RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4275
(182 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 = 200 bits (510), Expect = 8e-66
Identities = 75/156 (48%), Positives = 100/156 (64%), Gaps = 3/156 (1%)
Query: 8 FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
F +L L+P L+R +G + PT IQ IP +L+ D IG A+TGSGKT AF +PIL+K
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60
Query: 68 W--CEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKP 125
G AL+L PTRELA QI + LGK NL+V +I GG + Q ++L + P
Sbjct: 61 LDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGP 120
Query: 126 HIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
HIV+ATPGRL D L+ L+++K+LVLDEADR+
Sbjct: 121 HIVVATPGRLLDLLER-GKLDLSKVKYLVLDEADRM 155
>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 = 192 bits (490), Expect = 2e-59
Identities = 69/163 (42%), Positives = 99/163 (60%), Gaps = 4/163 (2%)
Query: 2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
E F L L+P L++ + +G + PT IQ A IP +L D +G A+TG+GKT AF
Sbjct: 25 EKTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFL 84
Query: 62 LPILQK--WCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQG 118
LP+LQK + + AL+L PTRELA QI ++ LGK + LRV+++ GG+ + Q
Sbjct: 85 LPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQI 144
Query: 119 KELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
+ L + IV+ATPGRL D + L+ ++ LVLDEADR+
Sbjct: 145 EALKRGVDIVVATPGRLLDLIKR-GKLDLSGVETLVLDEADRM 186
>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 = 158 bits (402), Expect = 6e-50
Identities = 66/136 (48%), Positives = 84/136 (61%), Gaps = 1/136 (0%)
Query: 30 TEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQ 89
T IQ IP +L+ +D + A TGSGKTLAF LPILQ G ALVL PTRELA Q
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQ 60
Query: 90 IGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAK-KPHIVIATPGRLADHLDTCNTFSLN 148
I ++ L K++ LRV+++TGG + +Q ++L K K I++ TPGRL D L L
Sbjct: 61 IYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLK 120
Query: 149 RIKFLVLDEADRLSLM 164
+K LVLDEA RL M
Sbjct: 121 NLKLLVLDEAHRLLDM 136
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 143 bits (362), Expect = 7e-41
Identities = 65/156 (41%), Positives = 88/156 (56%), Gaps = 2/156 (1%)
Query: 6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL 65
+F+ L L P L+ +G T IQ +P +L +D I AKTGSGKT AF L +L
Sbjct: 4 TAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLL 63
Query: 66 QKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVM-NLRVSIITGGMDMVDQGKELAKK 124
QK + + ALVL PTRELA Q+ + L + + N++V + GG+ M Q L
Sbjct: 64 QKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHG 123
Query: 125 PHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR 160
HI++ TPGR+ DHL T L+ + LVLDEADR
Sbjct: 124 AHIIVGTPGRILDHLRK-GTLDLDALNTLVLDEADR 158
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 136 bits (346), Expect = 7e-39
Identities = 64/158 (40%), Positives = 91/158 (57%), Gaps = 5/158 (3%)
Query: 8 FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
F++L+L+ L+ Q G PT IQ IP L+ D +G A TG+GKT AF LP LQ
Sbjct: 3 FSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQH 62
Query: 68 WCEDP--YGIFA--LVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAK 123
+ P L+LTPTRELA Q+ DQ L K +L ++ ITGG+ ++ + ++
Sbjct: 63 LLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSE 122
Query: 124 KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
IV+ATPGRL ++ N F ++ L+LDEADR+
Sbjct: 123 NQDIVVATPGRLLQYIKEEN-FDCRAVETLILDEADRM 159
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 123 bits (311), Expect = 6e-36
Identities = 55/142 (38%), Positives = 74/142 (52%), Gaps = 4/142 (2%)
Query: 25 GVKTPTEIQKAIIPHVL-NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT 83
G + QK I +L D I A TGSGKTLA LP L+ G LVL PT
Sbjct: 5 GFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGR-VLVLVPT 63
Query: 84 RELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAK-KPHIVIATPGRLADHLDTC 142
RELA Q ++ LG + L+V + GG +Q ++L K I++ TPGRL D L+
Sbjct: 64 RELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLEN- 122
Query: 143 NTFSLNRIKFLVLDEADRLSLM 164
+ SL+ + ++LDEA RL
Sbjct: 123 DKLSLSNVDLVILDEAHRLLDG 144
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 125 bits (316), Expect = 2e-34
Identities = 66/164 (40%), Positives = 94/164 (57%), Gaps = 7/164 (4%)
Query: 7 SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
SF L L+P ++R G + PT IQ+ IP VL D + A+TG+GKT F LP+LQ
Sbjct: 2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61
Query: 67 KWCEDPYG------IFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE 120
+ AL+LTPTRELA QIG+ K +N+R ++ GG+ + Q +
Sbjct: 62 HLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMK 121
Query: 121 LAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM 164
L +++ATPGRL D L+ N L++++ LVLDEADR+ M
Sbjct: 122 LRGGVDVLVATPGRLLD-LEHQNAVKLDQVEILVLDEADRMLDM 164
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 124 bits (313), Expect = 1e-33
Identities = 66/165 (40%), Positives = 90/165 (54%), Gaps = 2/165 (1%)
Query: 1 MEDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAF 60
M + +F DL L ++ +G + P+ IQ IPH+LN D +G A+TGSGKT AF
Sbjct: 1 MAEFETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAF 60
Query: 61 ALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMN-LRVSIITGGMDMVDQGK 119
+LP+L + LVL PTRELA Q+ + K M + V + GG Q +
Sbjct: 61 SLPLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLR 120
Query: 120 ELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM 164
L + P IV+ TPGRL DHL T L+++ LVLDEAD + M
Sbjct: 121 ALRQGPQIVVGTPGRLLDHLKR-GTLDLSKLSGLVLDEADEMLRM 164
>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 = 113 bits (286), Expect = 9e-33
Identities = 51/126 (40%), Positives = 66/126 (52%), Gaps = 3/126 (2%)
Query: 44 EDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL 103
D + A TGSGKTLA LPIL+ G LVL PTRELA Q+ ++ L +
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQ-VLVLAPTRELANQVAERLKELFGE-GI 58
Query: 104 RVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSL 163
+V + GG + Q K L+ K IV+ TPGRL D L+ SL ++ L+LDEA RL
Sbjct: 59 KVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELER-LKLSLKKLDLLILDEAHRLLN 117
Query: 164 MTSLKF 169
Sbjct: 118 QGFGLL 123
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 119 bits (299), Expect = 1e-31
Identities = 66/166 (39%), Positives = 88/166 (53%), Gaps = 6/166 (3%)
Query: 4 PIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALP 63
P+ SF ++++ + G PT IQ P L+ D IG A+TGSGKTLAF LP
Sbjct: 128 PVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLP 187
Query: 64 ILQKWCEDPY-----GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQG 118
+ P G LVL PTRELA QI +Q G +R ++ GG+ Q
Sbjct: 188 AIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPKRGQI 247
Query: 119 KELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM 164
L + I+IA PGRL D L++ N +L R+ +LVLDEADR+ M
Sbjct: 248 YALRRGVEILIACPGRLIDFLES-NVTNLRRVTYLVLDEADRMLDM 292
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 111 bits (278), Expect = 7e-29
Identities = 61/164 (37%), Positives = 88/164 (53%), Gaps = 8/164 (4%)
Query: 3 DPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFAL 62
PI SF+ L P L+ +T G + PT IQ IP L+ + A TGSGKT +F +
Sbjct: 118 PPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLV 177
Query: 63 PILQKWC-------EDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMV 115
PI+ + C + A+VLTPTREL Q+ DQ VLGK + + +++ GG M
Sbjct: 178 PIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMP 237
Query: 116 DQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEAD 159
Q + + +++ TPGRL D L + + L+ + LVLDE D
Sbjct: 238 QQLYRIQQGVELIVGTPGRLIDLL-SKHDIELDNVSVLVLDEVD 280
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 106 bits (267), Expect = 2e-27
Identities = 61/165 (36%), Positives = 84/165 (50%), Gaps = 9/165 (5%)
Query: 8 FTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK 67
F D L P L+ +G T IQ ++ + L D IG A+TG+GKT AF + I+ +
Sbjct: 89 FHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQ 148
Query: 68 WCEDPYG-------IFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKE 120
+ P AL++ PTREL QI L K L V GGMD Q K+
Sbjct: 149 LLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMDFDKQLKQ 208
Query: 121 L-AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLM 164
L A+ I++ATPGRL D + L+ ++ +VLDEADR+ M
Sbjct: 209 LEARFCDILVATPGRLLD-FNQRGEVHLDMVEVMVLDEADRMLDM 252
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 104 bits (261), Expect = 6e-27
Identities = 59/160 (36%), Positives = 87/160 (54%), Gaps = 1/160 (0%)
Query: 2 EDPIKSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFA 61
++ + SF LKLN L+R + G + P+ IQ+ I +L+ D IG A++G+GKT F
Sbjct: 24 DEIVDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFV 83
Query: 62 LPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKEL 121
+ LQ D AL+L PTRELA QI L LG + +R GG + D +L
Sbjct: 84 IAALQLIDYDLNACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKL 143
Query: 122 AKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
H+V+ TPGR+ D +D ++ +K +LDEAD +
Sbjct: 144 KAGVHMVVGTPGRVYDMIDK-RHLRVDDLKLFILDEADEM 182
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 105 bits (262), Expect = 1e-26
Identities = 60/165 (36%), Positives = 89/165 (53%), Gaps = 13/165 (7%)
Query: 7 SFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQ 66
+F+ L+P L+ ++ G T IQ +P L D G A+TG+GKTLAF + ++
Sbjct: 10 TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMN 69
Query: 67 KWC----------EDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVD 116
+ EDP AL+L PTRELA QI + G + LR +++ GG+D
Sbjct: 70 RLLSRPALADRKPEDPR---ALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDK 126
Query: 117 QGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
Q + L + ++IATPGRL D++ SL+ + VLDEADR+
Sbjct: 127 QRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRM 171
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 92.7 bits (231), Expect = 1e-22
Identities = 58/171 (33%), Positives = 82/171 (47%), Gaps = 11/171 (6%)
Query: 6 KSFTDLKLNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALP-- 63
+ F+D L+P ++ + G T IQ +P L D G A+TG+GKT+AF
Sbjct: 8 QKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATF 67
Query: 64 --ILQKWCEDPYGIF---ALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQG 118
+L + + AL++ PTRELA QI L + L++ + GG Q
Sbjct: 68 HYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQL 127
Query: 119 KELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKF 169
K L I+I T GRL D+ N +L I+ +VLDEADR M L F
Sbjct: 128 KVLESGVDILIGTTGRLIDYAKQ-NHINLGAIQVVVLDEADR---MFDLGF 174
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 74.2 bits (183), Expect = 8e-16
Identities = 41/152 (26%), Positives = 72/152 (47%), Gaps = 9/152 (5%)
Query: 13 LNPWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDP 72
L+P + + + T Q+ IP + + E+ + A TGSGKT A LP++ +
Sbjct: 8 LDPRVREWFKRKF-TSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLG 66
Query: 73 Y-----GIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHI 127
GI+AL ++P + L I + + + + V++ G ++ K L PHI
Sbjct: 67 KGKLEDGIYALYISPLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHI 126
Query: 128 VIATPGRLADHLDTCNTFS--LNRIKFLVLDE 157
+I TP LA L F L ++++++DE
Sbjct: 127 LITTPESLAILL-NSPKFRELLRDVRYVIVDE 157
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 65.1 bits (159), Expect = 9e-13
Identities = 40/128 (31%), Positives = 64/128 (50%), Gaps = 9/128 (7%)
Query: 32 IQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIG 91
Q+A+ +L+DE+ + A TGSGKTL L IL E G + + P + LA +
Sbjct: 36 QQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLE--GGGKVVYIVPLKALAEEKY 93
Query: 92 DQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSL-NRI 150
++F L + + +RV I TG D+ E + +++ TP +L D L T S +
Sbjct: 94 EEFSRL-EELGIRVGISTGDYDL---DDERLARYDVIVTTPEKL-DSL-TRKRPSWIEEV 147
Query: 151 KFLVLDEA 158
+V+DE
Sbjct: 148 DLVVIDEI 155
>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 = 59.0 bits (143), Expect = 1e-10
Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 20/129 (15%)
Query: 42 NDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQ---FLVLG 98
+ + TGSGKT +F LPIL DP AL+L PT LA DQ L
Sbjct: 84 EGRNVVVTTGTGSGKTESFLLPILDHLLRDPSAR-ALLLYPTNALAN---DQAERLRELI 139
Query: 99 KVM--NLRVSIITGGMDMVDQGKE---LAKKPHIVIATPGRLADHLDTCNT----FSLNR 149
+ + TG D + + P I++ P L +L N + L
Sbjct: 140 SDLPGKVTFGRYTG--D-TPPEERRAIIRNPPDILLTNPDML-HYLLLRNHDAWLWLLRN 195
Query: 150 IKFLVLDEA 158
+K+LV+DE
Sbjct: 196 LKYLVVDEL 204
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 50.3 bits (121), Expect = 1e-07
Identities = 45/153 (29%), Positives = 72/153 (47%), Gaps = 25/153 (16%)
Query: 27 KTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL-------QKW-CEDPYGIFAL 78
T T Q+ IP + ++ + + TGSGKTLA L I+ ++ ED ++ L
Sbjct: 31 GTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELED--KVYCL 88
Query: 79 VLTPTRELA-----------YQIGDQFLVLG-KVMNLRVSIITGGMDMVDQGKELAKKPH 126
++P R L +I + G ++ +RV+I TG ++ K L K PH
Sbjct: 89 YVSPLRALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPH 148
Query: 127 IVIATPGRLADHLDTCNTFS--LNRIKFLVLDE 157
I+I TP LA L F L +K++++DE
Sbjct: 149 ILITTPESLAILL-NSPKFREKLRTVKWVIVDE 180
>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 = 44.5 bits (106), Expect = 1e-05
Identities = 38/114 (33%), Positives = 50/114 (43%), Gaps = 5/114 (4%)
Query: 28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQK--WCEDP-YGIFALVLTPTR 84
TP Q + L + A TGSGKTLA LP L E P G+ L +TP R
Sbjct: 13 TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKPKKGLHTLYITPLR 72
Query: 85 ELAYQIGDQFLVLGKVMNL--RVSIITGGMDMVDQGKELAKKPHIVIATPGRLA 136
LA I + + L RV TG ++ ++ K P I++ TP LA
Sbjct: 73 ALAVDIARNLQAPIEELGLPIRVETRTGDTSSSERARQRKKPPDILLTTPESLA 126
>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative
DEAH-box helicase. A conserved gene neighborhood
widely spread in the Actinobacteria contains this
uncharacterized DEAH-box family helicase encoded
convergently towards an operon of genes for protein
homologous to type II secretion and pilus formation
proteins. The context suggests that this helicase may
play a role in conjugal transfer of DNA.
Length = 742
Score = 44.0 bits (104), Expect = 2e-05
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 4/79 (5%)
Query: 15 PWLIRQCQTIGVKTPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYG 74
P ++ + G+ P + Q + T SGK+LA+ LP+L +DP
Sbjct: 23 PDVVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDP-R 81
Query: 75 IFALVLTPTRELAYQIGDQ 93
AL L PT+ LA DQ
Sbjct: 82 ATALYLAPTKALAA---DQ 97
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 41.7 bits (98), Expect = 9e-05
Identities = 31/113 (27%), Positives = 42/113 (37%), Gaps = 19/113 (16%)
Query: 52 TGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGG 111
TG+GKT+ A I + LVL PT+EL Q + +N + I GG
Sbjct: 64 TGAGKTVVAAEAIAE------LKRSTLVLVPTKELLDQWAEALKKFLL-LNDEIGIYGGG 116
Query: 112 MDMVDQGKELAKKPHIVIAT--PGRLADHLDTCNTFSLNRIKFLVLDEADRLS 162
KEL + +AT LD F N ++ DE L
Sbjct: 117 E------KELEPA-KVTVATVQTLARRQLLD---EFLGNEFGLIIFDEVHHLP 159
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 36.9 bits (86), Expect = 0.004
Identities = 28/121 (23%), Positives = 52/121 (42%), Gaps = 13/121 (10%)
Query: 53 GSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGM 112
GSGKTL AL +L G ++ PT LA Q + L + + V+++TG +
Sbjct: 266 GSGKTLVAALAMLAAI---EAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSL 322
Query: 113 DMVDQGKELAK----KPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLK 168
+ + L + H+V+ T + + ++ R+ +++DE R + K
Sbjct: 323 KGKRRKELLETIASGQIHLVVGTHALIQEKVE------FKRLALVIIDEQHRFGVEQRKK 376
Query: 169 F 169
Sbjct: 377 L 377
>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 = 36.7 bits (85), Expect = 0.005
Identities = 36/136 (26%), Positives = 51/136 (37%), Gaps = 25/136 (18%)
Query: 33 QKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGD 92
Q +I VL DC TG GK+L + LP L C D + V++P L + D
Sbjct: 16 QLEVINAVLLGRDCFVVMPTGGGKSLCYQLPAL---CSDGITL---VISPLISL---MED 66
Query: 93 QFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPH---------IVIATPGRLADHLDTCN 143
Q V+ L+ S I Q KE K ++ TP + +
Sbjct: 67 Q------VLQLKASGIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQ 120
Query: 144 TF-SLNRIKFLVLDEA 158
T I + +DEA
Sbjct: 121 TLEERKGITLIAVDEA 136
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 35.3 bits (81), Expect = 0.016
Identities = 41/138 (29%), Positives = 66/138 (47%), Gaps = 24/138 (17%)
Query: 33 QKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGD 92
Q+ II ++ D TG GK+L + LP L C GI LV++P L I D
Sbjct: 465 QREIINATMSGYDVFVLMPTGGGKSLTYQLPAL--ICP---GI-TLVISPLVSL---IQD 515
Query: 93 QFLVLGKVMNLRVSIITGGMDMVDQGK---ELAK---KPHIVIATPGRLAD------HLD 140
Q + L + N+ + ++ GM+ +Q + EL+ K ++ TP ++A HL+
Sbjct: 516 QIMNLLQA-NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLE 574
Query: 141 TCNTFSLNRIKFLVLDEA 158
N+ L + V+DEA
Sbjct: 575 NLNSRGL--LARFVIDEA 590
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 34.8 bits (81), Expect = 0.017
Identities = 36/127 (28%), Positives = 54/127 (42%), Gaps = 34/127 (26%)
Query: 49 CAKTGSGKTLAFALPI---LQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNL-- 103
TG GKT L I L K G L+L PT+ L Q + F K +N+
Sbjct: 35 VLPTGLGKTAIALLVIAERLHK-----KGGKVLILAPTKPLVEQHAEFFR---KFLNIPE 86
Query: 104 -RVSIITGGMDMVDQGKELAKKPHIVIATP---------GRLADHLDTCNTFSLNRIKFL 153
++ + TG + ++ EL +K +++ATP GR+ SL + L
Sbjct: 87 EKIVVFTGEVS-PEKRAELWEKAKVIVATPQVIENDLIAGRI----------SLEDVSLL 135
Query: 154 VLDEADR 160
+ DEA R
Sbjct: 136 IFDEAHR 142
>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 = 35.0 bits (81), Expect = 0.017
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 33 QKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL 65
Q+ II HVL+ D + TG GK+L + +P L
Sbjct: 18 QEEIISHVLDGRDVLVVMPTGGGKSLCYQVPAL 50
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 31.8 bits (73), Expect = 0.17
Identities = 22/83 (26%), Positives = 39/83 (46%), Gaps = 7/83 (8%)
Query: 53 GSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGGM 112
GSGKT+ L +L G A ++ PT LA Q + + + +RV+++TG +
Sbjct: 293 GSGKTVVALLAMLAAI---EAGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSL 349
Query: 113 DMVDQGKELAK----KPHIVIAT 131
+ + L + + IV+ T
Sbjct: 350 KGKARKEILEQLASGEIDIVVGT 372
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 31.9 bits (73), Expect = 0.17
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 33 QKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL 65
Q+ II +L+ +D + TG GK+L + +P L
Sbjct: 22 QQEIIDALLSGKDTLVVMPTGGGKSLCYQIPAL 54
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 31.6 bits (72), Expect = 0.20
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 33 QKAIIPHVLNDEDCIGCAKTGSGKTLAFALPIL 65
Q+ II VL+ DC+ TG GK+L + +P L
Sbjct: 30 QQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPAL 62
>gnl|CDD|162276 TIGR01266, fum_ac_acetase, fumarylacetoacetase. This enzyme
catalyzes the final step in the breakdown of tyrosine or
phenylalanine to fumarate and acetoacetate [Energy
metabolism, Amino acids and amines].
Length = 415
Score = 31.0 bits (70), Expect = 0.32
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 72 PYGIFALVLTPTRELAYQIGDQFLVLGKVMNL 103
PYG+F+ + + IGDQ L L + +L
Sbjct: 17 PYGVFSTQANSSPRIGVAIGDQILDLSVIAHL 48
>gnl|CDD|187632 cd05374, 17beta-HSD-like_SDR_c, 17beta hydroxysteroid
dehydrogenase-like, classical (c) SDRs.
17beta-hydroxysteroid dehydrogenases are a group of
isozymes that catalyze activation and inactivation of
estrogen and androgens. SDRs are a functionally diverse
family of oxidoreductases that have a single domain with
a structurally conserved Rossmann fold (alpha/beta
folding pattern with a central beta-sheet), an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 248
Score = 30.3 bits (69), Expect = 0.40
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 9/58 (15%)
Query: 104 RVSIITG-----GMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLD 156
+V +ITG G+ + LA + + VIAT R D L++ + ++ L LD
Sbjct: 1 KVVLITGCSSGIGLALA---LALAAQGYRVIAT-ARNPDKLESLGELLNDNLEVLELD 54
>gnl|CDD|234947 PRK01362, PRK01362, putative translaldolase; Provisional.
Length = 214
Score = 30.1 bits (69), Expect = 0.44
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 113 DMVDQGKELAK-KPHIVIATPGRLADHLDTCNTFSLNRIK 151
M+ +G+ELAK P++V+ P + L S IK
Sbjct: 65 GMIKEGRELAKIAPNVVVKIP-MTPEGLKAVKALSKEGIK 103
>gnl|CDD|222875 PHA02558, uvsW, UvsW helicase; Provisional.
Length = 501
Score = 30.4 bits (69), Expect = 0.53
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 2/67 (2%)
Query: 28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELA 87
P Q + L + + T +GK+L L L ++ + Y L++ PT L
Sbjct: 114 EPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYL--LSRYYLENYEGKVLIIVPTTSLV 171
Query: 88 YQIGDQF 94
Q+ D F
Sbjct: 172 TQMIDDF 178
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 28.3 bits (64), Expect = 0.92
Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 5/39 (12%)
Query: 52 TGSGKTL-AFALPILQKWCEDPYGIFALVLTPTRELAYQ 89
TGSGKTL A AL L + P ++L Q
Sbjct: 27 TGSGKTLTAAALI---ARLAKGKKKV-LFVVPRKDLLEQ 61
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 29.7 bits (67), Expect = 1.0
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 28 TPTEIQKAIIPHVLNDEDCIGCAKTGSGKTL 58
Q+ I + E + CA T SGKT+
Sbjct: 119 ELDPFQQEAIAILERGESVLVCAPTSSGKTV 149
>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 29.2 bits (66), Expect = 1.0
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 126 HIVIAT---PGRLADHLDTCNTFSLNRIKFLVLDEADRL 161
++A PG A +DT + R K L +D D L
Sbjct: 78 LQLVANAQKPGGKAAFIDTEHALDPERAKQLGVDLLDNL 116
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 29.1 bits (66), Expect = 1.2
Identities = 33/120 (27%), Positives = 49/120 (40%), Gaps = 27/120 (22%)
Query: 52 TGSGKT-----LA--FALPILQKWCEDPYGIFALVLTPTRELAYQIG--DQFLVLGKVMN 102
TG GKT LA +AL + AL+ T Y+IG +Q K+M
Sbjct: 230 TGVGKTTTLAKLAARYAL------LYGKKKV-ALITLDT----YRIGAVEQLKTYAKIMG 278
Query: 103 LRVSIITGGMDMVDQGKELAKKPHIVIATPGR------LADHLDTCNTFSLNRIK-FLVL 155
+ V ++ ++ ++L I+I T GR L + L FS I +LVL
Sbjct: 279 IPVEVVYDPKELAKALEQLRDCDVILIDTAGRSQRDKRLIEELKALIEFSGEPIDVYLVL 338
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli [DNA metabolism, DNA replication,
recombination, and repair].
Length = 850
Score = 29.0 bits (65), Expect = 1.5
Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 8/85 (9%)
Query: 39 HVLNDEDCIGCAKTGSGKTLAFALPIL-QKWCEDPYGIFALVLTPTRELAYQIGDQFL-V 96
+ + E + A TG+GKTL + LP L E P ++ T T+ L Q+ ++ + +
Sbjct: 260 QLTHSEKSLIEAPTGTGKTLGYLLPALYYAITEKP----VVISTNTKVLQSQLLEKDIPL 315
Query: 97 LGKVMN--LRVSIITGGMDMVDQGK 119
L +++N + ++I G + + GK
Sbjct: 316 LNEILNFKINAALIKGKSNYLSLGK 340
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 28.9 bits (65), Expect = 1.7
Identities = 15/77 (19%), Positives = 31/77 (40%), Gaps = 8/77 (10%)
Query: 88 YQIG--DQFLVLGKVMNLRVSIITGGMDMVDQGKELAKKPHIVIATPGR------LADHL 139
Y+IG +Q +M + + ++ ++ + + L I++ T GR + L
Sbjct: 244 YRIGAVEQLKTYADIMGVPLEVVYSPKELAEAIEALRDCDVILVDTAGRSQYDKEKIEEL 303
Query: 140 DTCNTFSLNRIKFLVLD 156
S + +LVL
Sbjct: 304 KELIDVSHSIEVYLVLS 320
>gnl|CDD|237844 PRK14873, PRK14873, primosome assembly protein PriA; Provisional.
Length = 665
Score = 28.7 bits (65), Expect = 2.0
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 105 VSIIT-GGMDMVDQGKELAKKPHIVIATPG 133
V ++T GG +VD + P +V+ATPG
Sbjct: 454 VPVVTSGGDQVVD---TVDAGPALVVATPG 480
>gnl|CDD|163426 TIGR03714, secA2, accessory Sec system translocase SecA2. Members
of this protein family are homologous to SecA and part
of the accessory Sec system. This system, including both
five core proteins for export and a variable number of
proteins for glycosylation, operates in certain
Gram-positive pathogens for the maturation and delivery
of serine-rich glycoproteins such as the cell surface
glycoprotein GspB in Streptococcus gordonii [Protein
fate, Protein and peptide secretion and trafficking].
Length = 762
Score = 28.1 bits (63), Expect = 2.8
Identities = 32/125 (25%), Positives = 48/125 (38%), Gaps = 26/125 (20%)
Query: 51 KTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKV---MNLRVSI 107
KTG GKTL +P+ G A+++T LA + +G V + L VS+
Sbjct: 91 KTGEGKTLTATMPLYLNALT---GKGAMLVTTNDYLAKR---DAEEMGPVYEWLGLTVSL 144
Query: 108 ITGGMDMVDQGKELAKKPH-------IVIATPGRLA-DHL-----DTCNTFSLNRIKFLV 154
G +D D +E IV T L D+L L +++
Sbjct: 145 --GVVDDPD--EEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVI 200
Query: 155 LDEAD 159
+DE D
Sbjct: 201 VDEVD 205
>gnl|CDD|187841 cd09710, Cas3_I-D, CRISPR/Cas system-associated protein Cas3;
Distinct diverged subfamily of Cas3 helicase domain.
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;
Diverged DNA helicase Cas3'; signature gene for Type I
and subtype I-D.
Length = 353
Score = 27.9 bits (62), Expect = 2.8
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 6/40 (15%)
Query: 50 AKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQ 89
A TG+GKTLA+ P+L A+ L PT L
Sbjct: 21 APTGAGKTLAWLTPLLHG------ENKAIALYPTNALIED 54
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 27.7 bits (62), Expect = 3.5
Identities = 24/91 (26%), Positives = 37/91 (40%), Gaps = 20/91 (21%)
Query: 52 TGSGKT-----LA--FALPILQKWCEDPYGIFALVLTPTRELAYQIG--DQFLVLGKVMN 102
TG GKT LA F L + AL+ T T Y+IG +Q +++
Sbjct: 204 TGVGKTTTLAKLAARFVL------EHGKKKV-ALITTDT----YRIGAVEQLKTYAEILG 252
Query: 103 LRVSIITGGMDMVDQGKELAKKPHIVIATPG 133
+ V + ++ + L K I+I T G
Sbjct: 253 VPVKVARDPKELAEALDRLRDKDLILIDTAG 283
>gnl|CDD|234127 TIGR03158, cas3_cyano, CRISPR-associated helicase Cas3, subtype
CYANO. CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) is a widespread family of
prokaryotic direct repeats with spacers of unique
sequence between consecutive repeats. This protein
family is a CRISPR-associated (Cas) family strictly
associated with the Cyano subtype of CRISPR/Cas locus,
found in several species of Cyanobacteria and several
archaeal species. It contains helicase motifs and
appears to represent the Cas3 protein of the Cyano
subtype of CRISPR/Cas system [Mobile and
extrachromosomal element functions, Other].
Length = 357
Score = 27.9 bits (62), Expect = 3.5
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 6/40 (15%)
Query: 50 AKTGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQ 89
A TG+GKTLA+ P+L + L PT L
Sbjct: 21 APTGAGKTLAWLTPLLHG------ENDTIALYPTNALIED 54
>gnl|CDD|235778 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein;
Validated.
Length = 860
Score = 27.9 bits (62), Expect = 4.2
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 1 MEDPIKSFTDLKLNPW--LIRQCQTIGVKTPTEIQK-AIIPHVLNDEDCIGCAK 51
MED ++ D K PW L+++ + + +K A IP ++ + DC C K
Sbjct: 548 MEDELELIADNK-KPWKLLLQEFWELFLPVVVTAEKEAFIPRIVTEIDCPKCHK 600
>gnl|CDD|236659 PRK10158, PRK10158, 23S rRNA/tRNA pseudouridine synthase A;
Provisional.
Length = 219
Score = 27.3 bits (60), Expect = 4.3
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 124 KPHIVIATPGRLADHLDTCNTFSLNRIK--FLVLDEADRLSLMTS 166
KP +++ PGRL +H D+ T RI+ + + RL + TS
Sbjct: 28 KPSGLLSVPGRLEEHKDSVMT----RIQRDYPQAESVHRLDMATS 68
>gnl|CDD|221427 pfam12114, Period_C, Period protein 2/3C-terminal region. This
domain is found in eukaryotes. This domain is typically
between 164 to 200 amino acids in length. This domain is
found associated with pfam08447.
Length = 190
Score = 27.0 bits (60), Expect = 5.2
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 32 IQKAIIPHVLNDEDCIGCAKTGSGKTL 58
IQ +P ++ ++C+ C+ + SG T
Sbjct: 149 IQTGGLPAAIDLQECVTCSSSSSGSTD 175
>gnl|CDD|182464 PRK10441, PRK10441, iron-enterobactin transporter membrane protein;
Provisional.
Length = 335
Score = 27.4 bits (61), Expect = 5.3
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 76 FALVLTPTRELAYQIGDQFLVLGKVMNLRVSIIT 109
L+ TP L I + LV G+ LRVS+++
Sbjct: 284 VTLLATPALLLFADIIGRLLVPGE---LRVSVVS 314
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 26.5 bits (59), Expect = 5.5
Identities = 18/123 (14%), Positives = 34/123 (27%), Gaps = 43/123 (34%)
Query: 46 CIGCAKTGSGKTLAFALPILQKWCEDPYGIFALVLTPT-----RELAYQIGDQFLVLGKV 100
G + GSGKT L++ + + ++L +I +
Sbjct: 9 LTGES--GSGKTTL-----LRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSG 61
Query: 101 MNLRVSIITGGMDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADR 160
++++ + D L L++DEA
Sbjct: 62 GTTA--------ELLEA-----------------ILDALKRR------GRPLLIIDEAQH 90
Query: 161 LSL 163
LSL
Sbjct: 91 LSL 93
>gnl|CDD|203709 pfam07652, Flavi_DEAD, Flavivirus DEAD domain.
Length = 146
Score = 26.1 bits (58), Expect = 7.5
Identities = 15/32 (46%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 53 GSGKTLAFALPILQKWCEDPYGIFALVLTPTR 84
G+GKT LP L + C D + LVL PTR
Sbjct: 12 GAGKTRKV-LPELVRECIDR-RLRTLVLAPTR 41
>gnl|CDD|236749 PRK10742, PRK10742, putative methyltransferase; Provisional.
Length = 250
Score = 26.7 bits (59), Expect = 7.8
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 61 ALPIL-QKW--CEDPYGIFALVLTPTR 84
AL +L +W D + ALVLTP
Sbjct: 15 ALSVLAARWGLEHDEDNLMALVLTPEH 41
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 25.8 bits (56), Expect = 9.6
Identities = 20/125 (16%), Positives = 31/125 (24%), Gaps = 30/125 (24%)
Query: 52 TGSGKTLAFALPILQKWCEDPYGIFALVLTPTRELAYQIGDQFLVLGKVMNLRVSIITGG 111
GSGKT + ++ G+ + E +V GK + G
Sbjct: 11 PGSGKTTLARA-LARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG------SG 63
Query: 112 MDMVDQGKELAKKPHIVIATPGRLADHLDTCNTFSLNRIKFLVLDEADRLSLMTSLKFFF 171
+ LA+K + L+LDE L
Sbjct: 64 ELRLRLALALARKLKPDV-----------------------LILDEITSLLDAEQEALLL 100
Query: 172 FFFFL 176
L
Sbjct: 101 LLEEL 105
>gnl|CDD|235648 PRK05932, PRK05932, RNA polymerase factor sigma-54; Reviewed.
Length = 455
Score = 26.3 bits (59), Expect = 9.7
Identities = 11/40 (27%), Positives = 14/40 (35%), Gaps = 13/40 (32%)
Query: 71 DPYGIFA-------------LVLTPTRELAYQIGDQFLVL 97
DP G+ A L TP + A +I L L
Sbjct: 166 DPAGVGARDLQECLLLQLEQLDDTPRLDEAMEIISDHLDL 205
>gnl|CDD|188632 cd00452, KDPG_aldolase, KDPG and KHG aldolase. KDPG and KHG
aldolase. This family belongs to the class I adolases
whose reaction mechanism involves Schiff base formation
between a substrate carbonyl and lysine residue in the
active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG)
aldolase, is best known for its role in the
Entner-Doudoroff pathway of bacteria, where it catalyzes
the reversible cleavage of KDPG to pyruvate and
glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate
(KHG) aldolase, which has enzymatic specificity toward
glyoxylate, forming KHG in the presence of pyruvate, and
is capable of regulating glyoxylate levels in the
glyoxylate bypass, an alternate pathway when bacteria
are grown on acetate carbon sources.
Length = 190
Score = 25.9 bits (58), Expect = 9.8
Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 6/30 (20%)
Query: 13 LNPWLIRQCQ------TIGVKTPTEIQKAI 36
L+P +++ GV TPTEI +A+
Sbjct: 85 LDPEVVKAANRAGIPLLPGVATPTEIMQAL 114
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
0.326 0.143 0.440
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: 9,574,892
Number of extensions: 899622
Number of successful extensions: 1453
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1403
Number of HSP's successfully gapped: 69
Length of query: 182
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 91
Effective length of database: 6,901,388
Effective search space: 628026308
Effective search space used: 628026308
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.5 bits)