RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16353
(132 letters)
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 105 bits (264), Expect = 2e-27
Identities = 40/107 (37%), Positives = 60/107 (56%), Gaps = 2/107 (1%)
Query: 23 LCSSLNKPEVQWKIVV--LHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKY 80
L K E+ + + L+ ++ E+Q VF P G RK+VL+TNIAE+S+T+P ++Y
Sbjct: 275 TAEWLEKAELGDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIAETSLTIPGIRY 334
Query: 81 VVDFCLTKVLTVAEGSNYSSLQLEWASESSCQQRAGRVGRVSEGRVY 127
V+D L K + + L+ E S++S QRAGR GR G Y
Sbjct: 335 VIDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRTGPGICY 381
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 74.9 bits (185), Expect = 5e-19
Identities = 23/90 (25%), Positives = 43/90 (47%), Gaps = 18/90 (20%)
Query: 31 EVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVL 90
E+ K+ LH + +E+++ + +F G K++++T++AE + +P V V+ + L
Sbjct: 9 ELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDL---- 64
Query: 91 TVAEGSNYSSLQLEWASESSCQQRAGRVGR 120
S +S QR GR GR
Sbjct: 65 --------------PWSPASYIQRIGRAGR 80
>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 = 71.4 bits (176), Expect = 1e-17
Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 20/95 (21%)
Query: 27 LNKPEVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
L KP + K+ LH + +E+++ + F G K++++T++A I +PDV V+++ L
Sbjct: 3 LRKPGI--KVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60
Query: 87 TKVLTVAEGSNYSSLQLEWASESSCQQRAGRVGRV 121
+ +S QR GR GR
Sbjct: 61 ------------------PWNPASYIQRIGRAGRA 77
>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model
represents HrpB, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria,
but also in a few species of other lineages. The member
from Rhizobium meliloti has been designated HelO. HrpB
is typically about 800 residues in length, while its
paralog HrpA (TIGR01967), also uncharacterized, is about
1300 amino acids long. Related characterized eukarotic
proteins are RNA helicases associated with pre-mRNA
processing [Unknown function, Enzymes of unknown
specificity].
Length = 819
Score = 75.2 bits (185), Expect = 6e-17
Identities = 34/98 (34%), Positives = 52/98 (53%), Gaps = 2/98 (2%)
Query: 30 PEVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKV 89
+V I L+ + QD P G RK+VL+TNIAE+S+T+ ++ V+D L +V
Sbjct: 235 SDVL--ICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARV 292
Query: 90 LTVAEGSNYSSLQLEWASESSCQQRAGRVGRVSEGRVY 127
+ + L+ S++S QRAGR GR+ G Y
Sbjct: 293 ARFDPKTGITRLETVRISQASATQRAGRAGRLEPGVCY 330
>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional.
Length = 1294
Score = 72.4 bits (178), Expect = 7e-16
Identities = 41/101 (40%), Positives = 58/101 (57%), Gaps = 17/101 (16%)
Query: 36 IVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTVAEG 95
I+ L++ + +Q+ VF R+IVL+TN+AE+S+TVP +KYV+D A
Sbjct: 316 ILPLYARLSNSEQNRVFQ--SHSGRRIVLATNVAETSLTVPGIKYVID------PGTARI 367
Query: 96 SNYS------SLQLEWASESSCQQRAGRVGRVSEG---RVY 127
S YS L +E S++S QR GR GRVSEG R+Y
Sbjct: 368 SRYSYRTKVQRLPIEPISQASANQRKGRCGRVSEGICIRLY 408
>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model
represents HrpA, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria
and a few high-GC Gram-positive bacteria. HrpA is about
1300 amino acids long, while its paralog HrpB, also
uncharacterized, is about 800 amino acids long. Related
characterized eukarotic proteins are RNA helicases
associated with pre-mRNA processing [Unknown function,
Enzymes of unknown specificity].
Length = 1283
Score = 71.3 bits (175), Expect = 2e-15
Identities = 38/102 (37%), Positives = 59/102 (57%), Gaps = 17/102 (16%)
Query: 35 KIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTVAE 94
+I+ L++ + ++Q VF P R+IVL+TN+AE+S+TVP + YV+D ++
Sbjct: 308 EILPLYARLSNKEQQRVFQ--PHSGRRIVLATNVAETSLTVPGIHYVIDTGTARI----- 360
Query: 95 GSNYSS------LQLEWASESSCQQRAGRVGRVSEG---RVY 127
S YS L +E S++S QR GR GRV+ G R+Y
Sbjct: 361 -SRYSYRTKVQRLPIEPISQASANQRKGRCGRVAPGICIRLY 401
>gnl|CDD|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional.
Length = 812
Score = 65.3 bits (160), Expect = 2e-13
Identities = 29/69 (42%), Positives = 43/69 (62%)
Query: 56 PPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTVAEGSNYSSLQLEWASESSCQQRA 115
P G RK+VL+TNIAE+S+T+ ++ VVD L +V + + L + S++S QRA
Sbjct: 262 PAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRA 321
Query: 116 GRVGRVSEG 124
GR GR+ G
Sbjct: 322 GRAGRLEPG 330
>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 = 50.3 bits (121), Expect = 7e-09
Identities = 31/116 (26%), Positives = 49/116 (42%), Gaps = 23/116 (19%)
Query: 15 FSPNISLL--LCSSLNKPEVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESS 72
F P+ +L L L KP + K+ LH +E+++ V F G ++++T++
Sbjct: 34 FCPSKKMLDELAELLRKPGI--KVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARG 91
Query: 73 ITVPDVKYVVDFCLTKVLTVAEGSNYSSLQLEWASESSCQQRAGRVGRV-SEGRVY 127
I +P+V V+ NY S SS QR GR GR +G
Sbjct: 92 IDLPNVSVVI--------------NYDL----PWSPSSYLQRIGRAGRAGQKGTAI 129
>gnl|CDD|226583 COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA
uptake (late competence protein) [DNA replication,
recombination, and repair].
Length = 441
Score = 42.8 bits (101), Expect = 1e-05
Identities = 31/119 (26%), Positives = 50/119 (42%), Gaps = 23/119 (19%)
Query: 15 FSPNISLL--LCSSLNKPEVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESS 72
F P I + + ++L K + I +HS ++ + F G ++++T I E
Sbjct: 311 FFPEIETMEQVAAALKKKLPKETIASVHSEDQHRKEKV--EAFRDGKITLLITTTILERG 368
Query: 73 ITVPDVKYVVDFCLTKVLTVAEGSNYSSLQLEWASESSCQQRAGRVGRVSE---GRVYY 128
+T P+V V AE + +ES+ Q AGRVGR E G V +
Sbjct: 369 VTFPNVDVFV--------LGAEHRVF--------TESALVQIAGRVGRSLERPTGDVLF 411
>gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional.
Length = 675
Score = 42.3 bits (100), Expect = 2e-05
Identities = 25/66 (37%), Positives = 34/66 (51%), Gaps = 12/66 (18%)
Query: 62 IVLSTNIAESSITVPDVKYVVDFCLTKVLTVAE---GSNYSSLQLEWASESSCQQRAGRV 118
I++ST ESS+T+ + +V D T + V E G + S+S QR GRV
Sbjct: 449 IIISTPYLESSVTIRNATHVYD---TGRVYVPEPFGGKE------MFISKSMRTQRKGRV 499
Query: 119 GRVSEG 124
GRVS G
Sbjct: 500 GRVSPG 505
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 41.9 bits (99), Expect = 3e-05
Identities = 22/87 (25%), Positives = 38/87 (43%), Gaps = 18/87 (20%)
Query: 46 EQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTVAEGSNYSSLQLEW 105
++Q + +F G ++++T++ E + +P+V V+ V
Sbjct: 412 KEQKEIIDQFRKGEYNVLVATSVGEEGLDIPEVDLVI--FYEPV---------------- 453
Query: 106 ASESSCQQRAGRVGRVSEGRVYYMVTR 132
SE QR GR GR +GRV +VT
Sbjct: 454 PSEIRSIQRKGRTGRKRKGRVVVLVTE 480
>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 = 40.5 bits (95), Expect = 9e-05
Identities = 30/110 (27%), Positives = 49/110 (44%), Gaps = 21/110 (19%)
Query: 23 LCSSLNKPEVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVV 82
L SL K +K+ LH +P+E++D +F G +++++T++A + +PDV +V+
Sbjct: 289 LAESLRK--RGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVI 346
Query: 83 DFCLTKVLTVAEGSNYSSLQLEWASESSCQQRAGRVGR-VSEGRVYYMVT 131
NY L E R GR GR +G VT
Sbjct: 347 --------------NY---DLPLDPEDYV-HRIGRTGRAGRKGVAISFVT 378
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 36.4 bits (85), Expect = 0.002
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 19/88 (21%)
Query: 45 KEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTVAEGSNYSSLQLE 104
KEQ + + +F G +++ST++AE + +P V V+ F Y +
Sbjct: 410 KEQIE-ILDKFRAGEFNVLVSTSVAEEGLDIPSVDLVI-F-------------YEPV--- 451
Query: 105 WASESSCQQRAGRVGRVSEGRVYYMVTR 132
SE QR GR GR EGRV ++ +
Sbjct: 452 -PSEIRSIQRKGRTGRQEEGRVVVLIAK 478
>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd). All
proteins in this family for which functions are known
are DNA-dependent ATPases that function in the process
of transcription-coupled DNA repair in which the repair
of the transcribed strand of actively transcribed genes
is repaired at a higher rate than the repair of
non-transcribed regions of the genome and than the
non-transcribed strand of the same gene. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). This family is
closely related to the RecG and UvrB families [DNA
metabolism, DNA replication, recombination, and repair].
Length = 926
Score = 35.4 bits (82), Expect = 0.005
Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 2/49 (4%)
Query: 30 PEVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDV 78
PE +I + H + + + + V F G ++++ T I E+ I +P+
Sbjct: 685 PEA--RIAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNA 731
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 34.0 bits (78), Expect = 0.012
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 34 WKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDF 84
W + +H +E++ V F G I+++T++A + V DVKYV++F
Sbjct: 402 WPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRGLDVKDVKYVINF 452
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 33.5 bits (77), Expect = 0.019
Identities = 13/55 (23%), Positives = 28/55 (50%)
Query: 23 LCSSLNKPEVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPD 77
L L K ++ + +LH + ++++ V F G I+++T + E + VP+
Sbjct: 472 LYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVPN 526
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 33.0 bits (76), Expect = 0.029
Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 23/86 (26%)
Query: 22 LLCSSLNKPEVQWKIV------VLHS-----------------SIPKEQQDLVFTRFPPG 58
LLC L +PEV IV +H + + +++ R G
Sbjct: 235 LLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDG 294
Query: 59 VRKIVLSTNIAESSITVPDVKYVVDF 84
++++T++A I + DV +V++F
Sbjct: 295 RVNVLVATDVAARGIDIDDVSHVINF 320
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 33.0 bits (75), Expect = 0.031
Identities = 14/53 (26%), Positives = 34/53 (64%)
Query: 34 WKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
+++ VL +P+++++ + RF G +I+++T++A + + VKYV ++ L
Sbjct: 282 YRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDL 334
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 30.3 bits (69), Expect = 0.32
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 30 PEVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDV 78
PE +I V H + + + + V F G +++ T I E+ I +P+
Sbjct: 828 PEA--RIAVAHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNA 874
>gnl|CDD|216166 pfam00872, Transposase_mut, Transposase, Mutator family.
Length = 381
Score = 30.0 bits (68), Expect = 0.33
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 50 LVFTRFPPGVRKIVLSTNIAES 71
L F FP + + STN E
Sbjct: 321 LAFYDFPAQHWRRIRSTNAIER 342
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 29.6 bits (67), Expect = 0.49
Identities = 23/92 (25%), Positives = 40/92 (43%), Gaps = 19/92 (20%)
Query: 40 HSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTVAEGSNYS 99
H+ + E+++ V F K++++TN I PDV++V+ + L +
Sbjct: 261 HAGLSNEERERVQQAFLNDEIKVMVATNAFGMGIDKPDVRFVIHYDLPGSI--------- 311
Query: 100 SLQLEWASESSCQQ--RAGRVGRVSEGRVYYM 129
ES Q+ RAGR G +E + Y
Sbjct: 312 --------ESYYQETGRAGRDGLPAEAILLYS 335
>gnl|CDD|226186 COG3660, COG3660, Predicted nucleoside-diphosphate-sugar epimerase
[Cell envelope biogenesis, outer membrane].
Length = 329
Score = 28.7 bits (64), Expect = 0.87
Identities = 15/69 (21%), Positives = 21/69 (30%), Gaps = 10/69 (14%)
Query: 7 GTFSPHATFSPNISLLLCSSLNKPEVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLST 66
G + F + + S L K L S F+R P K +L
Sbjct: 169 GGNNKAFVFQEDKAHQFASLLVKILENQGGSFLIS----------FSRRTPDTVKSILKN 218
Query: 67 NIAESSITV 75
N+ S V
Sbjct: 219 NLNSSPGIV 227
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 27.6 bits (62), Expect = 2.6
Identities = 13/55 (23%), Positives = 26/55 (47%)
Query: 23 LCSSLNKPEVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPD 77
L L + K+ ++H + ++D V F G I+++T + E + VP+
Sbjct: 497 LYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDVPN 551
>gnl|CDD|227632 COG5322, COG5322, Predicted dehydrogenase [General function
prediction only].
Length = 351
Score = 27.2 bits (60), Expect = 2.7
Identities = 12/51 (23%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 19 ISLLLCSSLNKPEVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIA 69
I+ + L P+V K ++L + + +Q L + G R ++S + A
Sbjct: 179 IASAIARWLA-PKVGVKELLLRDAEARNRQRLTLLQEELG-RGKIMSLDYA 227
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 26.7 bits (59), Expect = 3.9
Identities = 11/48 (22%), Positives = 27/48 (56%)
Query: 39 LHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCL 86
+H + ++ +DL+ F G +++++T++ I V V V+++ L
Sbjct: 297 MHGDMDQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDL 344
>gnl|CDD|145415 pfam02251, PA28_alpha, Proteasome activator pa28 alpha subunit.
PA28 activator complex (also known as 11s regulator of
20S proteasome) is a ring shaped hexameric structure of
alternating alpha and beta subunits. This family
represents the alpha subunit. The activator complex
binds to the 20S proteasome ana simulates peptidase
activity in and ATP-independent manner.
Length = 64
Score = 25.3 bits (56), Expect = 4.0
Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 18/63 (28%)
Query: 30 PEVQWKIVVLHSSIPKEQQDLVFTRFPPGVRKIV---------------LSTNIAESSIT 74
PE + K+ S+ KE + LV FP KI+ LS A +I
Sbjct: 3 PENKKKVDAFRQSLTKEAERLVSNFFP---EKILELDALLKEPILNIHDLSQLHAPLNIP 59
Query: 75 VPD 77
+PD
Sbjct: 60 IPD 62
>gnl|CDD|225865 COG3328, COG3328, Transposase and inactivated derivatives [DNA
replication, recombination, and repair].
Length = 379
Score = 26.6 bits (59), Expect = 4.4
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 50 LVFTRFPPGVRKIVLSTNIAES 71
L F FP +RKI+ +TN ES
Sbjct: 300 LPFFAFPSEIRKIIYTTNAIES 321
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 26.6 bits (59), Expect = 4.5
Identities = 18/88 (20%), Positives = 35/88 (39%), Gaps = 18/88 (20%)
Query: 38 VLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVLTVAEGSN 97
+ PKE+++ + RF G K++++ + + + +PD +
Sbjct: 311 AITGETPKEEREAILERFRTGGIKVLVTVKVLDEGVDIPDAD-----------VLIILRP 359
Query: 98 YSSLQLEWASESSCQQRAGRVGRVSEGR 125
S +L QR GR R +EG+
Sbjct: 360 TGSRRLF-------IQRLGRGLRPAEGK 380
>gnl|CDD|221340 pfam11958, DUF3472, Domain of unknown function (DUF3472). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria, eukaryotes and viruses.
This domain is typically between 174 to 190 amino acids
in length. This domain has a single completely conserved
residue G that may be functionally important.
Length = 184
Score = 26.2 bits (58), Expect = 4.6
Identities = 7/28 (25%), Positives = 10/28 (35%)
Query: 92 VAEGSNYSSLQLEWASESSCQQRAGRVG 119
V+ +SS +A E R G
Sbjct: 105 VSLNGGHSSFLENFAPELGNLSRVAYYG 132
>gnl|CDD|215592 PLN03126, PLN03126, Elongation factor Tu; Provisional.
Length = 478
Score = 26.5 bits (58), Expect = 5.1
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 1 MVDIKPGTFSPHATFSPNISLL 22
MV KPG+ +PH F + +L
Sbjct: 370 MVLAKPGSITPHTKFEAIVYVL 391
>gnl|CDD|132992 cd06974, TerD_like, Uncharacterized proteins involved in stress
response, similar to tellurium resistance terD.
Tellurium resistance terD like proteins. This family is
composed of uncharacterized proteins involved in stress
response, such as the tellurium resistance proteins,
chemical-damaging agent resistance proteins, and
general stress proteins from a variety of organisms.
The tellurium resistance proteins are homologous
terA,-D,-E,-F,-Z,-X gene products, which confer
tellurium resistance mediated by plasmids. Currently,
the biochemical mechanism of tellurium resistance
remains unknown. The family also contains several ter
gene homologues, YceC, YceD, YceE, for which there is
no clear evidence for any involvement in the tellurium
resistance. A putative cAMP-binding protin CABP1 shows
a significant similarity to the terD protein and is
also included in this family.
Length = 162
Score = 26.1 bits (58), Expect = 5.8
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 46 EQQDLVFTRFPPGVRKIVLSTNIAES 71
E + R PP +R+IV + I E
Sbjct: 68 ETITVDLDRLPPDIRRIVFTVTIYEG 93
>gnl|CDD|222158 pfam13474, SnoaL_3, SnoaL-like domain. This family contains a
large number of proteins that share the SnoaL fold.
Length = 121
Score = 25.8 bits (57), Expect = 6.1
Identities = 6/12 (50%), Positives = 6/12 (50%)
Query: 33 QWKIVVLHSSIP 44
WKI H S P
Sbjct: 108 GWKIAHYHLSFP 119
>gnl|CDD|237301 PRK13200, psaA, photosystem I P700 chlorophyll a apoprotein A1;
Provisional.
Length = 766
Score = 25.9 bits (57), Expect = 7.5
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 36 IVVLHSSIPKEQQDLVFTRFPPGVRKIVLSTNIAESSITV 75
IV+ H S K Q D+ T G + N A+S+IT+
Sbjct: 619 IVIFHFSW-KMQSDVWGTVNADGSVSHITGGNFAQSAITI 657
>gnl|CDD|239908 cd04461, S1_Rrp5_repeat_hs8_sc7, S1_Rrp5_repeat_hs8_sc7: Rrp5
Homo sapiens S1 repeat 8 (hs8) and Saccharomyces
cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a
trans-acting factor important for biogenesis of both
the 40S and 60S eukaryotic ribosomal subunits. Rrp5
has two distinct regions, an N-terminal region
containing tandemly repeated S1 RNA-binding domains (12
S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in
H. sapiens Rrp5) and a C-terminal region containing
tetratricopeptide repeat (TPR) motifs thought to be
involved in protein-protein interactions. Mutational
studies have shown that each region represents a
specific functional domain. Deletions within the
S1-containing region inhibit pre-rRNA processing at
either site A3 or A2, whereas deletions within the TPR
region confer an inability to support cleavage of
A0-A2. This CD includes H. sapiens S1 repeat 8 and S.
cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but
not in prokaryotes or archaea.
Length = 83
Score = 24.9 bits (55), Expect = 7.9
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 51 VFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLT-KVLTV 92
VF F G+ + + I++ +T P + +T KV +V
Sbjct: 30 VFVEFLGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSV 72
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 25.9 bits (57), Expect = 8.1
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 12/54 (22%)
Query: 82 VDFCLTKVL--TVAEGSNYSSLQLEWASESSCQQ---RAGRVGRVSEGRVYYMV 130
VDF ++V+ ++A G +EW S QQ RAGR G+VY +V
Sbjct: 504 VDFPASQVIFESLAMG-------IEWLSVREFQQMLGRAGRPDYHDRGKVYLLV 550
>gnl|CDD|177010 CHL00071, tufA, elongation factor Tu.
Length = 409
Score = 25.7 bits (57), Expect = 9.0
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 1 MVDIKPGTFSPHATFSPNISLL 22
MV KPGT +PH F + +L
Sbjct: 301 MVLAKPGTITPHTKFEAQVYIL 322
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 25.9 bits (57), Expect = 9.4
Identities = 21/90 (23%), Positives = 35/90 (38%), Gaps = 25/90 (27%)
Query: 35 KIVVLHSSIPK----EQQDLVFTRFPPGVRKIVLSTNIAESSITVPDVKYVVDFCLTKVL 90
K+++LHS E++ + F IV++T + E+ + + D +
Sbjct: 466 KVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQVIEAGVDI-DFDVL--------- 515
Query: 91 TVAEGSNYSSLQLEWASESSCQQRAGRVGR 120
+ L A S QRAGRV R
Sbjct: 516 -------ITEL----APIDSLIQRAGRVNR 534
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 0.132 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: 6,426,230
Number of extensions: 527971
Number of successful extensions: 420
Number of sequences better than 10.0: 1
Number of HSP's gapped: 408
Number of HSP's successfully gapped: 42
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
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 (21.8 bits)
S2: 53 (24.1 bits)