RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3103
(217 letters)
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 84.7 bits (210), Expect = 4e-19
Identities = 50/155 (32%), Positives = 77/155 (49%), Gaps = 29/155 (18%)
Query: 61 VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIYDIALWLGFGKPTVY 120
+HLLG+ +RGPVLE++V RMR R ++ IR V +SAT+PN ++A WL K
Sbjct: 155 IHLLGDRTRGPVLESIVARMR------RLNELIRIVGLSATLPNAEEVADWLN-AKL--- 204
Query: 121 AQIDDSFRPVKLTKIVRGFP----------TKPSQSTFQFEMMLSYKLKSIIMQYSDNKP 170
++ +RPV L RG P K + + L L+S+ ++
Sbjct: 205 --VESDWRPVPL---RRGVPYVGAFLGADGKKKTWPLLIDNLALELVLESL----AEGGQ 255
Query: 171 TLIFCATRKGVEHTCTILRQEMSIQTSPEVREIVD 205
L+F +RK E T LR +MS S + + ++D
Sbjct: 256 VLVFVHSRKEAEKTAKKLRIKMSATLSDDEKIVLD 290
Score = 56.6 bits (137), Expect = 2e-09
Identities = 15/44 (34%), Positives = 26/44 (59%)
Query: 18 SNIMDNKLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYLMILV 61
D +L +++ + +HHAG+ EDR ++E FR G + +LV
Sbjct: 302 PTSEDEELAELVLRGVAFHHAGLPREDRQLVEDAFRKGKIKVLV 345
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 54.5 bits (131), Expect = 8e-09
Identities = 24/62 (38%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 1 MSIQTSPEVREI-VDKCMSNIMDNKLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYLMI 59
M IQ PE + V +N+ D+ L +ML + +HHAG+S E R IE++FR+ Y+ +
Sbjct: 255 MLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKV 314
Query: 60 LV 61
+V
Sbjct: 315 IV 316
Score = 52.2 bits (125), Expect = 4e-08
Identities = 47/165 (28%), Positives = 74/165 (44%), Gaps = 27/165 (16%)
Query: 57 LMIL--VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIYDIALWLGF 114
L++ +H++G+E RGP LE V+ R V R +A+SAT+ N ++A WL
Sbjct: 138 LIVADEIHIIGDEDRGPTLETVLSSARYVNPD------ARILALSATVSNANELAQWLN- 190
Query: 115 GKPTVYAQIDDSFRPV--KLTKIVRGFPTKPSQSTFQFEMMLSYKLKSIIMQYSDNKPTL 172
+ I +FRPV KL + R Q ++ +K + +D L
Sbjct: 191 -----ASLIKSNFRPVPLKLGILYRKRLILDGYERSQVDINSL--IKETV---NDGGQVL 240
Query: 173 IFCATRKGVEHTCTILRQEMSIQTSPEVREI-VDKCMSNMMDNKL 216
+F ++RK E EM IQ PE + V +N+ D+ L
Sbjct: 241 VFVSSRKNAEDYA-----EMLIQHFPEFNDFKVSSENNNVYDDSL 280
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 51.4 bits (123), Expect = 1e-07
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 5 TSPEVR---EIVDKCMSNIMDNKLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYLMILV 61
T PE+R E+ D N + KLK LR + +HHAG+ +R +IE FR G + ++
Sbjct: 267 TKPELRALKELADSLEENPTNEKLKKALRGGVAFHHAGLGRTERVLIEDAFREGLIKVIT 326
Score = 44.0 bits (104), Expect = 2e-05
Identities = 44/163 (26%), Positives = 69/163 (42%), Gaps = 24/163 (14%)
Query: 61 VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIYDIALWLGFGKPTVY 120
+HL+G RG LE ++ M + ++Q + +SAT+ N ++A WL
Sbjct: 147 IHLIGSYDRGATLEMILTHM--LGRAQ-------ILGLSATVGNAEELAEWLN------A 191
Query: 121 AQIDDSFRPVKLTKIV--RGFPTKPSQSTFQFEMMLSYKLKSIIMQYSDNKPTLIFCATR 178
+ +RPVKL K V +GF +F L + K L+F TR
Sbjct: 192 ELVVSDWRPVKLRKGVFYQGFLFWEDGKIERFPNSW-ESL--VYDAVKKGKGALVFVNTR 248
Query: 179 KGVEHTCTILRQEM-SIQTSPEVR---EIVDKCMSNMMDNKLK 217
+ E L +++ T PE+R E+ D N + KLK
Sbjct: 249 RSAEKEALELAKKIKRFLTKPELRALKELADSLEENPTNEKLK 291
>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional.
Length = 737
Score = 46.9 bits (112), Expect = 3e-06
Identities = 26/73 (35%), Positives = 39/73 (53%), Gaps = 14/73 (19%)
Query: 61 VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIYDIALWLGFGKPTVY 120
VHL+ +RGP LE + ++R + Q VA+SATI N ++A WL
Sbjct: 146 VHLIDSANRGPTLEVTLAKLR---RLNPDLQ---VVALSATIGNADELADWLD------- 192
Query: 121 AQIDDS-FRPVKL 132
A++ DS +RP+ L
Sbjct: 193 AELVDSEWRPIDL 205
Score = 42.6 bits (101), Expect = 7e-05
Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 3/60 (5%)
Query: 1 MSIQTSPEVREIVDKCMSNI---MDNKLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYL 57
++ E+ E+ ++ L D + +HHAG+S E R ++E FR +
Sbjct: 271 LTAAERAELAELAEEIREVSDTETSKDLADCVAKGAAFHHAGLSREHRELVEDAFRDRLI 330
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 43.9 bits (104), Expect = 4e-05
Identities = 27/112 (24%), Positives = 43/112 (38%), Gaps = 23/112 (20%)
Query: 29 LRSSIGYHHAGMSPEDRTIIEQLFRSGYLMILVHLLGEESRGPVLEAVVCRMRTVQKSQR 88
LR+ + Y + + ++ VH +G+ RG V E V+
Sbjct: 216 LRN-MLYRGSESLRDIEWVV---------FDEVHYIGDRERGVVWEEVIIL--------- 256
Query: 89 ASQPIRFVAVSATIPNIYDIALWLGF--GKPTVYAQIDDSFRPVKLTKIVRG 138
+RFV +SAT+PN + A W+ +P + RPV L V
Sbjct: 257 LPDHVRFVFLSATVPNAEEFAEWIQRVHSQPIH--VVSTEHRPVPLEHFVYV 306
Score = 37.0 bits (86), Expect = 0.006
Identities = 15/62 (24%), Positives = 33/62 (53%), Gaps = 9/62 (14%)
Query: 8 EVREIVDKCMSNIMDN---------KLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYLM 58
+REI+D + ++ + ++ +L I HHAG+ P + ++E+LF+ G +
Sbjct: 413 AIREIIDHAIGDLAEEDRELPLQILEISALLLRGIAVHHAGLLPAIKELVEELFQEGLVK 472
Query: 59 IL 60
++
Sbjct: 473 VV 474
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 39.1 bits (92), Expect = 1e-04
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 24 KLKDMLRS---SIGYHHAGMSPEDRTIIEQLFRSGYLMILV 61
+L ++L+ + H G+S E+R I F +G + +LV
Sbjct: 2 ELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLV 42
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 40.9 bits (96), Expect = 3e-04
Identities = 31/115 (26%), Positives = 52/115 (45%), Gaps = 21/115 (18%)
Query: 61 VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIYDIALWLGFGKPTVY 120
+H L +E RGP L+ ++ R+R + +F+ +SAT+ N ++A LG K +Y
Sbjct: 347 IHTLEDEERGPRLDGLIGRLRYLFPGA------QFIYLSATVGNPEELAKKLG-AKLVLY 399
Query: 121 AQIDDSFRPVKLTK---IVRGFPTKPS------QSTFQFEMMLSYKLKSIIMQYS 166
+ RPV L + R K + F E Y+ ++I+ YS
Sbjct: 400 DE-----RPVPLERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIVFTYS 449
>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 = 37.0 bits (86), Expect = 0.006
Identities = 25/107 (23%), Positives = 42/107 (39%), Gaps = 2/107 (1%)
Query: 87 QRASQPIRFVAVSATIPNIYDIALWLGFGKPTVYAQIDDSFRPVKLTKIVRGFPTKPSQS 146
+R P++ + SAT+ N + A L FG+ +D+ P L VR P +
Sbjct: 227 RRYGSPLQIICTSATLANPGEFAEEL-FGRDFEVP-VDEDGSPRGLRYFVRREPPIRELA 284
Query: 147 TFQFEMMLSYKLKSIIMQYSDNKPTLIFCATRKGVEHTCTILRQEMS 193
L+ + + TL+F +RK VE R+ +
Sbjct: 285 ESIRRSALAELATLAALLVRNGIQTLVFFRSRKQVELLYLSPRRRLV 331
Score = 29.7 bits (67), Expect = 1.3
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 36 HHAGMSPEDRTIIEQLFRSG 55
+ AG+ E+R IE F+ G
Sbjct: 344 YRAGLHREERRRIEAEFKEG 363
>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 = 32.5 bits (75), Expect = 0.023
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 32 SIGYHHAGMSPEDRTIIEQLFRSGYLMILV 61
+ H G+S E+R I + FR+G +LV
Sbjct: 9 KVARLHGGLSQEEREEILEDFRNGKSKVLV 38
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 34.5 bits (80), Expect = 0.035
Identities = 33/159 (20%), Positives = 65/159 (40%), Gaps = 23/159 (14%)
Query: 61 VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIYDIALWL-GFGKPTV 119
+H L E RG L + R+R + + + +SAT+ ++A +L GFG P
Sbjct: 158 IHALAESKRGVQLALSLERLRELAG------DFQRIGLSATVGPPEEVAKFLVGFGDPCE 211
Query: 120 YAQIDDSF-RPVKLTKIVRGFPTKPSQSTFQFEMMLSYKLKSIIMQYSDNKPTLIFCATR 178
+D S + +++ K++ + ++ ++ ++ + TLIF TR
Sbjct: 212 I--VDVSAAKKLEI-KVISPVEDLIYDEELWAALYE--RIAELVKKH---RTTLIFTNTR 263
Query: 179 KGVEHTCTILRQEMSIQT-------SPEVREIVDKCMSN 210
G E L++ S E+R V++ +
Sbjct: 264 SGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKE 302
>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 = 33.0 bits (76), Expect = 0.041
Identities = 12/47 (25%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 15 KCMSNIMDNKLKDMLRSSIGYHHAGMSPEDRTIIEQLFRSGYLMILV 61
K M + + L+ + H S E+R + + FR G +++LV
Sbjct: 38 KKMLDELAELLRK-PGIKVAALHGDGSQEEREEVLKDFREGEIVVLV 83
>gnl|CDD|132287 TIGR03243, arg_catab_AOST, arginine and ornithine
succinyltransferase subunits. In many bacteria, the
sole member of this protein family is arginine
N-succinyltransferase (EC 2.3.1.109), the AstA protein
of the arginine succinyltransferase (ast) pathway.
However, in Pseudomonas aeruginosa and several other
species, a tandem gene pair encodes alpha and beta
subunits of a heterodimer that is designated arginine
and ornithine succinyltransferase (AOST).
Length = 335
Score = 33.0 bits (76), Expect = 0.087
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 5/34 (14%)
Query: 70 GPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIP 103
GP LEA V +R V++S+R V V + P
Sbjct: 254 GPTLEAEVDDIRAVRESRRVP-----VKVGESAP 282
>gnl|CDD|132288 TIGR03244, arg_catab_AstA, arginine N-succinyltransferase. In many
bacteria, the arginine succinyltransferase (ast) pathway
operon consists of five genes, including this protein,
arginine N-succinyltransferase (EC 2.3.1.109). In a few
species, such as Pseudomonas aeruginosa, the member of
this family is encoded adjacent to a paralog, and the
two polypeptides form a heterodimeric enzyme, active on
both arginine and ornithine. In such species, this
polypeptide may be treated as the beta subunit of an
enzyme that may be named either arginine
N-succinyltransferase (AST) or arginine and orthithine
N-succinyltransferase (AOST) [Energy metabolism, Amino
acids and amines].
Length = 336
Score = 32.3 bits (74), Expect = 0.16
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 70 GPVLEAVVCRMRTVQKSQRASQPI 93
GP LEA V +R V++S+ +
Sbjct: 254 GPTLEAEVADIRAVRESRLVPVAV 277
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 30.2 bits (68), Expect = 0.57
Identities = 16/77 (20%), Positives = 29/77 (37%), Gaps = 11/77 (14%)
Query: 57 LMIL--VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIYDIALWLGF 114
L+IL H L + G LE ++ + + ++ + +SAT P + L L
Sbjct: 132 LVILDEAHRLLDGGFGDQLEKLLKLLP---------KNVQLLLLSATPPEEIENLLELFL 182
Query: 115 GKPTVYAQIDDSFRPVK 131
P P++
Sbjct: 183 NDPVFIDVGFTPLEPIE 199
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 30.0 bits (68), Expect = 1.2
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 32 SIGYHHAGMSPEDRTIIEQLFRSGYLMILV 61
S G +HAG+S E+R ++Q F + + ++V
Sbjct: 256 SAGAYHAGLSNEERERVQQAFLNDEIKVMV 285
>gnl|CDD|218349 pfam04958, AstA, Arginine N-succinyltransferase beta subunit.
Arginine N-succinyltransferase EC:2.3.1.109 catalyzes
the transfer of succinyl-CoA to arginine to produce
succinylarginine. This is the first step in arginine
catabolism by the arginine succinyltransferase pathway.
Length = 337
Score = 29.4 bits (67), Expect = 1.6
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 70 GPVLEAVVCRMRTVQKSQRA 89
GP +EA +RTV++S+RA
Sbjct: 256 GPTVEARTDDIRTVRESRRA 275
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 29.5 bits (66), Expect = 1.6
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 36 HHAGMSPEDRTIIEQLFRSGYLMILV 61
HH +S E R I EQ +SG L +V
Sbjct: 307 HHGSVSKEQRAITEQALKSGELRCVV 332
>gnl|CDD|184395 PRK13919, PRK13919, putative RNA polymerase sigma E protein;
Provisional.
Length = 186
Score = 28.7 bits (64), Expect = 1.6
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 30 RSSIGYHHAGMSPEDRTIIEQLFRSGY 56
R+ +G +SPE+R +IE L+ GY
Sbjct: 126 RTRLGRALKALSPEERRVIEVLYYQGY 152
>gnl|CDD|146132 pfam03338, Pox_J1, Poxvirus J1 protein.
Length = 145
Score = 28.0 bits (63), Expect = 2.1
Identities = 19/93 (20%), Positives = 38/93 (40%), Gaps = 11/93 (11%)
Query: 26 KDMLRSSIGYHHAGMSPEDRTIIE----QLFRSGYLMILVHLLGEE---SRGPVLEAVVC 78
KD L +IGY + +S E R +I+ + R + I ++ ++G + + V+
Sbjct: 52 KDKL-EAIGYCYEPLSEEFRALIDFRDLKELRQLFNRIPINPDSGRVQVNKGYLSDFVIS 110
Query: 79 RMRTVQKSQRASQ-PIRFVA--VSATIPNIYDI 108
+R ++ P ++ NI I
Sbjct: 111 LIRLKRELGLDLPKPTTYIDPRDDPAFSNILSI 143
>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 = 27.9 bits (63), Expect = 4.6
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 33 IGYHHAGMSPEDRTIIEQLFRSGYLMILV 61
I HH + E R +E +G L +V
Sbjct: 278 IALHHGSLDREQRRWVEAAMAAGRLRAVV 306
Score = 27.5 bits (62), Expect = 6.3
Identities = 25/136 (18%), Positives = 51/136 (37%), Gaps = 19/136 (13%)
Query: 49 EQLFRSGYLMIL--VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIY 106
+LF+ +++ H L RG LE + R+R + +R +SATI N+
Sbjct: 135 ARLFKDLRCVVVDEWHELAGSKRGDQLELALARLRRLAPG------LRRWGLSATIGNLE 188
Query: 107 DIALWL---GFGKPT-VYAQIDDSFRPVKLTKIVRGFPTKPSQSTFQFEMMLSYKLKSII 162
+ L G V ++ + + + ++ + + + L +
Sbjct: 189 EARRVLLGVGGAPAVLVRGKLP---KAIPVISLLPESEERFPWAGH----LGLRALPEVY 241
Query: 163 MQYSDNKPTLIFCATR 178
+ + TL+F TR
Sbjct: 242 AEIDQARTTLVFTNTR 257
>gnl|CDD|227314 COG4981, COG4981, Enoyl reductase domain of yeast-type FAS1 [Lipid
metabolism].
Length = 717
Score = 27.9 bits (62), Expect = 4.6
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 20/75 (26%)
Query: 81 RTVQKSQRASQPIRFVAVSATIPNIYDIAL------------WLGFGKPTVYAQIDDSFR 128
R VQK++ + PI V +SA IP++ + A+ ++ F KP QI
Sbjct: 112 RLVQKARASGAPIDGVVISAGIPSL-EEAVELIEELGDDGFPYVAF-KPGTIEQIR---- 165
Query: 129 PVKLTKIVRGFPTKP 143
+ +I + PT P
Sbjct: 166 --SVIRIAKANPTFP 178
>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 = 27.2 bits (61), Expect = 5.5
Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 12/55 (21%)
Query: 57 LMIL--VHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSATIP-NIYDI 108
L++L H L + G LE ++ R+ + + +SAT+P N+ D+
Sbjct: 124 LLVLDEAHRLLDMGFGDDLEEILSRLPP---------DRQILLLSATLPRNLEDL 169
>gnl|CDD|240255 PTZ00070, PTZ00070, 40S ribosomal protein S2; Provisional.
Length = 257
Score = 27.3 bits (61), Expect = 5.9
Identities = 13/54 (24%), Positives = 18/54 (33%), Gaps = 16/54 (29%)
Query: 47 IIEQLFRSGYLMILVHLLGEESRGPVLEAVVCRMRTVQKSQRASQPIRFVAVSA 100
I++ F L +E V ++ VQK A Q RF A
Sbjct: 70 IVDHFFAESKLK-------DE---------VMKIMPVQKQTSAGQRTRFKAFVV 107
>gnl|CDD|239131 cd02666, Peptidase_C19J, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 343
Score = 27.1 bits (60), Expect = 6.8
Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 6/50 (12%)
Query: 11 EIVDKCMSNIMDNKLKDMLRSSIGYHHAGMSPEDRTI----IEQLFRSGY 56
+ V +C+ N++ ++ I AG ED I++LF
Sbjct: 99 QDVTECIDNVLFQ--LEVALEPISNAFAGPDTEDDKEQSDLIKRLFSGKT 146
>gnl|CDD|236078 PRK07726, PRK07726, DNA topoisomerase III; Provisional.
Length = 658
Score = 27.4 bits (62), Expect = 6.9
Identities = 14/42 (33%), Positives = 18/42 (42%), Gaps = 13/42 (30%)
Query: 47 IIEQLFRSGYL-------------MILVHLLGEESRGPVLEA 75
IIE+LF+ GYL L+ L EE P + A
Sbjct: 521 IIEKLFKRGYLEKKGKYIHATDKGKQLIDALPEELTSPDMTA 562
>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 = 27.0 bits (60), Expect = 8.3
Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 3/40 (7%)
Query: 16 CMSNIMDNKLKDMLRS---SIGYHHAGMSPEDRTIIEQLF 52
C S ++ L++ + G +HAG+ R + F
Sbjct: 233 CPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKF 272
>gnl|CDD|239853 cd04388, RhoGAP_p85, RhoGAP_p85: RhoGAP (GTPase-activator protein
[GAP] for Rho-like small GTPases) domain present in the
p85 isoforms of the regulatory subunit of the class IA
PI3K (phosphatidylinositol 3'-kinase). This domain is
also called Bcr (breakpoint cluster region protein)
homology (BH) domain. Class IA PI3Ks are heterodimers,
containing a regulatory subunit (p85) and a catalytic
subunit (p110) and are activated by growth factor
receptor tyrosine kinases (RTKs); this activation is
mediated by the p85 subunit. p85 isoforms, alpha and
beta, contain a C-terminal p110-binding domain flanked
by two SH2 domains, an N-terminal SH3 domain, and a
RhoGAP domain flanked by two proline-rich regions. Small
GTPases cluster into distinct families, and all act as
molecular switches, active in their GTP-bound form but
inactive when GDP-bound. The Rho family of GTPases
activates effectors involved in a wide variety of
developmental processes, including regulation of
cytoskeleton formation, cell proliferation and the JNK
signaling pathway. GTPases generally have a low
intrinsic GTPase hydrolytic activity but there are
family-specific groups of GAPs that enhance the rate of
GTP hydrolysis by several orders of magnitude.
Length = 200
Score = 26.4 bits (58), Expect = 9.4
Identities = 12/40 (30%), Positives = 21/40 (52%)
Query: 71 PVLEAVVCRMRTVQKSQRASQPIRFVAVSATIPNIYDIAL 110
PV ++ R + VQ S +Q +R + S +P+ Y + L
Sbjct: 88 PVYSEMISRAQEVQSSDEYAQLLRKLIRSPNLPHQYWLTL 127
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
0.322 0.134 0.388
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: 10,716,996
Number of extensions: 975382
Number of successful extensions: 983
Number of sequences better than 10.0: 1
Number of HSP's gapped: 974
Number of HSP's successfully gapped: 51
Length of query: 217
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 124
Effective length of database: 6,812,680
Effective search space: 844772320
Effective search space used: 844772320
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 (21.9 bits)
S2: 57 (25.6 bits)