RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1539
(175 letters)
>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 = 121 bits (307), Expect = 3e-35
Identities = 39/107 (36%), Positives = 59/107 (55%), Gaps = 4/107 (3%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN--VYVLVMCHT 91
F + T Q IP + G D++ QA++G GKTA F++ L++L+ + L++ T
Sbjct: 19 FEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPT 78
Query: 92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
RELA QI++ + K+ N+KV V +GG I K LK P IV
Sbjct: 79 RELALQIAEVARKLGKHT-NLKVVVIYGGTSIDKQIRKLK-RGPHIV 123
>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 = 106 bits (266), Expect = 3e-27
Identities = 50/134 (37%), Positives = 73/134 (54%), Gaps = 12/134 (8%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYV--LVMCHT 91
F E T Q IP + G D+L QA++G GKTA F+L LQ++ + YV L++ T
Sbjct: 49 FEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPT 108
Query: 92 RELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV----G-----LVN 142
RELA QI++E + K + ++V V +GG+ I+K E LK IV G +
Sbjct: 109 RELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKR-GVDIVVATPGRLLDLIKR 167
Query: 143 YETNLSGVVVNVMD 156
+ +LSGV V+D
Sbjct: 168 GKLDLSGVETLVLD 181
>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 = 96.2 bits (240), Expect = 1e-25
Identities = 35/101 (34%), Positives = 52/101 (51%), Gaps = 1/101 (0%)
Query: 38 TSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ 97
T Q + IP + G D+L QA +G GKT F+L LQ L LV+ TRELA Q
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60
Query: 98 ISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
I +E ++ K + ++V + GG +++ LK I+
Sbjct: 61 IYEELKKLFKIL-GLRVALLTGGTSLKEQARKLKKGKADIL 100
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 83.7 bits (208), Expect = 2e-19
Identities = 42/105 (40%), Positives = 63/105 (60%), Gaps = 1/105 (0%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
+ E T Q + +P + G D++ QAK+G GKTA F L LQ+L+ V LV+C TRE
Sbjct: 24 YTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRE 83
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
LA Q++KE R ++++ NIKV GG+P+ + L+ H I+
Sbjct: 84 LADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLE-HGAHII 127
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 73.3 bits (180), Expect = 1e-16
Identities = 29/102 (28%), Positives = 50/102 (49%), Gaps = 3/102 (2%)
Query: 38 TSFQHECIPQAVLG-MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAF 96
+Q E I + G D++ A +G GKT +L L+ L+ VLV+ TRELA
Sbjct: 10 RPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKR-GKGGRVLVLVPTRELAE 68
Query: 97 QISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
Q ++E ++ + VG+ +GG ++ L++ I+
Sbjct: 69 QWAEELKKLGPSLGLKVVGL-YGGDSKREQLRKLESGKTDIL 109
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 74.8 bits (184), Expect = 3e-16
Identities = 56/156 (35%), Positives = 76/156 (48%), Gaps = 29/156 (18%)
Query: 27 RIGESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSN---- 82
R Q +RE T Q + IP + G D++ A++G GKTA F L LQ L T +
Sbjct: 14 RAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGR 73
Query: 83 --VYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVGL 140
V L++ TRELA QI + +SKY+ NI+ V FGG+ I NPQ++ L
Sbjct: 74 RPVRALILTPTRELAAQIGENVRDYSKYL-NIRSLVVFGGVSI----------NPQMMKL 122
Query: 141 VNYETNLSGVVVNVMDVRSGGWWLDLE---ALILSK 173
GV V V + G LDLE A+ L +
Sbjct: 123 ------RGGVDVLVA---TPGRLLDLEHQNAVKLDQ 149
>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 = 69.3 bits (170), Expect = 2e-15
Identities = 31/87 (35%), Positives = 44/87 (50%), Gaps = 4/87 (4%)
Query: 52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN 111
D+L A +G GKT +L L+ L++ VLV+ TRELA Q+++ +
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLK-GGQVLVLAPTRELANQVAERLKELFGE--G 57
Query: 112 IKVGVFFGGLPIQKDEEYLKTHNPQIV 138
IKVG GG I K +E L + IV
Sbjct: 58 IKVGYLIGGTSI-KQQEKLLSGKTDIV 83
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 72.2 bits (177), Expect = 3e-15
Identities = 45/131 (34%), Positives = 67/131 (51%), Gaps = 19/131 (14%)
Query: 41 QHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISK 100
Q ECIP + G D+L A++G GKTA F L L L+ +LV+ TRELA Q+++
Sbjct: 33 QAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAE 92
Query: 101 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKT--HNPQIV-------------GLVNYET 145
FSK+M + V +GG Q+ + L+ PQIV G ++ +
Sbjct: 93 AMTDFSKHMRGVNVVALYGG---QRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDL-S 148
Query: 146 NLSGVVVNVMD 156
LSG+V++ D
Sbjct: 149 KLSGLVLDEAD 159
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 67.3 bits (165), Expect = 1e-13
Identities = 34/105 (32%), Positives = 52/105 (49%), Gaps = 6/105 (5%)
Query: 38 TSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQL----ETTDSNVYVLVMCHTRE 93
T+ Q E IP A+ G D+L A +G GKTA F+L LQ L +L++ TRE
Sbjct: 25 TAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRE 84
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIV 138
LA Q++ + +K+ +++ + GG+ E N IV
Sbjct: 85 LAMQVADQARELAKH-THLDIATITGGVAYMNHAEVFSE-NQDIV 127
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 60.0 bits (146), Expect = 4e-11
Identities = 31/98 (31%), Positives = 49/98 (50%), Gaps = 8/98 (8%)
Query: 30 ESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVY----- 84
E + F T Q +P + G D+ QA++G GKT F+ AT L + +
Sbjct: 24 EKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQ 83
Query: 85 --VLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGG 120
L+M TRELA QI + E ++ + +K+G+ +GG
Sbjct: 84 PRALIMAPTRELAVQIHADAEPLAQ-ATGLKLGLAYGG 120
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 57.1 bits (138), Expect = 4e-10
Identities = 35/106 (33%), Positives = 53/106 (50%), Gaps = 1/106 (0%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRE 93
F + ++ Q I + G D + QA+SG GKTA FV+A LQ ++ + L++ TRE
Sbjct: 48 FEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRE 107
Query: 94 LAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG 139
LA QI K Y+ ++ GG ++ D LK +VG
Sbjct: 108 LAQQIQKVVLALGDYL-KVRCHACVGGTVVRDDINKLKAGVHMVVG 152
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 51.1 bits (122), Expect = 5e-08
Identities = 31/105 (29%), Positives = 52/105 (49%), Gaps = 8/105 (7%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD-------SNVYVL 86
F T Q + + + G D + +A++G GKTA F+++ + QL T L
Sbjct: 107 FPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRAL 166
Query: 87 VMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK 131
++ TREL QI+K+ +KY + + V F GG+ K + L+
Sbjct: 167 IIAPTRELVVQIAKDAAALTKY-TGLNVMTFVGGMDFDKQLKQLE 210
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 50.5 bits (121), Expect = 8e-08
Identities = 34/94 (36%), Positives = 49/94 (52%), Gaps = 6/94 (6%)
Query: 34 FREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATL-----QQLETTDSNVYVLVM 88
F E T Q + P A+ G D++ A++G GKT F+L + Q L VLV+
Sbjct: 150 FTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVL 209
Query: 89 CHTRELAFQISKEYERFSKYMSNIKVGVFFGGLP 122
TRELA QI ++ +F S I+ V +GG+P
Sbjct: 210 APTRELAEQIREQCNKFGA-SSKIRNTVAYGGVP 242
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 50.3 bits (120), Expect = 1e-07
Identities = 33/109 (30%), Positives = 55/109 (50%), Gaps = 8/109 (7%)
Query: 30 ESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNV------ 83
ES F T Q +P A+ G D+ QA++G GKT F++A + +L + +
Sbjct: 25 ESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPED 84
Query: 84 -YVLVMCHTRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLK 131
L++ TRELA QI K+ +F + ++ + +GG+ K E L+
Sbjct: 85 PRALILAPTRELAIQIHKDAVKFGADLG-LRFALVYGGVDYDKQRELLQ 132
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 40.9 bits (96), Expect = 1e-04
Identities = 35/134 (26%), Positives = 59/134 (44%), Gaps = 16/134 (11%)
Query: 38 TSFQHECIPQAVLGMDILCQAKSGMGKTAVFVL------ATLQQLETTDS-NVYVLVMCH 90
T Q + IP A+ G +L A +G GKTA F++ T++ ++ N +V+
Sbjct: 145 TPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTP 204
Query: 91 TRELAFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVG--------LVN 142
TREL Q+ + + K + K + GG + + ++ IVG L
Sbjct: 205 TRELCVQVEDQAKVLGKGLP-FKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSK 263
Query: 143 YETNLSGVVVNVMD 156
++ L V V V+D
Sbjct: 264 HDIELDNVSVLVLD 277
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 38.6 bits (90), Expect = 9e-04
Identities = 32/134 (23%), Positives = 54/134 (40%), Gaps = 23/134 (17%)
Query: 10 GVTVKVLSSRNRREKEDRI-GESQPFREQTSF-------QHECIPQAV----LGMDILCQ 57
G + LSS+ E D + E P + +F Q E + V +
Sbjct: 2 GDLKQYLSSKGAEELADYVLDEGLPLKLIVAFEFELRPYQEEALDALVKNRRTERRGVIV 61
Query: 58 AKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIKVGVF 117
+G GKT V A + LV+ T+EL Q ++ ++F + N ++G++
Sbjct: 62 LPTGAGKTVVAAEAI------AELKRSTLVLVPTKELLDQWAEALKKF--LLLNDEIGIY 113
Query: 118 FGGLPIQKDEEYLK 131
GG +K+ E K
Sbjct: 114 GGG---EKELEPAK 124
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 34.7 bits (80), Expect = 0.020
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 53 DILCQAKSGMGKTAVFVLATLQQL-ETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN 111
++L A +G GKT + +LA L L E VY+ + LA + +E+ R +
Sbjct: 49 NVLISAPTGSGKTLIALLAILSTLLEGGGKVVYI---VPLKALAEEKYEEFSRLEEL--G 103
Query: 112 IKVGVFFGGLP 122
I+VG+ G
Sbjct: 104 IRVGISTGDYD 114
>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 = 32.4 bits (74), Expect = 0.097
Identities = 26/120 (21%), Positives = 49/120 (40%), Gaps = 14/120 (11%)
Query: 29 GESQPFREQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVM 88
G + + Q + + G +++ +G GKT F+L L L S +L+
Sbjct: 67 GIERLYS----HQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLY 122
Query: 89 CHTRELAFQISKEYERFSKYMSN----IKVGVFFGGLPIQKDEEYLKTHNPQIVGLVNYE 144
T LA + ER + +S+ + G + G P ++ + + P I+ L N +
Sbjct: 123 -PTNALAND---QAERLRELISDLPGKVTFGRYTGDTP-PEERRAIIRNPPDIL-LTNPD 176
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 32.3 bits (74), Expect = 0.11
Identities = 19/99 (19%), Positives = 38/99 (38%), Gaps = 8/99 (8%)
Query: 45 IPQAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYER 104
I L + L +G+GKT + + +L VL + T+ L Q ++ +
Sbjct: 23 IAAKALFKNTLVVLPTGLGKTFIAAMVIANRLRWFGG--KVLFLAPTKPLVLQHAEFCRK 80
Query: 105 FSKYMSNIKVGVFFGGLPIQKDEEYLKTHN-----PQIV 138
+ + ++ G + ++ EE PQ+V
Sbjct: 81 VTG-IPEDEIAALTGEVRPEEREELWAKKKVFVATPQVV 118
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 29.8 bits (68), Expect = 0.71
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 9/77 (11%)
Query: 55 LCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI-- 112
L +G+GKTA+ +L ++L VL++ T+ L Q E F K++ NI
Sbjct: 33 LVVLPTGLGKTAIALLVIAERLHKKGGK--VLILAPTKPLVEQ---HAEFFRKFL-NIPE 86
Query: 113 -KVGVFFGGLPIQKDEE 128
K+ VF G + +K E
Sbjct: 87 EKIVVFTGEVSPEKRAE 103
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 30.0 bits (68), Expect = 0.75
Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 8/83 (9%)
Query: 52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS- 110
M+ L Q G GKT V LA L ++ V +M T LA Q Y ++
Sbjct: 257 MNRLLQGDVGSGKTLVAALAMLA---AIEAGYQVALMAPTEILAEQ---HYNSLRNLLAP 310
Query: 111 -NIKVGVFFGGLPIQKDEEYLKT 132
I+V + G L ++ +E L+T
Sbjct: 311 LGIEVALLTGSLKGKRRKELLET 333
>gnl|CDD|187839 cd09708, Csf4_U, CRISPR/Cas system-associated DinG family helicase
Csf4. CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
DinG family DNA helicase.
Length = 632
Score = 29.9 bits (67), Expect = 0.75
Identities = 26/102 (25%), Positives = 39/102 (38%), Gaps = 8/102 (7%)
Query: 36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQL-ETTDSNVYVLVMCHTREL 94
EQ F C+ + +A +G+GKT ++A L L E D + + V L
Sbjct: 1 EQALFYRNCLTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKERPDQKIAIAVPTLA--L 58
Query: 95 AFQISKEYERFSKYMSNIKV-GVFFGG----LPIQKDEEYLK 131
Q+ E ER + V FF G + +E L
Sbjct: 59 MGQLWSELERLTAEGLAGPVQAGFFPGSQEFVSPGALQELLD 100
>gnl|CDD|234113 TIGR03117, cas_csf4, CRISPR type AFERR-associated DEAD/DEAH-box
helicase Csf4. Members of this family show up near
CRISPR repeats in Acidithiobacillus ferrooxidans ATCC
23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens
DSM 15236. In the latter two species, the CRISPR/cas
locus is found on a plasmid. This family is one of
several characteristic of a type of CRISPR-associated
(cas) gene cluster we designate Aferr after A.
ferrooxidans, where it is both chromosomal and the only
type of cas gene cluster found. The gene is designated
csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein
1), as it lies farthest (fourth closest) from the
repeats in the A. ferrooxidans genome [Mobile and
extrachromosomal element functions, Other].
Length = 636
Score = 29.9 bits (67), Expect = 0.75
Identities = 26/102 (25%), Positives = 39/102 (38%), Gaps = 8/102 (7%)
Query: 36 EQTSFQHECIPQAVLGMDILCQAKSGMGKTAVFVLATLQQL-ETTDSNVYVLVMCHTREL 94
EQ F C+ + +A +G+GKT ++A L L E D + + V L
Sbjct: 1 EQALFYLNCLTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKERPDQKIAIAVPTLA--L 58
Query: 95 AFQISKEYERFSKYMSNIKV-GVFFGG----LPIQKDEEYLK 131
Q+ E ER + V FF G + +E L
Sbjct: 59 MGQLWSELERLTAEGLAGPVQAGFFPGSQEFVSPGALQELLD 100
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are components
of TFIIH, a complex that is involved in nucleotide
excision repair and transcription initiation. Also known
as MAT1 (menage a trois 1). 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 = 309
Score = 29.4 bits (66), Expect = 0.97
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 11/80 (13%)
Query: 71 ATLQQLETTDSNVYVLVMCHTRELAFQISKEYERF-----SKYMSNIKVGVFFGGLPIQK 125
A L +LET+ L+ H + + ++ + E+ + + + IK+G +P+QK
Sbjct: 182 ALLDELETSTLPAAELIAQHKKN-SVKLEMQVEKPKPEKPNTFSTGIKMGYQISLVPVQK 240
Query: 126 DEEYLKTHNPQIVGLVNYET 145
EE L + P +N ET
Sbjct: 241 SEEALYPYQP-----LNIET 255
>gnl|CDD|129307 TIGR00203, cydB, cytochrome d oxidase, subunit II (cydB). part of
a two component cytochrome D terminal complex. Terminal
reaction in the aerobic respiratory chain [Energy
metabolism, Electron transport].
Length = 378
Score = 27.5 bits (61), Expect = 3.8
Identities = 18/57 (31%), Positives = 23/57 (40%), Gaps = 4/57 (7%)
Query: 114 VGVFFG----GLPIQKDEEYLKTHNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDL 166
GV FG G+P DE + L+N + L GV M + G WL L
Sbjct: 134 FGVAFGNLLQGVPFDFDENLRVHYTGSFFQLLNPFSLLCGVTSLGMCITHGAMWLQL 190
>gnl|CDD|234013 TIGR02785, addA_Gpos, helicase-exonuclease AddAB, AddA subunit,
Firmicutes type. AddAB, also called RexAB, substitutes
for RecBCD in several bacterial lineages. These DNA
recombination proteins act before synapse and are
particularly important for DNA repair of
double-stranded breaks by homologous recombination. The
term AddAB is used broadly, with AddA homologous
between the Firmicutes (as modeled here) and the
alphaproteobacteria, while the partner AddB proteins
show no strong homology across the two groups of
species [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1230
Score = 27.7 bits (62), Expect = 4.2
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 51 GMDILCQAKSGMGKTAVFVLATLQQL 76
G DIL A +G GKTAV V ++++
Sbjct: 14 GQDILVSASAGSGKTAVLVERIIRKI 39
>gnl|CDD|215681 pfam00054, Laminin_G_1, Laminin G domain.
Length = 131
Score = 26.5 bits (59), Expect = 4.4
Identities = 6/29 (20%), Positives = 12/29 (41%)
Query: 111 NIKVGVFFGGLPIQKDEEYLKTHNPQIVG 139
++ ++ GGLP + +P G
Sbjct: 90 DVDGPLYVGGLPSLAVKLRRLAISPSFDG 118
>gnl|CDD|236749 PRK10742, PRK10742, putative methyltransferase; Provisional.
Length = 250
Score = 27.0 bits (60), Expect = 5.3
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 52 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTR 92
M I ++G G A+ VLA LE + N+ LV+
Sbjct: 1 MKICLIDETGAGDGALSVLAARWGLEHDEDNLMALVLTPEH 41
>gnl|CDD|99709 cd05826, Sortase_B_2, Sortase B (SrtB) or subfamily-2 sortases are
membrane cysteine transpeptidases found in gram-positive
bacteria that anchor surface proteins to peptidoglycans
of the bacterial cell wall envelope. This involves a
transpeptidation reaction in which the surface protein
substrate is cleaved at a conserved cell wall sorting
signal and covalently linked to peptidoglycan for
display on the bacterial surface. Sortases are grouped
into different classes and subfamilies based on
sequence, membrane topology, genomic positioning, and
cleavage site preference. Sortase B cleaves surface
protein precursors between threonine and asparagine at a
conserved NPQTN motif with subsequent covalent linkage
to peptidoglycan. It is required for anchoring the
heme-iron binding surface protein IsdC to the cell wall
envelope and the gene encoding Sortase B is located
within the isd locus in S. aureus and B. anthracis. It
may also play a role in pathogenesis. Sortase B contains
an N-terminal region that functions as both a signal
peptide for secretion and a stop-transfer signal for
membrane anchoring. At the C-terminus, it contains the
catalytic TLXTC signature sequence, where X is usually a
serine. Genes encoding SrtB and its targets are
generally clustered in the same locus.
Length = 209
Score = 26.4 bits (59), Expect = 6.6
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 111 NIKVGVFFGGLPIQKDEEYLKTH 133
N+K G FG L KD+E+ K H
Sbjct: 102 NMKNGSMFGDLDKYKDKEFFKKH 124
>gnl|CDD|215094 PLN00188, PLN00188, enhanced disease resistance protein (EDR2);
Provisional.
Length = 719
Score = 27.1 bits (60), Expect = 7.1
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 9 HGVTVKVLSSRNRREKEDRI 28
HG V VLS N++EK RI
Sbjct: 69 HGHMVYVLSVYNKKEKYHRI 88
>gnl|CDD|225841 COG3304, COG3304, Predicted membrane protein [Function unknown].
Length = 145
Score = 26.3 bits (58), Expect = 7.1
Identities = 9/34 (26%), Positives = 15/34 (44%)
Query: 133 HNPQIVGLVNYETNLSGVVVNVMDVRSGGWWLDL 166
H ++ N G ++N++ GWWL L
Sbjct: 58 HVDELTPAKNVLAGTGGALLNIIWFILFGWWLAL 91
>gnl|CDD|232933 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR
family. This gene is part of the type I restriction and
modification system which is composed of three
polypeptides R (restriction endonuclease), M
(modification) and S (specificity). This group of
enzymes recognize specific short DNA sequences and have
an absolute requirement for ATP (or dATP) and
S-adenosyl-L-methionine. They also catalyse the
reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar
site specificity.(J. Mol. Biol. 271 (3), 342-348
(1997)). Members of this family are assumed to differ
from each other in DNA site specificity [DNA metabolism,
Restriction/modification].
Length = 667
Score = 26.6 bits (59), Expect = 7.9
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 61 GMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSK 107
G GKT + A + LE N V + REL +Q+ KE++ K
Sbjct: 273 GSGKTLTMLFAARKALEL-LKNPKVFFVVDRRELDYQLMKEFQSLQK 318
>gnl|CDD|217683 pfam03709, OKR_DC_1_N, Orn/Lys/Arg decarboxylase, N-terminal
domain. This domain has a flavodoxin-like fold, and is
termed the "wing" domain because of its position in the
overall 3D structure.
Length = 111
Score = 25.7 bits (57), Expect = 8.1
Identities = 8/50 (16%), Positives = 20/50 (40%), Gaps = 9/50 (18%)
Query: 120 GLPIQKDEEYLKTHNPQIVGLVNYE---------TNLSGVVVNVMDVRSG 160
++ E L+ ++V + + T+++ VV++ D G
Sbjct: 3 IAASRELAEALERTGREVVYATSTDDLLSLIENFTDIAAVVLSWDDEARG 52
>gnl|CDD|132806 cd06896, PX_PI3K_C2_gamma, The phosphoinositide binding Phox
Homology Domain of the Gamma Isoform of Class II
Phosphoinositide 3-Kinases. The PX domain is a
phosphoinositide (PI) binding module present in many
proteins with diverse functions. The Phosphoinositide
3-Kinase (PI3K) family of enzymes catalyzes the
phosphorylation of the 3-hydroxyl group of the inositol
ring of phosphatidylinositol. PI3Ks play an important
role in a variety of fundamental cellular processes,
including cell motility, the Ras pathway, vesicle
trafficking and secretion, immune cell activation and
apoptosis. PI3Ks are divided into three main classes (I,
II, and III) based on their substrate specificity,
regulation, and domain structure. Class II PI3Ks
preferentially use PI as a substrate to produce PI3P,
but can also phosphorylate PI4P to produce PI(3,4)P2.
They function as monomers and do not associate with any
regulatory subunits. Class II enzymes contain an
N-terminal Ras binding domain, a lipid binding C2
domain, a PI3K homology domain of unknown function, an
ATP-binding cataytic domain, a PX domain, and a second
C2 domain at the C-terminus. The class II gamma isoform,
PI3K-C2gamma, is expressed in the liver, breast, and
prostate. It's biological function remains unknown. The
PX domain is involved in targeting of proteins to
PI-enriched membranes, and may also be involved in
protein-protein interaction.
Length = 101
Score = 25.6 bits (56), Expect = 8.7
Identities = 11/43 (25%), Positives = 22/43 (51%)
Query: 71 ATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNIK 113
AT+ SN+Y++ + + L K +E+FS+ S ++
Sbjct: 2 ATILGFSKKSSNLYLVQVTQSCNLVSLTEKSFEQFSELHSQLQ 44
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
0.321 0.135 0.399
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,677,424
Number of extensions: 772434
Number of successful extensions: 677
Number of sequences better than 10.0: 1
Number of HSP's gapped: 664
Number of HSP's successfully gapped: 36
Length of query: 175
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 85
Effective length of database: 6,945,742
Effective search space: 590388070
Effective search space used: 590388070
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: 56 (25.5 bits)