK GF
Sbjct: 92 NFYKEHPEVSALSSKEVDEIRKEKEITIIAGENVPKPVVSFEYTSFPDYILKSLKNAGFT 151
Query: 62 EPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVI 95
EPT IQ QGWPIALSGRDM+GIA+TGSGKTLA +
Sbjct: 152 EPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFL 185
Score = 105 bits (264), Expect = 4e-27
Identities = 38/68 (55%), Positives = 51/68 (75%)
Query: 94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
VINFD+PN EDY+HRIGRTGR + G +YTF TP+ + A++L+ VL EA QP+PP+L+
Sbjct: 449 VINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPDKYRLARDLVKVLREAKQPVPPELE 508
Query: 154 DLANSNPN 161
L+N N
Sbjct: 509 KLSNERSN 516
>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins
involved in ATP-dependent RNA unwinding, needed in a
variety of cellular processes including splicing,
ribosome biogenesis and RNA degradation. The name
derives from the sequence of the Walker B motif (motif
II). This domain contains the ATP- binding region.
Length = 203
Score = 79.5 bits (197), Expect = 4e-19
Identities = 25/43 (58%), Positives = 32/43 (74%)
Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
+L+ + GFE+PT IQA+ P LSGRD++G AQTGSGKT A
Sbjct: 10 LLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAA 52
>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 = 76.8 bits (189), Expect = 6e-17
Identities = 26/43 (60%), Positives = 32/43 (74%)
Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
+LQ LK GFEEPT IQ P+ L+GRD++G AQTG+GKT A
Sbjct: 40 LLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAA 82
Score = 61.0 bits (148), Expect = 2e-11
Identities = 24/63 (38%), Positives = 29/63 (46%)
Query: 94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQLQ 153
VIN+D P EDY+HRIGRTGR G A +F T + + I E P L
Sbjct: 345 VINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLP 404
Query: 154 DLA 156
Sbjct: 405 LDE 407
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 75.6 bits (186), Expect = 1e-16
Identities = 36/81 (44%), Positives = 47/81 (58%)
Query: 13 RLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWP 72
LS S+ E R+K EI VKG +P P + P +L +L+ G+E PT IQ Q P
Sbjct: 94 GLSSSQAELLRRKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIP 153
Query: 73 IALSGRDMVGIAQTGSGKTLA 93
ALSGR ++ A TGSGKT +
Sbjct: 154 AALSGRSLLVSADTGSGKTAS 174
Score = 61.7 bits (150), Expect = 9e-12
Identities = 31/88 (35%), Positives = 44/88 (50%), Gaps = 11/88 (12%)
Query: 77 GRDMVGIAQTGSGKTLAVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKE 136
G D++ + Q VI FD PN+ ++YIH+IGR R GTA F + E
Sbjct: 431 GVDLLRVRQ--------VIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNEEDRNLFPE 482
Query: 137 LIAVLTEASQPIPPQLQDLANSNPNSKG 164
L+A+L + IP ++LANS G
Sbjct: 483 LVALLKSSGAAIP---RELANSRYLGSG 507
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 61.0 bits (149), Expect = 1e-11
Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 5/72 (6%)
Query: 93 AVINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVLTEASQPIPPQL 152
AVIN++ E ++HRIGRTGR S G A + P ++A + E
Sbjct: 313 AVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPEEMQRANAI-----EDYLGRKLNW 367
Query: 153 QDLANSNPNSKG 164
+ L + +P S
Sbjct: 368 EPLPSLSPLSGV 379
Score = 56.0 bits (136), Expect = 7e-10
Identities = 23/46 (50%), Positives = 31/46 (67%)
Query: 48 PNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
P A+L +L G+ E T IQAQ P L+G+D++ A+TGSGKT A
Sbjct: 12 PPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAA 57
>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 = 57.2 bits (139), Expect = 3e-11
Identities = 16/32 (50%), Positives = 18/32 (56%)
Query: 94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTF 125
VIN+D P S Y+ RIGR GR GTA
Sbjct: 100 VINYDLPWSPSSYLQRIGRAGRAGQKGTAILL 131
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 58.1 bits (141), Expect = 1e-10
Identities = 22/43 (51%), Positives = 31/43 (72%)
Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
V++ L+ +GF T IQA P+ L+GRD+ G AQTG+GKT+A
Sbjct: 19 VVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMA 61
Score = 52.3 bits (126), Expect = 2e-08
Identities = 17/32 (53%), Positives = 23/32 (71%)
Query: 94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTF 125
V N+D P+ EDY+HRIGRTGR +SG + +
Sbjct: 327 VFNYDLPDDCEDYVHRIGRTGRAGASGHSISL 358
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 54.2 bits (131), Expect = 8e-10
Identities = 19/30 (63%), Positives = 22/30 (73%)
Query: 64 TAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
T IQAQ P LSG+D++ A TGSGKTLA
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLA 30
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 54.9 bits (133), Expect = 2e-09
Identities = 23/42 (54%), Positives = 31/42 (73%)
Query: 52 LQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
L+ L+ +G+ PTAIQA+ P AL GRD++G A TG+GKT A
Sbjct: 13 LEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAA 54
Score = 51.5 bits (124), Expect = 3e-08
Identities = 19/29 (65%), Positives = 22/29 (75%)
Query: 94 VINFDYPNSSEDYIHRIGRTGRCASSGTA 122
VINFD P S++ Y+HRIGRTGR GTA
Sbjct: 317 VINFDMPRSADTYLHRIGRTGRAGRKGTA 345
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 54.4 bits (131), Expect = 2e-09
Identities = 24/44 (54%), Positives = 31/44 (70%)
Query: 94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKEL 137
VIN+D P S E+YIHRIGR+GR G A F TP++ +Q KE+
Sbjct: 339 VINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPDDIEQLKEI 382
Score = 46.7 bits (111), Expect = 1e-06
Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 13/79 (16%)
Query: 33 NNIPCPTQELTEGCFPNAVLQH--LKG---QGFEEPTAIQAQGWPIALSGRDMVGIAQTG 87
I E+ + F L L+G GFE+P+AIQ +G L G D +G AQ+G
Sbjct: 17 GTIESNYDEIVD-SFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSG 75
Query: 88 SGKT-------LAVINFDY 99
+GKT L +I++D
Sbjct: 76 TGKTATFVIAALQLIDYDL 94
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 54.1 bits (130), Expect = 4e-09
Identities = 23/43 (53%), Positives = 33/43 (76%)
Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
+L+ L G+E+P+ IQA+ P L+GRD++G+AQTGSGKT A
Sbjct: 17 ILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAA 59
Score = 46.4 bits (110), Expect = 2e-06
Identities = 18/32 (56%), Positives = 22/32 (68%)
Query: 94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTF 125
V+N+D P SE Y+HRIGRTGR +G A F
Sbjct: 317 VVNYDIPMDSESYVHRIGRTGRAGRAGRALLF 348
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 53.0 bits (128), Expect = 1e-08
Identities = 21/67 (31%), Positives = 29/67 (43%), Gaps = 7/67 (10%)
Query: 49 NAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA----VIN---FDYPN 101
+ ++ + F T Q P SG +++ IA TGSGKT A VIN
Sbjct: 9 DPRVREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKG 68
Query: 102 SSEDYIH 108
ED I+
Sbjct: 69 KLEDGIY 75
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 51.0 bits (122), Expect = 2e-08
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 55 LKGQGFEEPTAIQAQGWPIALSG-RDMVGIAQTGSGKTLAVINF 97
++ GFE Q + LSG RD++ A TGSGKTLA +
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLP 44
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 51.5 bits (123), Expect = 3e-08
Identities = 24/46 (52%), Positives = 30/46 (65%)
Query: 50 AVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAVI 95
A+L L+ GF T IQA P+AL G D+ G AQTG+GKTLA +
Sbjct: 19 ALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFL 64
Score = 43.4 bits (102), Expect = 2e-05
Identities = 17/32 (53%), Positives = 21/32 (65%)
Query: 94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTF 125
V N+D P +EDY+HRIGRT R G A +F
Sbjct: 329 VYNYDLPFDAEDYVHRIGRTARLGEEGDAISF 360
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 51.3 bits (123), Expect = 3e-08
Identities = 21/41 (51%), Positives = 28/41 (68%)
Query: 51 VLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKT 91
+L+ + QG+ EPT IQ Q P L GRD++ AQTG+GKT
Sbjct: 12 ILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKT 52
Score = 51.0 bits (122), Expect = 5e-08
Identities = 18/29 (62%), Positives = 24/29 (82%)
Query: 94 VINFDYPNSSEDYIHRIGRTGRCASSGTA 122
V+N++ PN EDY+HRIGRTGR A++G A
Sbjct: 317 VVNYELPNVPEDYVHRIGRTGRAAATGEA 345
>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 = 46.7 bits (112), Expect = 8e-08
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 94 VINFDYPNSSEDYIHRIGRTGR 115
VIN+D P + YI RIGR GR
Sbjct: 55 VINYDLPWNPASYIQRIGRAGR 76
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 49.9 bits (119), Expect = 1e-07
Identities = 21/48 (43%), Positives = 30/48 (62%)
Query: 94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAVL 141
VINF P +DY+HRIGRTGR +SG + +F ++ Q E+ +L
Sbjct: 407 VINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGEDDAFQLPEIEELL 454
Score = 39.1 bits (91), Expect = 5e-04
Identities = 19/35 (54%), Positives = 22/35 (62%)
Query: 59 GFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
GF T IQAQ L+G D +G AQTG+GKT A
Sbjct: 106 GFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAA 140
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 44.1 bits (105), Expect = 1e-06
Identities = 13/22 (59%), Positives = 14/22 (63%)
Query: 94 VINFDYPNSSEDYIHRIGRTGR 115
VI +D P S YI RIGR GR
Sbjct: 59 VIIYDLPWSPASYIQRIGRAGR 80
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 34.6 bits (80), Expect = 0.007
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 78 RDMVGIAQTGSGKTLAVINF 97
RD++ A TGSGKTLA +
Sbjct: 1 RDVLLAAPTGSGKTLAALLP 20
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 35.6 bits (83), Expect = 0.008
Identities = 18/39 (46%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 56 KGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAV 94
+G+ P Q + W AL GR + IA TGSGKTLA
Sbjct: 8 AARGWT-PRPFQLEMWAAALEGRSGLLIAPTGSGKTLAG 45
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 34.6 bits (80), Expect = 0.018
Identities = 15/45 (33%), Positives = 22/45 (48%)
Query: 94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELI 138
VI++D P S E Y GR GR A ++P + + + LI
Sbjct: 302 VIHYDLPGSIESYYQETGRAGRDGLPAEAILLYSPEDIRWQRYLI 346
Score = 28.0 bits (63), Expect = 2.9
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 49 NAVLQHLKG-QGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTL 92
VL+ + G F Q + LSG+D + + TG GK+L
Sbjct: 6 QQVLKQVFGYASFRPG---QQEIIDALLSGKDTLVVMPTGGGKSL 47
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 34.7 bits (80), Expect = 0.019
Identities = 18/47 (38%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 48 PNAVLQHLKGQGFEE--PTAIQAQGWPIALSGRDMVGIAQTGSGKTL 92
+ VL+ LKG G +E Q LS +++ A TGSGKTL
Sbjct: 17 DDRVLEILKGDGIDELFN-PQQEAVEKGLLSDENVLISAPTGSGKTL 62
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 33.5 bits (77), Expect = 0.043
Identities = 13/39 (33%), Positives = 18/39 (46%)
Query: 55 LKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
L G E + Q + GR++V TGSGKT +
Sbjct: 63 LVKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTES 101
>gnl|CDD|165387 PHA03108, PHA03108, poly(A) polymerase small subunit; Provisional.
Length = 300
Score = 31.6 bits (72), Expect = 0.16
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 94 VINFDYPNSSEDYIH 108
V+NFDYPN D+ H
Sbjct: 248 VLNFDYPNQEYDFFH 262
>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative
DEAH-box helicase. A conserved gene neighborhood
widely spread in the Actinobacteria contains this
uncharacterized DEAH-box family helicase encoded
convergently towards an operon of genes for protein
homologous to type II secretion and pilus formation
proteins. The context suggests that this helicase may
play a role in conjugal transfer of DNA.
Length = 742
Score = 31.2 bits (71), Expect = 0.21
Identities = 16/47 (34%), Positives = 23/47 (48%)
Query: 47 FPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLA 93
V+ L+ G P QA+ +A +GR +V T SGK+LA
Sbjct: 21 AHPDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLA 67
>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 = 31.2 bits (71), Expect = 0.23
Identities = 14/47 (29%), Positives = 20/47 (42%)
Query: 94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTPNNGKQAKELIAV 140
VI++D P + E Y GR GR A ++P + K I
Sbjct: 296 VIHYDMPGNLESYYQEAGRAGRDGLPAEAILLYSPADIALLKRRIEQ 342
>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 = 30.5 bits (69), Expect = 0.36
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTP 128
VI++ P S E Y GR GR + F+ P
Sbjct: 298 VIHYSLPKSMESYYQESGRAGRDGLPSECHLFYAP 332
>gnl|CDD|236330 PRK08665, PRK08665, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 752
Score = 29.1 bits (66), Expect = 1.3
Identities = 20/80 (25%), Positives = 29/80 (36%), Gaps = 6/80 (7%)
Query: 45 GCFPNAVLQHLKGQGFEEPTAIQAQGWPIALSGRD--MVGIA---QTGSGKTLAVINFDY 99
G VL K + EE A + + R G QTG G +N D
Sbjct: 564 GSRDEQVLSTGKKEKKEEEPAAAVEPKKLEPRPRPKVTKGFTEKVQTGCGPLYVTVNEDE 623
Query: 100 PNSSEDYIHRIGRTGRCASS 119
E + +G+ G CA++
Sbjct: 624 GGPFEVFTT-LGKAGGCAAA 642
>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional.
Length = 737
Score = 28.8 bits (65), Expect = 1.4
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 7/49 (14%)
Query: 48 PNAVLQHLKGQGFEEPTAIQA----QGWPIALSGRDMVGIAQTGSGKTL 92
P V++ + +G EE QA G L G++++ T SGKTL
Sbjct: 9 PEGVIEFYEAEGIEELYPPQAEAVEAG---LLDGKNLLAAIPTASGKTL 54
>gnl|CDD|178584 PLN03007, PLN03007, UDP-glucosyltransferase family protein.
Length = 482
Score = 28.7 bits (64), Expect = 1.7
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 12 ARLSESEVEAFRQKK---EITVKGNNIPCPTQELTEGC 46
A++ E +EAF+ EI ++ N PC L EGC
Sbjct: 45 AKIFEKPIEAFKNLNPGLEIDIQIFNFPCVELGLPEGC 82
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 28.6 bits (64), Expect = 1.7
Identities = 19/75 (25%), Positives = 30/75 (40%), Gaps = 5/75 (6%)
Query: 23 RQKKEIT----VKGNNIPCPTQELTEGCFPNAVLQHLKGQGFEEPTAIQAQGWPIAL-SG 77
+ E+T V + E P + LK +G EE +Q L G
Sbjct: 173 LEDPELTRYDEVTAETDEVERVPVDELDIPEKFKRMLKREGIEELLPVQVLAVEAGLLEG 232
Query: 78 RDMVGIAQTGSGKTL 92
+++ ++ T SGKTL
Sbjct: 233 ENLLVVSATASGKTL 247
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 27.8 bits (62), Expect = 3.2
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 94 VINFDYPNSSEDYIHRIGRTGRCASSGTAYTFFTP 128
V++FD P + E Y GR GR A F+ P
Sbjct: 308 VVHFDIPRNIESYYQETGRAGRDGLPAEAMLFYDP 342
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 27.7 bits (62), Expect = 3.4
Identities = 15/43 (34%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 94 VINFDYPNSSE-DYIHRIGRTGRCASSGTAYTFFTPNNGKQAK 135
VI ++ P SE I R GRTGR G T +A
Sbjct: 447 VIFYE-PVPSEIRSIQRKGRTGR-KRKGRVVVLVTEGTRDEAY 487
>gnl|CDD|235708 PRK06131, PRK06131, dihydroxy-acid dehydratase; Validated.
Length = 571
Score = 27.5 bits (62), Expect = 3.6
Identities = 9/24 (37%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 66 IQAQGWP-IALSGRDMVGIAQTGS 88
++ QG+P GR ++GI T S
Sbjct: 25 MKNQGYPDELFDGRPIIGICNTWS 48
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 27.5 bits (62), Expect = 3.9
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 60 FEEPTAIQAQGWPIALSGRDMVGIAQTGSGKTLAV 94
F T Q P+ G++++ + TGSGKTLA
Sbjct: 30 FGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAA 64
>gnl|CDD|237272 PRK13017, PRK13017, dihydroxy-acid dehydratase; Provisional.
Length = 596
Score = 27.2 bits (61), Expect = 4.2
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 76 SGRDMVGIAQTGS 88
SG+ ++GIAQTGS
Sbjct: 45 SGKPIIGIAQTGS 57
>gnl|CDD|216796 pfam01935, DUF87, Domain of unknown function DUF87. The function
of this prokaryotic domain is unknown. It contains
several conserved aspartates and histidines that could
be metal ligands.
Length = 218
Score = 26.9 bits (60), Expect = 4.8
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 7/37 (18%)
Query: 66 IQAQGWPIALSGRDMVG-----IAQTGSGK--TLAVI 95
+ P+ L +V + TGSGK T+AV+
Sbjct: 7 LDGSEVPVYLDLNKLVSRHFAILGSTGSGKSNTVAVL 43
>gnl|CDD|133100 cd06242, M14-like_1_5, Peptidase M14-like domain; uncharacterized
subgroup. Peptidase M14-like domain of a functionally
uncharacterized subgroup of the M14 family of
metallocarboxypeptidases (MCPs). The M14 family are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. Two major subfamilies of the M14 family,
defined based on sequence and structural homology, are
the A/B and N/E subfamilies. Enzymes belonging to the
A/B subfamily are normally synthesized as inactive
precursors containing preceding signal peptide, followed
by an N-terminal pro-region linked to the enzyme; these
proenzymes are called procarboxypeptidases. The A/B
enzymes can be further divided based on their substrate
specificity; Carboxypeptidase A-like (CPA-like) enzymes
favor hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues lysine
or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate cleavages.
They contain an extra C-terminal transthyretin-like
domain, thought to be involved in folding or formation
of oligomers. MCPs can also be classified based on
their involvement in specific physiological processes;
the pancreatic MCPs participate only in alimentary
digestion and include carboxypeptidase A and B (A/B
subfamily), while others, namely regulatory MCPs or the
N/E subfamily, are involved in more selective reactions,
mainly in non-digestive tissues and fluids, acting on
blood coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily,
is that of succinylglutamate desuccinylase
/aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
(NAA), and deficiency in which is the established cause
of Canavan disease. Another subfamily (referred to as
subfamily C) includes an exceptional type of activity in
the MCP family, that of dipeptidyl-peptidase activity of
gamma-glutamyl-(L)-meso-diaminopimelate peptidase I
which is involved in bacterial cell wall metabolism.
Length = 268
Score = 27.0 bits (60), Expect = 5.2
Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 10/63 (15%)
Query: 34 NIPCPTQELTEGCFPNAVLQHLKGQGF----------EEPTAIQAQGWPIALSGRDMVGI 83
NIP + L+E F + L+ +G + + A GR+ +G+
Sbjct: 181 NIPKNIRTLSESLFVPNAGKALEAKGLRWEPYFTGSVGNDIILIQEDTTAAQIGRNAMGL 240
Query: 84 AQT 86
Q
Sbjct: 241 TQA 243
>gnl|CDD|144813 pfam01358, PARP_regulatory, Poly A polymerase regulatory subunit.
Length = 295
Score = 27.0 bits (60), Expect = 5.3
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 94 VINFDYPNSSEDYIH 108
V NFDYPN DY H
Sbjct: 245 VNNFDYPNQEYDYFH 259
>gnl|CDD|225763 COG3222, COG3222, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 211
Score = 26.7 bits (59), Expect = 5.9
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 1/44 (2%)
Query: 11 AARLSESEVEAFRQKKEITVKGNNIPCPTQELTEGCFPNAVLQH 54
RL+ S V+AF + + G + P T EL F A+LQ
Sbjct: 90 GDRLARSHVDAFDGSYPVLIIGMDCPGLTAELLADAF-TALLQI 132
>gnl|CDD|172310 PRK13772, PRK13772, formimidoylglutamase; Provisional.
Length = 314
Score = 26.6 bits (59), Expect = 7.1
Identities = 21/69 (30%), Positives = 28/69 (40%), Gaps = 20/69 (28%)
Query: 66 IQAQGWPIALSGRDMV------GI-----AQTGSGKTLAVINFDYPNSSEDYIHRIGRTG 114
+ A P+ L G V G+ AQ G+ + +IN D H RT
Sbjct: 113 LAAGARPLVLGGGHEVAWGTWQGLRAHLDAQGDRGR-VLIINLD--------AHFDLRTS 163
Query: 115 RCASSGTAY 123
R ASSGT +
Sbjct: 164 RPASSGTPF 172
>gnl|CDD|234948 PRK01372, ddl, D-alanine--D-alanine ligase; Reviewed.
Length = 304
Score = 26.2 bits (59), Expect = 8.5
Identities = 16/65 (24%), Positives = 24/65 (36%), Gaps = 25/65 (38%)
Query: 49 NAVLQHLKGQGFE---------EPTAIQAQGWP----IALSGR-----------DMVGIA 84
AVL L+ G++ ++ G AL GR +++GI
Sbjct: 26 AAVLAALREAGYDAHPIDPGEDIAAQLKELG-FDRVFNALHGRGGEDGTIQGLLELLGIP 84
Query: 85 QTGSG 89
TGSG
Sbjct: 85 YTGSG 89
>gnl|CDD|176244 cd08284, FDH_like_2, Glutathione-dependent formaldehyde
dehydrogenase related proteins, child 2.
Glutathione-dependent formaldehyde dehydrogenases (FDHs)
are members of the zinc-dependent/medium chain alcohol
dehydrogenase family. Formaldehyde dehydrogenase (FDH)
is a member of the zinc-dependent/medium chain alcohol
dehydrogenase family. FDH converts formaldehyde and NAD
to formate and NADH. The initial step in this process
the spontaneous formation of a
S-(hydroxymethyl)glutathione adduct from formaldehyde
and glutathione, followed by FDH-mediated oxidation (and
detoxification) of the adduct to S-formylglutathione.
These tetrameric FDHs have a catalytic zinc that resides
between the catalytic and NAD(H)binding domains and a
structural zinc in a lobe of the catalytic domain. The
medium chain alcohol dehydrogenase family (MDR) has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 344
Score = 26.1 bits (58), Expect = 9.8
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 109 RIGRTGRCASSGTAYTFFTPN-NGKQAKELIAVLTEASQ--PIPPQLQD 154
R G++GRCA G +PN +G QA E + V +P L D
Sbjct: 96 RRGQSGRCAKGGLFGYAGSPNLDGAQA-EYVRVPFADGTLLKLPDGLSD 143
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
0.312 0.129 0.378
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: 8,122,655
Number of extensions: 713222
Number of successful extensions: 619
Number of sequences better than 10.0: 1
Number of HSP's gapped: 617
Number of HSP's successfully gapped: 58
Length of query: 165
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 75
Effective length of database: 6,945,742
Effective search space: 520930650
Effective search space used: 520930650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (24.9 bits)