RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6850
(118 letters)
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 102 bits (256), Expect = 4e-27
Identities = 45/88 (51%), Positives = 63/88 (71%), Gaps = 6/88 (6%)
Query: 13 LNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRIGRTGRFGK 72
+ F S +VLITT++LARGIDV+QV++VIN+D+P A E Y+HRIGR+GRFG+
Sbjct: 310 MREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLP------ASPENYIHRIGRSGRFGR 363
Query: 73 CGIAINLVDEHSVGVLKDIEKHFGKKIE 100
G+AIN V + LK+IE+H+ +IE
Sbjct: 364 KGVAINFVTPDDIEQLKEIERHYNTQIE 391
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 100 bits (250), Expect = 4e-26
Identities = 42/98 (42%), Positives = 60/98 (61%), Gaps = 6/98 (6%)
Query: 2 GKGPNTSSSSSLNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYL 61
G+ + ++ T + VL+ T+V ARGID++ V+ VINFDMP AD TYL
Sbjct: 277 GEMVQAKRNEAIKRLTDGRVNVLVATDVAARGIDIDDVSHVINFDMPR----SAD--TYL 330
Query: 62 HRIGRTGRFGKCGIAINLVDEHSVGVLKDIEKHFGKKI 99
HRIGRTGR G+ G AI+LV+ H +L IE++ + +
Sbjct: 331 HRIGRTGRAGRKGTAISLVEAHDHLLLGKIERYIEEPL 368
>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 = 99.5 bits (248), Expect = 1e-25
Identities = 42/107 (39%), Positives = 63/107 (58%), Gaps = 7/107 (6%)
Query: 11 SSLNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRIGRTGRF 70
+L F + +VL+ T+V ARG+D+ V+ VIN+D+P+D E Y+HRIGRTGR
Sbjct: 314 RALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDP------EDYVHRIGRTGRA 367
Query: 71 GKCGIAINLVDEH-SVGVLKDIEKHFGKKIELLDTEDIDDEGNFRNL 116
G+ G+AI+ V E V LK IEK +K+ +D+ + + L
Sbjct: 368 GRKGVAISFVTEEEEVKKLKRIEKRLERKLPSAVLLPLDEPEDAKLL 414
>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 = 76.1 bits (188), Expect = 5e-19
Identities = 32/78 (41%), Positives = 43/78 (55%), Gaps = 6/78 (7%)
Query: 2 GKGPNTSSSSSLNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYL 61
G G L F + VL+ T+V+ARGID+ V++VIN+D+P +YL
Sbjct: 60 GDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSP------SSYL 113
Query: 62 HRIGRTGRFGKCGIAINL 79
RIGR GR G+ G AI L
Sbjct: 114 QRIGRAGRAGQKGTAILL 131
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 79.8 bits (198), Expect = 9e-19
Identities = 32/83 (38%), Positives = 50/83 (60%), Gaps = 8/83 (9%)
Query: 18 SCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRIGRTGRFGKCGIAI 77
SC VL+ T+V ARG+D++ + VIN+++ D E ++HRIGRTGR G G+A+
Sbjct: 292 SCS--VLVATDVAARGLDIKALEAVINYELARDP------EVHVHRIGRTGRAGSKGLAL 343
Query: 78 NLVDEHSVGVLKDIEKHFGKKIE 100
+LV + IE + G+K+
Sbjct: 344 SLVAPEEMQRANAIEDYLGRKLN 366
>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 = 72.9 bits (180), Expect = 2e-18
Identities = 26/59 (44%), Positives = 36/59 (61%), Gaps = 6/59 (10%)
Query: 13 LNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRIGRTGRFG 71
L F + K KVL+ T+V RGID+ V +VIN+D+P + +Y+ RIGR GR G
Sbjct: 26 LEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNP------ASYIQRIGRAGRAG 78
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 76.5 bits (189), Expect = 1e-17
Identities = 37/87 (42%), Positives = 48/87 (55%), Gaps = 6/87 (6%)
Query: 13 LNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRIGRTGRFGK 72
L FT +L+ T+V ARG+ + VT V N+D+P DCE Y+HRIGRTGR G
Sbjct: 298 LEEFTRGDLDILVATDVAARGLHIPAVTHVFNYDLP------DDCEDYVHRIGRTGRAGA 351
Query: 73 CGIAINLVDEHSVGVLKDIEKHFGKKI 99
G +I+L E L IE + G I
Sbjct: 352 SGHSISLACEEYALNLPAIETYIGHSI 378
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 76.4 bits (188), Expect = 2e-17
Identities = 32/71 (45%), Positives = 52/71 (73%), Gaps = 6/71 (8%)
Query: 23 VLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRIGRTGRFGKCGIAINLVDE 82
+LI T+V ARG+DVE++++V+N+D+P+ D E+Y+HRIGRTGR G+ G A+ V+
Sbjct: 298 ILIATDVAARGLDVERISLVVNYDIPM------DSESYVHRIGRTGRAGRAGRALLFVEN 351
Query: 83 HSVGVLKDIEK 93
+L++IE+
Sbjct: 352 RERRLLRNIER 362
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 69.9 bits (172), Expect = 3e-17
Identities = 24/59 (40%), Positives = 35/59 (59%), Gaps = 6/59 (10%)
Query: 13 LNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRIGRTGRFG 71
L+ F + K KVL+ T+V RG+D+ V +VI +D+P +Y+ RIGR GR G
Sbjct: 30 LDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWSP------ASYIQRIGRAGRAG 82
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 74.1 bits (182), Expect = 1e-16
Identities = 39/90 (43%), Positives = 58/90 (64%), Gaps = 10/90 (11%)
Query: 12 SLNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRIGRTGRFG 71
+L F S +VL+ T++ ARG+D+E++ V+N+++P N D Y+HRIGRTGR
Sbjct: 287 ALADFKSGDIRVLVATDIAARGLDIEELPHVVNYELP---NVPED---YVHRIGRTGRAA 340
Query: 72 KCGIAINL--VDEHSVGVLKDIEKHFGKKI 99
G A++L VDEH +L+DIEK K+I
Sbjct: 341 ATGEALSLVCVDEH--KLLRDIEKLLKKEI 368
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 73.8 bits (181), Expect = 1e-16
Identities = 37/99 (37%), Positives = 54/99 (54%), Gaps = 6/99 (6%)
Query: 2 GKGPNTSSSSSLNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYL 61
G P +L F K +VL+ T+V RGI ++ ++ VINF +P D + Y+
Sbjct: 367 GDVPQHKRIKTLEGFREGKIRVLVATDVAGRGIHIDGISHVINFTLP------EDPDDYV 420
Query: 62 HRIGRTGRFGKCGIAINLVDEHSVGVLKDIEKHFGKKIE 100
HRIGRTGR G G++I+ E L +IE+ G+KI
Sbjct: 421 HRIGRTGRAGASGVSISFAGEDDAFQLPEIEELLGRKIS 459
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 71.9 bits (176), Expect = 6e-16
Identities = 38/98 (38%), Positives = 53/98 (54%), Gaps = 6/98 (6%)
Query: 2 GKGPNTSSSSSLNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYL 61
G P S LN F + ++L+ T+V ARG+ ++ V V N+D+P D E Y+
Sbjct: 289 GDVPQKKRESLLNRFQKGQLEILVATDVAARGLHIDGVKYVYNYDLPFD------AEDYV 342
Query: 62 HRIGRTGRFGKCGIAINLVDEHSVGVLKDIEKHFGKKI 99
HRIGRT R G+ G AI+ E L DIE + +KI
Sbjct: 343 HRIGRTARLGEEGDAISFACERYAMSLPDIEAYIEQKI 380
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 69.4 bits (170), Expect = 4e-15
Identities = 30/64 (46%), Positives = 40/64 (62%), Gaps = 6/64 (9%)
Query: 13 LNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRIGRTGRFGK 72
LN F + K ++I T+V +RG+DV+ V VINFD P + E Y+HRIGRTGR G
Sbjct: 420 LNEFKTGKSPIMIATDVASRGLDVKDVKYVINFDFPNQI------EDYVHRIGRTGRAGA 473
Query: 73 CGIA 76
G +
Sbjct: 474 KGAS 477
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 58.6 bits (142), Expect = 3e-11
Identities = 28/79 (35%), Positives = 43/79 (54%), Gaps = 6/79 (7%)
Query: 13 LNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRIGRTGRFGK 72
+ SF + V++ T VL RG+D+ +V VI FDMP + Y+H+IGR R G+
Sbjct: 411 MKSFLVGEVPVIVATGVLGRGVDLLRVRQVIIFDMP------NTIKEYIHQIGRASRMGE 464
Query: 73 CGIAINLVDEHSVGVLKDI 91
G AI V+E + ++
Sbjct: 465 KGTAIVFVNEEDRNLFPEL 483
>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 = 41.6 bits (98), Expect = 3e-05
Identities = 27/85 (31%), Positives = 37/85 (43%), Gaps = 6/85 (7%)
Query: 5 PNTSSSSSLNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRI 64
N + + F KV++ TN GID V VI++DMP + E+Y
Sbjct: 259 SNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIHYDMP------GNLESYYQEA 312
Query: 65 GRTGRFGKCGIAINLVDEHSVGVLK 89
GR GR G AI L + +LK
Sbjct: 313 GRAGRDGLPAEAILLYSPADIALLK 337
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 38.0 bits (89), Expect = 4e-04
Identities = 22/75 (29%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 20 KEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRIGRTGRFGKCGIAINL 79
+ KV++ TN GID V VI++D+P E+Y GR GR G AI L
Sbjct: 280 EIKVMVATNAFGMGIDKPDVRFVIHYDLP------GSIESYYQETGRAGRDGLPAEAILL 333
Query: 80 VDEHSVGVLKDIEKH 94
+ + + +
Sbjct: 334 YSPEDIRWQRYLIEQ 348
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 35.5 bits (82), Expect = 0.003
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 18/85 (21%)
Query: 22 KVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRIGRTGRFGKCGIAINL-- 79
++++ T GI+ V V++FD+P ++ E+Y GR GR G A+
Sbjct: 288 QIVVATVAFGMGINKPNVRFVVHFDIPRNI------ESYYQETGRAGRDGLPAEAMLFYD 341
Query: 80 ----------VDEHSVGVLKDIEKH 94
++E G +DIE+H
Sbjct: 342 PADMAWLRRCLEEKPAGQQQDIERH 366
>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 = 35.5 bits (82), Expect = 0.003
Identities = 19/79 (24%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 22 KVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRIGRTGRFGKCGIAINLVD 81
+V++ T GI+ V VI++ +P M E+Y GR GR G
Sbjct: 278 QVVVATVAFGMGINKPDVRFVIHYSLPKSM------ESYYQESGRAGRDGLPSECHLFYA 331
Query: 82 EHSVGVLKDI--EKHFGKK 98
+ L+ + E+ G++
Sbjct: 332 PADINRLRRLLMEEPDGQQ 350
>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'. All proteins in this
family for which functions are known are components of
the primosome which is involved in replication, repair,
and recombination.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 = 505
Score = 33.9 bits (78), Expect = 0.011
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 12 SLNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMPIDMNG---QADCETY--LHRI-G 65
LN F + K +LI T ++A+G VT+V D ++ +A + L ++ G
Sbjct: 304 LLNQFANGKADILIGTQMIAKGHHFPNVTLVGVLDADSGLHSPDFRAAERGFQLLTQVAG 363
Query: 66 RTGRFGKCGIAI 77
R GR G I
Sbjct: 364 RAGRAEDPGQVI 375
>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 = 32.0 bits (73), Expect = 0.058
Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 9/62 (14%)
Query: 22 KVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLH--RIGRTGRFGKCGIAINL 79
+I TN L GID+ + VI G R GR GR G+ + + +
Sbjct: 366 LGVIATNALELGIDIGSLDAVI-------AYGYPGVSVLSFRQRAGRAGRRGQESLVLVV 418
Query: 80 VD 81
+
Sbjct: 419 LR 420
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 30.4 bits (69), Expect = 0.16
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 12/51 (23%)
Query: 22 KVLITTNVLARGIDVEQVTIVINFD---MPIDMNGQADCETYLHRIGRTGR 69
VL+ T+V G+D+ +V +VI ++ I + R GRTGR
Sbjct: 427 NVLVATSVGEEGLDIPEVDLVIFYEPVPSEIRS---------IQRKGRTGR 468
>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 = 30.1 bits (68), Expect = 0.20
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 20 KEKVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRI-GRTGR 69
K +LITT +L RG+ V + + + + E+ L +I GR GR
Sbjct: 355 KITLLITTTILERGVTFPNVDVFV-----LGAEHRVFTESALVQIAGRVGR 400
>gnl|CDD|177953 PLN02319, PLN02319, aminomethyltransferase.
Length = 404
Score = 29.7 bits (67), Expect = 0.35
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 7/51 (13%)
Query: 48 PIDMNGQADCETYLHRIGRTGRFGKCGIAINLVDEHSVGVLKDI-EKHFGK 97
D+NG ADC + RTG G+ G I++ EH+V + K + EK GK
Sbjct: 209 ITDING-ADC-----FLTRTGYTGEDGFEISVPSEHAVDLAKALLEKSEGK 253
>gnl|CDD|106159 PRK13190, PRK13190, putative peroxiredoxin; Provisional.
Length = 202
Score = 28.7 bits (64), Expect = 0.66
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 74 GIAINLVDEHSVGVLKDIEKHFGKKIELLDTEDIDDE 110
G++++ + H + L+DIE+ FG KI DID E
Sbjct: 66 GLSVDSIYSH-IAWLRDIEERFGIKIPFPVIADIDKE 101
>gnl|CDD|224711 COG1798, DPH5, Diphthamide biosynthesis methyltransferase
[Translation, ribosomal structure and biogenesis].
Length = 260
Score = 28.4 bits (64), Expect = 0.66
Identities = 9/30 (30%), Positives = 17/30 (56%)
Query: 83 HSVGVLKDIEKHFGKKIELLDTEDIDDEGN 112
L+ +E+ GK++ LLD ED+++
Sbjct: 38 LLGSNLEKLEELIGKEVILLDREDLEENSR 67
>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 = 28.1 bits (63), Expect = 1.3
Identities = 25/94 (26%), Positives = 40/94 (42%), Gaps = 10/94 (10%)
Query: 2 GKGPNTSSSSSLNSFTSCKEKVLITTNVLARGIDVEQV-TIVINFDMPIDMNGQADCETY 60
G+ + F + +VL+ T ++ GID+ TI+I D G A
Sbjct: 694 GQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIE---RADKFGLAQ---- 746
Query: 61 LHRI-GRTGRFGKCGIAINLVDEHSVGVLKDIEK 93
L+++ GR GR K A L H + +D +K
Sbjct: 747 LYQLRGRVGRSKKKAYAYLLY-PHQKALTEDAQK 779
>gnl|CDD|220105 pfam09084, NMT1, NMT1/THI5 like. This family contains the NMT1 and
THI5 proteins. These proteins are proposed to be
required for the biosynthesis of the pyrimidine moiety
of thiamine. They are regulated by thiamine.
Length = 216
Score = 27.5 bits (62), Expect = 1.3
Identities = 13/63 (20%), Positives = 21/63 (33%), Gaps = 10/63 (15%)
Query: 3 KGPNTSSSSSLN-----SFTSCKEKVLITTNVLARGIDVEQVTIV----INFDMPIDMNG 53
K S L S E+ L+ + G D VT+V + + + G
Sbjct: 81 KDSGIKSPKDLKGKRIGYSGSPFEEALLKAMLAKAGGDPSDVTLVNVGGTSLSPAL-LTG 139
Query: 54 QAD 56
+ D
Sbjct: 140 KVD 142
>gnl|CDD|235342 PRK05092, PRK05092, PII uridylyl-transferase; Provisional.
Length = 931
Score = 27.9 bits (63), Expect = 1.3
Identities = 9/18 (50%), Positives = 13/18 (72%), Gaps = 3/18 (16%)
Query: 80 VDEH---SVGVLKDIEKH 94
VDEH ++GVL +IE+
Sbjct: 494 VDEHTIRAIGVLAEIERG 511
>gnl|CDD|215353 PLN02654, PLN02654, acetate-CoA ligase.
Length = 666
Score = 27.6 bits (61), Expect = 1.7
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 8 SSSSSLNSFTSCKEKVLITTNVLARGIDV 36
S+ S CK KV+IT N + RG
Sbjct: 180 SAESLAQRIVDCKPKVVITCNAVKRGPKT 208
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 27.3 bits (61), Expect = 1.9
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 12/75 (16%)
Query: 12 SLNSFTSCKEKVLITTNVLARGIDVEQVTIV--INFDMPIDMNGQAD---CETYLHRI-- 64
L+ F + + +LI T ++A+G D VT+V ++ D + G D E +
Sbjct: 526 LLDQFANGEADILIGTQMIAKGHDFPNVTLVGVLDADTGL---GSPDFRASERTFQLLMQ 582
Query: 65 --GRTGRFGKCGIAI 77
GR GR GK G +
Sbjct: 583 VAGRAGRAGKPGEVV 597
>gnl|CDD|235231 PRK04160, PRK04160, diphthine synthase; Provisional.
Length = 258
Score = 27.1 bits (61), Expect = 2.0
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 88 LKDIEKHFGKKIELLDTEDIDDEG 111
++ +E+ GK+I +LD ED++ E
Sbjct: 43 IEKLEELIGKEIIVLDREDVEQES 66
>gnl|CDD|233007 TIGR00522, dph5, diphthine synthase. Alternate name: diphthamide
biosynthesis S-adenosylmethionine-dependent
methyltransferase. This protein participates in the
modification of a specific His of elongation factor 2 of
eukarotes and Archaea to diphthamide. The protein was
characterized in Saccharomyces cerevisiae and designated
DPH5 [Protein fate, Protein modification and repair].
Length = 257
Score = 26.7 bits (59), Expect = 3.3
Identities = 7/24 (29%), Positives = 18/24 (75%)
Query: 88 LKDIEKHFGKKIELLDTEDIDDEG 111
+++IE+ FGK++ +L+ D+++
Sbjct: 43 IEEIEEFFGKRVVVLERSDVEENS 66
>gnl|CDD|216003 pfam00579, tRNA-synt_1b, tRNA synthetases class I (W and Y).
Length = 291
Score = 26.1 bits (58), Expect = 5.0
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 30 LARGIDVEQVTIVINFDMP 48
LA G+D E+ IV N D
Sbjct: 75 LACGLDPEKSEIVNNSDWL 93
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 26.0 bits (58), Expect = 5.6
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 15/54 (27%)
Query: 23 VLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHR-------IGRTGR 69
VL+ N+L G+D+ +V++V D AD E +L IGR R
Sbjct: 499 VLVGINLLREGLDLPEVSLVAILD--------ADKEGFLRSERSLIQTIGRAAR 544
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 25.7 bits (57), Expect = 5.7
Identities = 9/32 (28%), Positives = 14/32 (43%)
Query: 87 VLKDIEKHFGKKIELLDTEDIDDEGNFRNLTN 118
V K+ E + L+DT +D+EG
Sbjct: 36 VRKEWELLPLGPVVLIDTPGLDEEGGLGRERV 67
>gnl|CDD|239652 cd03680, MM_CoA_mutase_ICM_like, Coenzyme
B12-dependent-methylmalonyl coenzyme A (CoA) mutase
(MCM) family, isobutyryl-CoA mutase (ICM)-like
subfamily; contains archaeal and bacterial proteins
similar to the large subunit of Streptomyces
cinnamonensis coenzyme B12-dependent ICM. ICM from S.
cinnamonensis is comprised of a large and a small
subunit. The holoenzyme appears to be an alpha2beta2
heterotetramer with up to 2 molecules of coenzyme B12
bound. The small subunit binds coenzyme B12. ICM
catalyzes the reversible rearrangement of n-butyryl-CoA
to isobutyryl-CoA, intermediates in fatty acid and
valine catabolism, which in S. cinnamonensis can be
converted to methylmalonyl-CoA and used in polyketide
synthesis.
Length = 538
Score = 26.1 bits (58), Expect = 5.7
Identities = 15/51 (29%), Positives = 20/51 (39%), Gaps = 14/51 (27%)
Query: 45 FDMPIDMNGQADCETYLHRIGRTGRFGKCGIAINLVDEHSVGVLKDIEKHF 95
FD+P M +D G GK G+AI+ L D+E F
Sbjct: 104 FDLPTLMGYDSDHPMAE------GEVGKVGVAID--------TLADMEILF 140
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 25.7 bits (57), Expect = 6.7
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 6/48 (12%)
Query: 22 KVLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYLHRIGRTGR 69
K ++ T+ L GID+ + +VI P +N +L RIGR G
Sbjct: 306 KAVVATSSLELGIDIGDIDLVIQLGSPKSVN------RFLQRIGRAGH 347
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 26.0 bits (58), Expect = 6.9
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 14/61 (22%)
Query: 13 LNSFTSCKEKVLITTNVLARGIDVEQVTIVINFDMP----IDMNGQADCETYLHRIGRTG 68
L+ F + + VL++T+V G+D+ V +VI F P I + R GRTG
Sbjct: 416 LDKFRAGEFNVLVSTSVAEEGLDIPSVDLVI-FYEPVPSEIRS---------IQRKGRTG 465
Query: 69 R 69
R
Sbjct: 466 R 466
>gnl|CDD|218979 pfam06295, DUF1043, Protein of unknown function (DUF1043). This
family consists of several hypothetical bacterial
proteins of unknown function.
Length = 128
Score = 25.2 bits (55), Expect = 7.4
Identities = 6/16 (37%), Positives = 12/16 (75%)
Query: 89 KDIEKHFGKKIELLDT 104
++++ HF + ELL+T
Sbjct: 46 QELKDHFAQSAELLET 61
>gnl|CDD|235329 PRK05007, PRK05007, PII uridylyl-transferase; Provisional.
Length = 884
Score = 25.7 bits (57), Expect = 8.2
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 80 VDEHSVGVLKDIEK 93
VDEH++ VL +E
Sbjct: 462 VDEHTIRVLLKLES 475
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in this
family for wich functions are known are DNA helicases
that function in the nucleotide excision repair and are
endonucleases that make the 3' incision next to DNA
damage. They are part of a pathway requiring UvrA, UvrB,
UvrC, and UvrD homologs. 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 = 655
Score = 25.3 bits (56), Expect = 8.6
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 15/54 (27%)
Query: 23 VLITTNVLARGIDVEQVTIVINFDMPIDMNGQADCETYL--HR-----IGRTGR 69
VL+ N+L G+D+ +V++V D AD E +L R IGR R
Sbjct: 495 VLVGINLLREGLDLPEVSLVAILD--------ADKEGFLRSERSLIQTIGRAAR 540
>gnl|CDD|223480 COG0403, GcvP, Glycine cleavage system protein P
(pyridoxal-binding), N-terminal domain [Amino acid
transport and metabolism].
Length = 450
Score = 25.3 bits (56), Expect = 9.1
Identities = 11/35 (31%), Positives = 21/35 (60%), Gaps = 4/35 (11%)
Query: 79 LVDEH----SVGVLKDIEKHFGKKIELLDTEDIDD 109
LV + ++ VL+ + G +IE++D +D+DD
Sbjct: 168 LVPKDVHPQTLDVLRTRAEGLGIEIEVVDADDLDD 202
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
0.317 0.137 0.392
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: 5,939,350
Number of extensions: 518429
Number of successful extensions: 543
Number of sequences better than 10.0: 1
Number of HSP's gapped: 519
Number of HSP's successfully gapped: 55
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
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 (21.6 bits)
S2: 53 (24.1 bits)