RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6093
(350 letters)
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 216 bits (553), Expect = 9e-64
Identities = 90/213 (42%), Positives = 121/213 (56%), Gaps = 20/213 (9%)
Query: 21 QNKSVFE---LGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWI 77
Q + VFE G RK+VLATNIAETS+TI I YV+D G K +D + + L+ E I
Sbjct: 302 QVR-VFEPAPGGKRKVVLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPI 360
Query: 78 SLANAKQRRGRAGRVQEGVCYHLYSRAREQTFQDYPLPEIQRTRLDEVVRTLESKKFKMV 137
S A+A QR GRAGR G+CY LYS F ++ LPEI RT L +V L+S
Sbjct: 361 SKASADQRAGRAGRTGPGICYRLYSEEDFLAFPEFTLPEILRTDLSGLVLQLKS------ 414
Query: 138 SRRFKVMLNTAFTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKL 197
+ + A P+ LDPP A++Q +L LL+ + ALDD LTPLG ++ L
Sbjct: 415 ---LGIGQDIAPFPF-------LDPPPEAAIQAALTLLQELGALDDSGKLTPLGKQMSLL 464
Query: 198 PLDPQIGKMLLMASIFSCVDPVFTVAASLGFKD 230
PLDP++ +MLL A C+ T+A+ L +D
Sbjct: 465 PLDPRLARMLLTAPEGGCLGEAATIASMLSEQD 497
>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 = 156 bits (395), Expect = 5e-42
Identities = 96/320 (30%), Positives = 153/320 (47%), Gaps = 64/320 (20%)
Query: 31 RKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAG 90
R+IVLATN+AETS+T+ I YV+D G ++S + + + L E IS A+A QR+GR G
Sbjct: 331 RRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCG 390
Query: 91 RVQEGVCYHLYSRAREQTFQDYPL---PEIQRTRLDEVVRTLESKKFKMVSRRFKVMLNT 147
RV G+C LYS E+ F P PEI RT L V+ + + + +
Sbjct: 391 RVAPGICIRLYS---EEDFNSRPEFTDPEILRTNLASVILQMLALRLGDI---------A 438
Query: 148 AFTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDE---HLTPLGYHLAKLPLDPQIG 204
AF P++ + PDP +++ +LL + ALDDDE LTP+G LA+LP+DP++
Sbjct: 439 AF-PFI-------EAPDPRAIRDGFRLLEELGALDDDEAEPQLTPIGRQLAQLPVDPRLA 490
Query: 205 KMLLMASIFSCVDPVFTVAASLGFKDAFYCPMIGKMLLMASIFSCVDPVFTVAASLGFKD 264
+MLL A C+ V +A++L +D PM
Sbjct: 491 RMLLEAHRLGCLQEVLIIASALSIQDPRERPM---------------------------- 522
Query: 265 AFYCPMNMEKDVDKQKNILAQGAKSDYVVLINAMQGWE---QALEHNYAHDYCRENFLTN 321
++ Q + + +SD++ +N + E QAL N + CR+ +L
Sbjct: 523 -------EKQQAADQAHARFKDPRSDFLSRVNLWRHIEEQRQALSANQFRNACRKQYLNY 575
Query: 322 NTLLLLRDMKDQFSRTMHEM 341
+ +D+ Q ++ + E+
Sbjct: 576 LRVREWQDIYRQLTQVVKEL 595
>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional.
Length = 1294
Score = 140 bits (355), Expect = 1e-36
Identities = 107/338 (31%), Positives = 160/338 (47%), Gaps = 74/338 (21%)
Query: 21 QNKSVFEL-GVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISL 79
QN+ VF+ R+IVLATN+AETS+T+ I YV+D G ++S + + + L E IS
Sbjct: 328 QNR-VFQSHSGRRIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQ 386
Query: 80 ANAKQRRGRAGRVQEGVCYHLYSRAREQTFQDYPL---PEIQRTRLDEVVRTLESKKFKM 136
A+A QR+GR GRV EG+C LYS E F P PEI RT L V+ +M
Sbjct: 387 ASANQRKGRCGRVSEGICIRLYS---EDDFLSRPEFTDPEILRTNLASVI-------LQM 436
Query: 137 VSRRFKVMLNTAFTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDE-----HLTPLG 191
+ + AF P+V + PD ++Q ++LL + A+ DE LTPLG
Sbjct: 437 TALGLGDI--AAF-PFV-------EAPDKRNIQDGVRLLEELGAITTDEQASAYKLTPLG 486
Query: 192 YHLAKLPLDPQIGKMLLMASIFSCVDPVFTVAASLGFKDAFYCPMIGKMLLMASIFSCVD 251
LA+LP+DP++ +M+L A CV V + ++L +D PM +
Sbjct: 487 RQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALSIQDPRERPMDKQQ----------- 535
Query: 252 PVFTVAASLGFKDAFYCPMNMEKD---VDKQKNILAQGAKSDYVVLINAMQGWEQALEHN 308
A+ EK DK+ + LA +V L N +Q ++AL N
Sbjct: 536 -----ASD-------------EKHRRFADKESDFLA------FVNLWNYLQEQQKALSSN 571
Query: 309 YAHDYCRENFLTNNTLLLLRDMKD---QFSRTMHEMNF 343
CR ++L L +R+ +D Q + + E+
Sbjct: 572 QFRRLCRTDYL---NYLRVREWQDIYTQLRQVVKELGI 606
>gnl|CDD|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional.
Length = 812
Score = 130 bits (330), Expect = 2e-33
Identities = 69/198 (34%), Positives = 101/198 (51%), Gaps = 19/198 (9%)
Query: 29 GVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGR 88
G RK+VLATNIAETS+TI+ I VVD G +++ FD K + L + IS A+ QR GR
Sbjct: 264 GRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGR 323
Query: 89 AGRVQEGVCYHLYSRAREQTFQDYPLPEIQRTRLDEVVRTLESKKFKMVSRRFKVMLNTA 148
AGR++ G+C HLYS+ + + PEI + L ++ L ++ L+
Sbjct: 324 AGRLEPGICLHLYSKEQAERAAAQSEPEILHSDLSGLLLELLQWGCHDPAQ-----LS-- 376
Query: 149 FTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKMLL 208
W LD P A++ + +LL+ + ALD LT G +A L DP++ ML+
Sbjct: 377 -----W-----LDQPPAAALAAAKRLLQQLGALDGQGRLTARGRKMAALGNDPRLAAMLV 426
Query: 209 MASIFSCVDPVFTVAASL 226
A + AA L
Sbjct: 427 AAKEDD--EAALATAAKL 442
>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 = 122 bits (307), Expect = 2e-30
Identities = 66/182 (36%), Positives = 93/182 (51%), Gaps = 17/182 (9%)
Query: 29 GVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGR 88
G RK+VLATNIAETS+TI+ I V+D G +++ FD K I L+ IS A+A QR GR
Sbjct: 261 GRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGR 320
Query: 89 AGRVQEGVCYHLYSRAREQTFQDYPLPEIQRTRLDEVVRTLESKKFKMVSRRFKVMLNTA 148
AGR++ GVCY L+S + Q PEI + L + L ++
Sbjct: 321 AGRLEPGVCYRLWSEEQHQRLPAQDEPEILQADLSGLALELA---------QWGA---KD 368
Query: 149 FTPYVWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKMLL 208
+ W LD P ++ + +LL+ + ALD LT G +A L P++ MLL
Sbjct: 369 PSDLRW-----LDAPPSVALAAARQLLQRLGALDAQGRLTAHGKAMAALGCHPRLAAMLL 423
Query: 209 MA 210
A
Sbjct: 424 SA 425
>gnl|CDD|218070 pfam04408, HA2, Helicase associated domain (HA2). This presumed
domain is about 90 amino acid residues in length. It is
found is a diverse set of RNA helicases. Its function is
unknown, however it seems likely to be involved in
nucleic acid binding.
Length = 91
Score = 89.6 bits (223), Expect = 2e-22
Identities = 33/63 (52%), Positives = 46/63 (73%)
Query: 171 SLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKMLLMASIFSCVDPVFTVAASLGFKD 230
+L+LL + ALDDD LTPLG +A+LPLDP++GKMLL+++ F C+D + T+AA L
Sbjct: 2 ALELLYELGALDDDGELTPLGRQMAELPLDPRLGKMLLLSAEFGCLDEILTIAAMLSVPS 61
Query: 231 AFY 233
FY
Sbjct: 62 PFY 64
>gnl|CDD|214852 smart00847, HA2, Helicase associated domain (HA2) Add an
annotation. This presumed domain is about 90 amino acid
residues in length. It is found is a diverse set of RNA
helicases. Its function is unknown, however it seems
likely to be involved in nucleic acid binding.
Length = 82
Score = 75.4 bits (186), Expect = 3e-17
Identities = 28/55 (50%), Positives = 37/55 (67%)
Query: 178 IDALDDDEHLTPLGYHLAKLPLDPQIGKMLLMASIFSCVDPVFTVAASLGFKDAF 232
+ ALDDD LTPLG +A+LPLDP++ KMLL A+ F C+D + T+ A L D
Sbjct: 2 LGALDDDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGDPR 56
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 51.1 bits (123), Expect = 1e-08
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 21/80 (26%)
Query: 15 SGLKHLQNKSVFEL---GVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIAT 71
GL + + + + G K+++AT++AE + + + V+ +D+
Sbjct: 19 GGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI--------IYDL------ 64
Query: 72 LKPEWISLANAKQRRGRAGR 91
S A+ QR GRAGR
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 = 50.2 bits (121), Expect = 3e-08
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 18/67 (26%)
Query: 26 FELGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQR 85
F G K+++AT++A I + D+ V+ N+D+ + A+ QR
Sbjct: 29 FRNGKSKVLVATDVAGRGIDLPDVNLVI--------NYDL----------PWNPASYIQR 70
Query: 86 RGRAGRV 92
GRAGR
Sbjct: 71 IGRAGRA 77
>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 = 40.7 bits (96), Expect = 2e-04
Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 19/69 (27%)
Query: 33 IVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRV 92
+++AT++ I + ++ V+ N+D+ S ++ QR GRAGR
Sbjct: 81 VLVATDVIARGIDLPNVSVVI--------NYDL----------PWSPSSYLQRIGRAGRA 122
Query: 93 -QEGVCYHL 100
Q+G L
Sbjct: 123 GQKGTAILL 131
>gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional.
Length = 675
Score = 41.9 bits (99), Expect = 4e-04
Identities = 33/142 (23%), Positives = 57/142 (40%), Gaps = 35/142 (24%)
Query: 33 IVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRV 92
I+++T E+S+TI + +V D G+ + K +IS + QR+GR GRV
Sbjct: 449 IIISTPYLESSVTIRNATHVYDTGRVYVPEP------FGGKEMFISKSMRTQRKGRVGRV 502
Query: 93 QEGVCYHLYSRAREQTFQ--DY---------------PLPE---IQRTRLDEVVRTLE-- 130
G + Y + + D LPE + + LD + +T E
Sbjct: 503 SPGTYVYFYDLDLLKPIKRIDSEFLHNYILYAKYFNLTLPEDLFVIPSNLDRLRKTEEYI 562
Query: 131 -------SKKFKMVSRRFKVML 145
K ++++S + ML
Sbjct: 563 DSFNISIEKWYEILSNYYVNML 584
>gnl|CDD|234640 PRK00110, PRK00110, hypothetical protein; Validated.
Length = 245
Score = 29.7 bits (68), Expect = 1.7
Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 15/64 (23%)
Query: 122 LDEVVRTLESKKFKMVSRRFKVMLNTAFTPYVWVPKQVLDPPDPASVQLSLKLLRLIDAL 181
+ V LE+ + S +P Q D + + KLL+LIDAL
Sbjct: 178 FEAVRDALEAAGLEAESAEV-----------TMIP-QNTVELDEETAE---KLLKLIDAL 222
Query: 182 DDDE 185
+D +
Sbjct: 223 EDLD 226
>gnl|CDD|217990 pfam04257, Exonuc_V_gamma, Exodeoxyribonuclease V, gamma subunit.
The Exodeoxyribonuclease V enzyme is a multi-subunit
enzyme comprised of the proteins RecB, RecC (this
family) and RecD. This enzyme plays an important role in
homologous genetic recombination, repair of double
strand DNA breaks resistance to UV irradiation and
chemical DNA-damage. The enzyme (EC:3.1.11.5) catalyzes
ssDNA or dsDNA-dependent ATP hydrolysis, hydrolysis of
ssDNA or dsDNA and unwinding of dsDNA. This family
consists of two AAA domains.
Length = 756
Score = 30.3 bits (69), Expect = 2.0
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 155 VPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAK 196
VP++ P S L+ +L+RL+ L D+ PL ++L+
Sbjct: 80 VPEE--SPFSKES--LTWRLMRLLPELLDEPEFAPLRHYLSD 117
>gnl|CDD|223110 COG0031, CysK, Cysteine synthase [Amino acid transport and
metabolism].
Length = 300
Score = 29.8 bits (68), Expect = 2.2
Identities = 13/46 (28%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 256 VAASLGFKDAFYCPMNMEKDVDKQKNILAQGAKSDYVVLINAMQGW 301
VAA+ G++ P M + +++K + A GA+ V+L G
Sbjct: 80 VAAAKGYRLIIVMPETMSQ--ERRKLLRALGAE---VILTPGAPGN 120
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 29.5 bits (67), Expect = 3.6
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 14/66 (21%)
Query: 84 QRRGRAGRVQEGVCYHLY------------SRAREQTFQD--YPLPEIQRTRLDEVVRTL 129
QR+GR GR +EG L SR +E+ ++ L I +L E+
Sbjct: 459 QRKGRTGRQEEGRVVVLIAKGTRDEAYYWSSRRKEKKMKEELKNLKGILNKKLQELDEEQ 518
Query: 130 ESKKFK 135
+ ++ +
Sbjct: 519 KGEEEE 524
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 28.8 bits (65), Expect = 4.6
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 8/39 (20%)
Query: 26 FELGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFD 64
G +++AT++A I IDD+ +V+ NFD
Sbjct: 291 LTDGRVNVLVATDVAARGIDIDDVSHVI--------NFD 321
>gnl|CDD|232905 TIGR00284, TIGR00284, dihydropteroate synthase-related protein.
This protein has been found so far only in the Archaea,
and in particular in those archaea that lack a
bacterial-type dihydropteroate synthase. The central
region of this protein shows considerable homology to
the amino-terminal half of dihydropteroate synthases,
while the carboxyl-terminal region shows homology to the
small, uncharacterized protein slr0651 of Synechocystis
PCC6803 [Unknown function, General].
Length = 499
Score = 28.7 bits (64), Expect = 4.9
Identities = 32/160 (20%), Positives = 61/160 (38%), Gaps = 18/160 (11%)
Query: 49 IVYVV-DCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRVQEGVCYHLYSRAREQ 107
I+YVV D K+ S + A + S A + + L+ ++
Sbjct: 347 ILYVVEDSYKSYRSTAEAA--EAA---KMASAARKLNSLPKD------IGTRLFVVKDKR 395
Query: 108 TFQDYPLPEIQRTRLDEVVRTLESKKFK--MVSRRFKVMLNTAFTPYVWVPKQVLDPPDP 165
+ P +R +D + +++ + V V++ T + P P ++ P
Sbjct: 396 RPPEPVEPPGERINVDYIEPSMDRTGYAKIQVDHERGVIMLTFY-PAGGEPVVTIEGKKP 454
Query: 166 ASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGK 205
S+ +L + +L EH +GY LAK + +GK
Sbjct: 455 TSILRALIRRFPVSSL---EHAGYIGYELAKAEIALALGK 491
>gnl|CDD|107289 cd06294, PBP1_ycjW_transcription_regulator_like, Ligand-binding
domain of uncharacterized transcription regulator ycjW
which is a member of the LacI-GalR family repressors.
This group includes the ligand-binding domain of
uncharacterized transcription regulator ycjW which is a
member of the LacI-GalR family repressors that are
composed of two functional domains: an N-terminal HTH
(helix-turn-helix) domain, which is responsible for the
DNA-binding specificity, and a C-terminal ligand-binding
domain, which is homologous to the sugar-binding domain
of ABC-type transport systems that contain the type I
periplasmic binding protein-like fold. As also observed
in the periplasmic binding proteins, the C-terminal
domain of the bacterial transcription repressor
undergoes a conformational change upon ligand binding
which in turn changes the DNA binding affinity of the
repressor.
Length = 270
Score = 28.7 bits (65), Expect = 4.9
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 280 KNILAQGAKSDYVVLINAMQGWEQALEHN 308
K I G D V + +QG++QALE +
Sbjct: 123 KKIAFVGGDLDLEVTQDRLQGYKQALEDH 151
>gnl|CDD|129609 TIGR00518, alaDH, alanine dehydrogenase. The family of known
L-alanine dehydrogenases includes representatives from
the Proteobacteria, Firmicutes, and Cyanobacteria, all
with about 50 % identity or better. An outlier to this
group in both sequence and gap pattern is the homolog
from Helicobacter pylori, an epsilon division
Proteobacteria, which must be considered a putative
alanine dehydrogenase. Related proteins include
saccharopine dehydrogenase and the N-terminal half of
the NAD(P) transhydrogenase alpha subunit. All of these
related proteins bind NAD and/or NADP [Energy
metabolism, Amino acids and amines].
Length = 370
Score = 28.3 bits (63), Expect = 5.5
Identities = 17/59 (28%), Positives = 21/59 (35%), Gaps = 6/59 (10%)
Query: 252 PVFTVAASLGFKDAFYCPMNMEKDVDKQKNILAQGAKSDYVVLINAMQGWEQALEHNYA 310
P + V + YC NM V K A YV+ + A GW A N A
Sbjct: 285 PTYAVHDVV-----HYCVANMPGAVPKTSTYALTNATMPYVLEL-ANHGWRAACRSNPA 337
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 28.5 bits (64), Expect = 6.3
Identities = 17/35 (48%), Positives = 19/35 (54%), Gaps = 8/35 (22%)
Query: 123 DEVVRTLESKKFKMVSRRFKV-------ML-NTAF 149
DEV + LE +K V RFKV ML NTAF
Sbjct: 107 DEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNTAF 141
>gnl|CDD|172668 PRK14180, PRK14180, bifunctional 5,10-methylene-tetrahydrofolate
dehydrogenase/ 5,10-methylene-tetrahydrofolate
cyclohydrolase; Provisional.
Length = 282
Score = 28.1 bits (62), Expect = 7.1
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 153 VWVPKQVLDPPDPASVQLSLKLLRLIDALDDDEHLTPLGYHLAKLPLDPQIGKMLLMASI 212
V + QV+ P+ + +LL LID L++D + + L +LPL I K ++ SI
Sbjct: 59 VGIDSQVITLPEHTTES---ELLELIDQLNNDSSVHAI---LVQLPLPAHINKNNVIYSI 112
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 28.2 bits (64), Expect = 8.1
Identities = 16/47 (34%), Positives = 18/47 (38%), Gaps = 10/47 (21%)
Query: 84 QRRGRAGRVQ-EGVCYHLYSRAREQTFQDYPLPEIQRTRLDEVVRTL 129
Q RGR GR + C LY PL E R RL + T
Sbjct: 568 QLRGRVGRGAAQSYCVLLY---------KDPLSETARERLKIMRETN 605
>gnl|CDD|218813 pfam05929, Phage_GPO, Phage capsid scaffolding protein (GPO) serine
peptidase. This family consists of several
bacteriophage capsid scaffolding proteins (GPO) and some
related bacterial sequences. GPO is thought to function
in both the assembly of proheads and the cleavage of
GPN. The family is found to function as a serine
peptidase, with a conserved Asp, His and Ser catalytic
triad, as in subtilisin, and as represented in
MEROPS:S73. The family includes GpO from Enterobacteria
phage P2 which cleaves itself and then becomes the
scaffold protein upon which the bacteriophage prohead is
built - a mechanism quite common amongst phages.
Length = 277
Score = 27.9 bits (62), Expect = 8.3
Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 2/88 (2%)
Query: 54 DCGKTKMSNFDVKDNIATLKPEWISLANAKQRRGRAGRVQEGVCYHLYSRAREQTFQDYP 113
D GK + V D+ A+L E +S + + + A R Q +L++ A E + +
Sbjct: 109 DTGKAYLVGLAVTDSPASLGTEMLSFSASAKHNPLAARKQNPD--NLFTVAEEVSLEFEE 166
Query: 114 LPEIQRTRLDEVVRTLESKKFKMVSRRF 141
E T L + V+ L KK RF
Sbjct: 167 TAETVPTNLFDRVKRLFKKKEASDDARF 194
>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 = 27.8 bits (62), Expect = 9.0
Identities = 22/122 (18%), Positives = 43/122 (35%), Gaps = 25/122 (20%)
Query: 24 SVFELGVRKIVLATNIAETSITIDDIVYVVDCGKTKMSNFDVKDNIATLKPEWISLANAK 83
F+ G ++++AT++A + I D+ +V+ N+D+ +
Sbjct: 317 EKFKDGELRVLVATDVAARGLDIPDVSHVI--------NYDLPLDPEDY----------V 358
Query: 84 QRRGRAGR-VQEGVCYHLYSRAREQTFQDYPLPEIQRT--RLDEVVRTLESKKFKMVSRR 140
R GR GR ++GV + E L I++ R L + +
Sbjct: 359 HRIGRTGRAGRKGVAISFVTEEEEVKK----LKRIEKRLERKLPSAVLLPLDEPEDAKLL 414
Query: 141 FK 142
Sbjct: 415 KT 416
>gnl|CDD|220291 pfam09561, RE_HpaII, HpaII restriction endonuclease. This family
includes the HpaII (recognises and cleaves C^CGG)
restriction endonuclease.
Length = 355
Score = 27.7 bits (62), Expect = 9.4
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 6/30 (20%)
Query: 94 EGVCYHLYSRAREQTFQDYPLPEIQRTRLD 123
E +CYH+Y+R F+DY T+L+
Sbjct: 303 EVLCYHIYNR---NQFEDY---LFNNTKLE 326
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
0.324 0.137 0.415
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,799,548
Number of extensions: 1714507
Number of successful extensions: 1960
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1949
Number of HSP's successfully gapped: 43
Length of query: 350
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 252
Effective length of database: 6,590,910
Effective search space: 1660909320
Effective search space used: 1660909320
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 59 (26.5 bits)