RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14082
(233 letters)
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 111 bits (278), Expect = 4e-28
Identities = 40/75 (53%), Positives = 58/75 (77%)
Query: 104 NPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT 163
K+++FVETKK + +T+ LR + A+CIHGDK Q++R +VLN+F+ GK+PI++AT
Sbjct: 375 RDGDKILIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIAT 434
Query: 164 DVAARGLDVEDVNTV 178
DVA+RGLDV+DV V
Sbjct: 435 DVASRGLDVKDVKYV 449
Score = 83.7 bits (207), Expect = 1e-18
Identities = 34/63 (53%), Positives = 44/63 (69%), Gaps = 2/63 (3%)
Query: 25 YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTPK 82
++LPA VHI+ Q ++ GDGPI LVLAPTRELA+QI+ +F SS +RN +GG PK
Sbjct: 184 FLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVAYGGVPK 243
Query: 83 GPQ 85
Q
Sbjct: 244 RGQ 246
Score = 49.4 bits (118), Expect = 5e-07
Identities = 21/50 (42%), Positives = 33/50 (66%)
Query: 167 ARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQDYEKEKRLFSLIRELGK 216
AR L E+ VN+GSL L+A HNI Q + VV+++EK +L L++ + +
Sbjct: 326 ARDLCKEEPVHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMR 375
>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 = 97.6 bits (243), Expect = 2e-23
Identities = 35/77 (45%), Positives = 49/77 (63%)
Query: 102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILV 161
+VIVFV TK+ VE++ +LR+ +HGD Q++RD L F+ G+ +LV
Sbjct: 269 KDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLV 328
Query: 162 ATDVAARGLDVEDVNTV 178
ATDVAARGLD+ DV+ V
Sbjct: 329 ATDVAARGLDIPDVSHV 345
Score = 58.6 bits (142), Expect = 4e-10
Identities = 20/64 (31%), Positives = 28/64 (43%), Gaps = 6/64 (9%)
Query: 25 YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNI---CIFGGTP 81
++LP I K AL+LAPTRELA QI ++ L + ++GG
Sbjct: 83 FLLPLLQKILKSVERKY---VSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVS 139
Query: 82 KGPQ 85
Q
Sbjct: 140 IRKQ 143
>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 = 90.8 bits (226), Expect = 3e-23
Identities = 30/71 (42%), Positives = 50/71 (70%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
KV++F +KK ++++ LR+ +HGD +Q++R+ VL DFR+G+ +LVATDV A
Sbjct: 30 KVLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIA 89
Query: 168 RGLDVEDVNTV 178
RG+D+ +V+ V
Sbjct: 90 RGIDLPNVSVV 100
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 84.9 bits (211), Expect = 4e-19
Identities = 32/69 (46%), Positives = 45/69 (65%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
+VF TKK+ +++ AL + SA+ +HGD Q+DRD VL F +LVATDVAARG
Sbjct: 246 VVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAARG 305
Query: 170 LDVEDVNTV 178
LD++ + V
Sbjct: 306 LDIKALEAV 314
Score = 43.6 bits (104), Expect = 4e-05
Identities = 23/45 (51%), Positives = 26/45 (57%), Gaps = 9/45 (20%)
Query: 47 ALVLAPTRELAQQIQTVAKE---FSSALRNICIF---GGTPKGPQ 85
ALVL PTRELA Q VAKE + + NI + GG P GPQ
Sbjct: 75 ALVLCPTRELADQ---VAKEIRRLARFIPNIKVLTLCGGVPMGPQ 116
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 74.2 bits (183), Expect = 1e-17
Identities = 23/59 (38%), Positives = 36/59 (61%)
Query: 120 EDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTV 178
E++ L+ +HG +Q++R+ +L+ F GK +LVATDVA RGLD+ V+ V
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLV 59
>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 = 74.1 bits (183), Expect = 2e-17
Identities = 26/53 (49%), Positives = 37/53 (69%)
Query: 126 LRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTV 178
LR+ +HG +Q++R+ +L DFR GK+ +LVATDVA RG+D+ DVN V
Sbjct: 3 LRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLV 55
>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 = 69.4 bits (171), Expect = 1e-14
Identities = 25/63 (39%), Positives = 37/63 (58%), Gaps = 5/63 (7%)
Query: 25 YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
+++P + +P + DGP AL+LAPTRELA QI VA++ L+ + I+GGT
Sbjct: 53 FLIPI---LEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSI 109
Query: 83 GPQ 85
Q
Sbjct: 110 DKQ 112
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 67.9 bits (166), Expect = 3e-13
Identities = 26/69 (37%), Positives = 46/69 (66%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
I++ T++KV+ +T+ + + C+HGD Q+DRD ++ +FR G +L+ TD+ ARG
Sbjct: 271 IIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTDLLARG 330
Query: 170 LDVEDVNTV 178
+DV+ V+ V
Sbjct: 331 IDVQQVSLV 339
Score = 39.8 bits (93), Expect = 7e-04
Identities = 20/36 (55%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 47 ALVLAPTRELAQQIQTVAKEFSSALRNIC--IFGGT 80
AL+LAPTRELAQQIQ V L+ C GGT
Sbjct: 99 ALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGT 134
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 67.3 bits (165), Expect = 4e-13
Identities = 26/71 (36%), Positives = 44/71 (61%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ IVFV T+++V ++ LR+ + + G+ Q R+ + G+ +LVATDVAA
Sbjct: 247 RSIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAA 306
Query: 168 RGLDVEDVNTV 178
RG+D++DV+ V
Sbjct: 307 RGIDIDDVSHV 317
Score = 41.5 bits (98), Expect = 2e-04
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 25 YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALR-NIC-IFGGTPK 82
++LPA H+ P ++ P L+L PTRELA Q+ A+E + +I I GG
Sbjct: 55 FLLPALQHLL-DFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAY 113
Query: 83 GPQ 85
Sbjct: 114 MNH 116
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 66.5 bits (162), Expect = 1e-12
Identities = 32/78 (41%), Positives = 49/78 (62%)
Query: 101 MAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPIL 160
++++ + +VFV TK VE + R L R + + GD Q+ R+ +LN F++G+ IL
Sbjct: 252 LSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEIL 311
Query: 161 VATDVAARGLDVEDVNTV 178
VATDVAARGL ++ V V
Sbjct: 312 VATDVAARGLHIDGVKYV 329
Score = 36.9 bits (85), Expect = 0.006
Identities = 19/37 (51%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 45 PIALVLAPTRELAQQIQTVAKEFSS--ALRNICIFGG 79
P AL+LAPTRELA QI A +F + LR ++GG
Sbjct: 85 PRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGG 121
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 63.8 bits (156), Expect = 6e-12
Identities = 29/71 (40%), Positives = 40/71 (56%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+ I+F TK + E+I L + H + GD Q+ R +L +F +G ILVATDVAA
Sbjct: 257 RAIIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAA 316
Query: 168 RGLDVEDVNTV 178
RGL + V V
Sbjct: 317 RGLHIPAVTHV 327
Score = 39.2 bits (92), Expect = 0.001
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 27 LPAAVH--ISHQEPV-KQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGG 79
L A H +SH P ++ + P AL++APTRELA QI A+ + A L+ +GG
Sbjct: 63 LTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGG 120
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 63.7 bits (155), Expect = 7e-12
Identities = 29/71 (40%), Positives = 43/71 (60%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+V+VF TK + L ++ + IHG+K+Q R L DF+ G +LVATD+AA
Sbjct: 247 QVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAA 306
Query: 168 RGLDVEDVNTV 178
RGLD+E++ V
Sbjct: 307 RGLDIEELPHV 317
Score = 47.5 bits (113), Expect = 2e-06
Identities = 25/64 (39%), Positives = 38/64 (59%), Gaps = 3/64 (4%)
Query: 25 YMLPAAVHISHQEPVKQGDGPI-ALVLAPTRELAQQIQTVAKEFSSAL--RNICIFGGTP 81
+ LP H+ ++P +G P+ AL+L PTRELA QI +++S L R++ +FGG
Sbjct: 55 FTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVS 114
Query: 82 KGPQ 85
PQ
Sbjct: 115 INPQ 118
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 61.8 bits (150), Expect = 4e-11
Identities = 33/90 (36%), Positives = 48/90 (53%), Gaps = 10/90 (11%)
Query: 99 YEMAKNPAF----------KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYV 148
+ M KN A I+FV TK ++ AL R +++ ++GD Q R+
Sbjct: 228 WGMRKNEALVRFLEAEDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQT 287
Query: 149 LNDFRQGKAPILVATDVAARGLDVEDVNTV 178
L + G+ IL+ATDVAARGLDVE ++ V
Sbjct: 288 LERLKDGRLDILIATDVAARGLDVERISLV 317
Score = 36.7 bits (85), Expect = 0.008
Identities = 17/38 (44%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 45 PIALVLAPTRELAQQIQTVAKEFSSALRNI---CIFGG 79
P LVLAPTRELA Q+ +FS +R + ++GG
Sbjct: 75 PQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGG 112
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 58.0 bits (140), Expect = 8e-10
Identities = 29/78 (37%), Positives = 45/78 (57%)
Query: 101 MAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPIL 160
+ +NP +V+VF K +V I L ++ +A + GD Q R L FR+GK +L
Sbjct: 330 VTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVL 389
Query: 161 VATDVAARGLDVEDVNTV 178
VATDVA RG+ ++ ++ V
Sbjct: 390 VATDVAGRGIHIDGISHV 407
Score = 31.0 bits (70), Expect = 0.48
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 45 PIALVLAPTRELAQQIQTVAKEFS 68
P AL++APTREL QI A +
Sbjct: 163 PRALIIAPTRELVVQIAKDAAALT 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 = 52.6 bits (127), Expect = 1e-08
Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 7/63 (11%)
Query: 25 YMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSA--LRNICIFGGTPK 82
++LP + ++ Q ALVLAPTRELA+QI K+ LR + GGT
Sbjct: 31 FLLPILQALLPKKGGPQ-----ALVLAPTRELAEQIYEELKKLFKILGLRVALLTGGTSL 85
Query: 83 GPQ 85
Q
Sbjct: 86 KEQ 88
Score = 30.3 bits (69), Expect = 0.53
Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 7/67 (10%)
Query: 101 MAKNPAFKVIVFVETKKKVEDITRALRR----ERHSAICIHGDKTQQDRDYVLNDFRQGK 156
+ K + +V T++ E I L++ + G + +++ L ++GK
Sbjct: 40 LPKKGGPQALVLAPTRELAEQIYEELKKLFKILGLRVALLTGGTSLKEQARKL---KKGK 96
Query: 157 APILVAT 163
A ILV T
Sbjct: 97 ADILVGT 103
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 48.7 bits (117), Expect = 9e-07
Identities = 29/87 (33%), Positives = 48/87 (55%), Gaps = 8/87 (9%)
Query: 100 EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAI------CIHGDK--TQQDRDYVLND 151
++ KNP ++IVF + + E I L +E A+ GDK +Q+++ +L+
Sbjct: 359 QLGKNPDSRIIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDK 418
Query: 152 FRQGKAPILVATDVAARGLDVEDVNTV 178
FR G+ +LV+T VA GLD+ V+ V
Sbjct: 419 FRAGEFNVLVSTSVAEEGLDIPSVDLV 445
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 47.0 bits (112), Expect = 3e-06
Identities = 16/71 (22%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
K ++F + +I + I G+ +++R+ +L FR G +LV V
Sbjct: 285 KTLIFASDVEHAYEIAKLFLAP-GIVEAITGETPKEEREAILERFRTGGIKVLVTVKVLD 343
Query: 168 RGLDVEDVNTV 178
G+D+ D + +
Sbjct: 344 EGVDIPDADVL 354
Score = 28.9 bits (65), Expect = 2.7
Identities = 15/40 (37%), Positives = 19/40 (47%)
Query: 47 ALVLAPTRELAQQIQTVAKEFSSALRNICIFGGTPKGPQD 86
LVL PT+EL Q K+F I I+GG K +
Sbjct: 83 TLVLVPTKELLDQWAEALKKFLLLNDEIGIYGGGEKELEP 122
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 45.9 bits (109), Expect = 4e-06
Identities = 23/64 (35%), Positives = 32/64 (50%), Gaps = 8/64 (12%)
Query: 24 QYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEF--SSALRNICIFGGTP 81
+LPA + K+G G LVL PTRELA+Q K+ S L+ + ++GG
Sbjct: 40 AALLPALEAL------KRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDS 93
Query: 82 KGPQ 85
K Q
Sbjct: 94 KREQ 97
>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 = 44.6 bits (106), Expect = 5e-06
Identities = 21/72 (29%), Positives = 27/72 (37%), Gaps = 7/72 (9%)
Query: 24 QYMLPAAVHISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSALRNICIF-GGTPK 82
+LP + G LVLAPTRELA Q+ KE + GGT
Sbjct: 16 AALLPILELL------DSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGTSI 69
Query: 83 GPQDCLPLHRFV 94
Q+ L +
Sbjct: 70 KQQEKLLSGKTD 81
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 46.2 bits (110), Expect = 5e-06
Identities = 28/85 (32%), Positives = 46/85 (54%), Gaps = 9/85 (10%)
Query: 103 KNPAFKVIVFVETKKKVEDITRALRRERHSAICI-------HGDK--TQQDRDYVLNDFR 153
KN +VIVF E + E+I L++ A GDK +Q+++ +++ FR
Sbjct: 363 KNGDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFR 422
Query: 154 QGKAPILVATDVAARGLDVEDVNTV 178
+G+ +LVAT V GLD+ +V+ V
Sbjct: 423 KGEYNVLVATSVGEEGLDIPEVDLV 447
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 44.6 bits (106), Expect = 2e-05
Identities = 22/69 (31%), Positives = 37/69 (53%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
I++ T+KKVE++ LR+ SA H + ++R+ V F + ++VAT+ G
Sbjct: 234 IIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMG 293
Query: 170 LDVEDVNTV 178
+D DV V
Sbjct: 294 IDKPDVRFV 302
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 44.0 bits (104), Expect = 3e-05
Identities = 29/122 (23%), Positives = 52/122 (42%), Gaps = 42/122 (34%)
Query: 101 MAKNPAF--------------KVIVFVETKKKVEDITRALRRERH--------------- 131
+AK+ ++ ++VETK+K + + L+ ++H
Sbjct: 321 LAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGA 380
Query: 132 -------------SAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTV 178
A+ IHG+K+ ++R V+ F G+ P++VAT V RG+D+ V V
Sbjct: 381 DLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLLRVRQV 440
Query: 179 NI 180
I
Sbjct: 441 II 442
Score = 37.1 bits (86), Expect = 0.006
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 10/73 (13%)
Query: 25 YMLPAAVH---ISHQEPVKQGDGPIALVLAPTRELAQQIQTVAKEFSSAL--RNICIFGG 79
+++P I P +Q P+A+VL PTREL Q++ AK L + + GG
Sbjct: 175 FLVPIISRCCTIRSGHPSEQ-RNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGG 233
Query: 80 TPKGPQDCLPLHR 92
Q L+R
Sbjct: 234 DAMPQQ----LYR 242
>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 = 41.2 bits (97), Expect = 3e-04
Identities = 19/69 (27%), Positives = 34/69 (49%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
I++ ++KKVE++ L + SA+ H + + R DF ++VAT+ G
Sbjct: 228 IIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMG 287
Query: 170 LDVEDVNTV 178
+D +V V
Sbjct: 288 IDKPNVRFV 296
>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 = 37.4 bits (87), Expect = 0.004
Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 4/85 (4%)
Query: 100 EMAKNPAFKVIVFVETKKKVEDITRALRRERH--SAICIHGDKTQQDRDYVLNDFRQGKA 157
E + V++F + +E + AL+++ + +H Q R + FR GK
Sbjct: 299 EKQRKTGRPVLIFFPEIETMEQVAAALKKKLPKETIASVHS--EDQHRKEKVEAFRDGKI 356
Query: 158 PILVATDVAARGLDVEDVNTVNIGS 182
+L+ T + RG+ +V+ +G+
Sbjct: 357 TLLITTTILERGVTFPNVDVFVLGA 381
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 36.5 bits (85), Expect = 0.009
Identities = 15/37 (40%), Positives = 24/37 (64%)
Query: 136 IHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDV 172
+HG +++ V+ +FR+G+ ILVAT V G+DV
Sbjct: 488 LHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDV 524
>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 = 0.019
Identities = 19/69 (27%), Positives = 35/69 (50%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
I++ ++KK E +T +L+ +A H RD V + F++ + ++VAT G
Sbjct: 230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMG 289
Query: 170 LDVEDVNTV 178
++ DV V
Sbjct: 290 INKPDVRFV 298
>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd). All
proteins in this family for which functions are known
are DNA-dependent ATPases that function in the process
of transcription-coupled DNA repair in which the repair
of the transcribed strand of actively transcribed genes
is repaired at a higher rate than the repair of
non-transcribed regions of the genome and than the
non-transcribed strand of the same gene. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). This family is
closely related to the RecG and UvrB families [DNA
metabolism, DNA replication, recombination, and repair].
Length = 926
Score = 35.0 bits (81), Expect = 0.028
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 7/66 (10%)
Query: 116 KKKVEDITRALRRERHSAICI-HGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVED 174
++ ++ R I I HG T+ + + V+ +F +G+ +LV T + G+D+ +
Sbjct: 677 ATQLRELVPEAR------IAIAHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPN 730
Query: 175 VNTVNI 180
NT+ I
Sbjct: 731 ANTIII 736
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 34.7 bits (80), Expect = 0.041
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 7/68 (10%)
Query: 119 VEDITRALRR------ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDV 172
VE+I +A R E AI HG +++ + V+NDF + +LV T + G+D+
Sbjct: 819 VENIQKAAERLAELVPEARIAIG-HGQMRERELERVMNDFHHQRFNVLVCTTIIETGIDI 877
Query: 173 EDVNTVNI 180
NT+ I
Sbjct: 878 PTANTIII 885
>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain. This is a family of proteins of
approximately 300 residues, found in plants and
vertebrates. They contain a highly conserved DDRGK
motif.
Length = 189
Score = 33.5 bits (77), Expect = 0.046
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 185 LSANHNIS--QVIEVVQDYEKEKRLFSLIRELGKYTLITQE 223
LSA + VIE +QD E + + +I + GKY I+ E
Sbjct: 120 LSAEFGLKTEDVIERIQDLEAQGSITGVIDDRGKYIYISPE 160
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 34.4 bits (79), Expect = 0.047
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDY----VLNDFRQGKAPILVAT 163
KV+V V T + ++ L+ + + +H T +DR+ + F+Q + I+VAT
Sbjct: 442 KVLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVAT 501
Query: 164 DVAARGLDV 172
V G+D+
Sbjct: 502 QVIEAGVDI 510
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 34.1 bits (79), Expect = 0.062
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 136 IHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDV 172
+HG ++D V+ F++G+ ILVAT V G+DV
Sbjct: 513 VHGRMKPAEKDAVMEAFKEGEIDILVATTVIEVGVDV 549
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 34.1 bits (79), Expect = 0.065
Identities = 15/69 (21%), Positives = 29/69 (42%), Gaps = 12/69 (17%)
Query: 110 IVFV---ETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILV--AT- 163
++FV + K+ E++ L +A ++ F +G+ +LV A+
Sbjct: 332 LIFVPSDKGKEYAEELAEYLEDLGINAELAISGFERK-----FEKFEEGEVDVLVGVASY 386
Query: 164 -DVAARGLD 171
V RG+D
Sbjct: 387 YGVLVRGID 395
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 33.8 bits (78), Expect = 0.083
Identities = 13/42 (30%), Positives = 24/42 (57%)
Query: 136 IHGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNT 177
HG +++ + V+ DF G+ +LV T + G+D+ + NT
Sbjct: 835 AHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANT 876
>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 = 33.4 bits (77), Expect = 0.099
Identities = 22/73 (30%), Positives = 38/73 (52%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAA 167
+V+V TKK ED+T L+ +H + +R ++ D R G+ +LV ++
Sbjct: 444 RVLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLR 503
Query: 168 RGLDVEDVNTVNI 180
GLD+ +V+ V I
Sbjct: 504 EGLDLPEVSLVAI 516
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 33.5 bits (77), Expect = 0.099
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 149 LNDFRQGKAPILVATDVAARGLDVEDVNTVNI 180
L+ F G+A IL+ T + A+G D +V V +
Sbjct: 527 LDQFANGEADILIGTQMIAKGHDFPNVTLVGV 558
>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 = 33.1 bits (76), Expect = 0.10
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 140 KTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNTVNI 180
+ + +LN F GKA IL+ T + A+G +V V +
Sbjct: 296 SRKGAHEALLNQFANGKADILIGTQMIAKGHHFPNVTLVGV 336
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 32.4 bits (75), Expect = 0.17
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 136 IHGDKTQQDRDYVLNDFRQGKAPILVATDV 165
+HG ++D V+ F+ G+ ILVAT V
Sbjct: 511 LHGRMKPAEKDAVMAAFKAGEIDILVATTV 540
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 32.2 bits (74), Expect = 0.23
Identities = 26/79 (32%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 102 AKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILV 161
AKN +V+V TKK ED+T L+ +H D +R ++ D R G+ +LV
Sbjct: 444 AKN--ERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLV 501
Query: 162 ATDVAARGLDVEDVNTVNI 180
++ GLD+ +V+ V I
Sbjct: 502 GINLLREGLDLPEVSLVAI 520
>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 = 0.31
Identities = 17/79 (21%), Positives = 41/79 (51%), Gaps = 8/79 (10%)
Query: 108 KVIVFVETKKKVEDITRALRRE--RHS-----AICIH-GDKTQQDRDYVLNDFRQGKAPI 159
+ +VF ++K+VE + + RR R A+ + +++R + +F++G+
Sbjct: 308 QTLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLG 367
Query: 160 LVATDVAARGLDVEDVNTV 178
++AT+ G+D+ ++ V
Sbjct: 368 VIATNALELGIDIGSLDAV 386
>gnl|CDD|224904 COG1993, COG1993, PII-like signaling protein [Signal transduction
mechanisms].
Length = 109
Score = 30.0 bits (68), Expect = 0.37
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 183 LQLSANHNISQVIEVVQDYEKEKRLFSLIRELGKYTLITQE 223
+LS + + V+EVV + EK +R + E+ K LIT E
Sbjct: 61 FRLSTDLPV--VVEVVDEEEKIERFLPELDEIIKNGLITLE 99
>gnl|CDD|111531 pfam02641, DUF190, Uncharacterized ACR, COG1993.
Length = 101
Score = 29.7 bits (67), Expect = 0.40
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 194 VIEVVQDYEKEKRLFSLIRELGKYTLITQE 223
++EVV E +R+ + I+E+ K LIT E
Sbjct: 67 IVEVVDREENIERVLNEIKEMIKNGLITVE 96
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 31.3 bits (72), Expect = 0.44
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 149 LNDFRQGKAPILVATDVAARGLDVEDVNTV 178
L F +G+A IL+ T + A+G D +V V
Sbjct: 473 LAQFARGEADILIGTQMLAKGHDFPNVTLV 502
>gnl|CDD|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3. This model
represents the highly conserved core region of an
alignment of Cas3, a protein found in association with
CRISPR repeat elements in a broad range of bacteria and
archaea. Cas3 appears to be a helicase, with regions
found by pfam00270 (DEAD/DEAH box helicase) and
pfam00271 (Helicase conserved C-terminal domain). Some
but not all members have an N-terminal HD domain region
(pfam01966) that is not included within this model
[Mobile and extrachromosomal element functions, Other].
Length = 358
Score = 30.9 bits (70), Expect = 0.50
Identities = 15/71 (21%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSA--ICIHGDKTQQDR----DYVLNDFRQGKAPILV 161
K+ + V T + ++ + L+ + +H T++DR +L + ++ + ++V
Sbjct: 224 KIAIIVNTVDRAQEFYQQLKENAPEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIV 283
Query: 162 ATDVAARGLDV 172
AT V LD+
Sbjct: 284 ATQVIEASLDI 294
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 31.2 bits (71), Expect = 0.53
Identities = 21/70 (30%), Positives = 31/70 (44%), Gaps = 12/70 (17%)
Query: 109 VIVFVETKK---KVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT-- 163
++FV K E++ LR +A IH +K + L DF +G+ +LV
Sbjct: 338 GLIFVPIDYGREKAEELAEYLRSHGINAELIHAEKEE-----ALEDFEEGEVDVLVGVAS 392
Query: 164 --DVAARGLD 171
V RGLD
Sbjct: 393 YYGVLVRGLD 402
>gnl|CDD|220490 pfam09954, DUF2188, Uncharacterized protein conserved in bacteria
(DUF2188). This domain, found in various hypothetical
bacterial proteins, has no known function.
Length = 61
Score = 28.0 bits (63), Expect = 0.79
Identities = 9/33 (27%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 115 TKKKVEDITRALRRERHSAICIHG-DKTQQDRD 146
T+ + + R L + + S + IHG D ++R+
Sbjct: 27 TQAEAIEAARELAKNQGSELVIHGRDGKIRERN 59
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 30.1 bits (68), Expect = 1.1
Identities = 15/62 (24%), Positives = 27/62 (43%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATDVAARG 169
IVF ++++ ++ AL + A H ++R V F + +V T A G
Sbjct: 444 IVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAAG 503
Query: 170 LD 171
+D
Sbjct: 504 VD 505
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 29.9 bits (67), Expect = 1.1
Identities = 25/120 (20%), Positives = 43/120 (35%), Gaps = 32/120 (26%)
Query: 108 KVIVFVETKKKVEDITRALRRE-------------------------RHSAICIHGDKTQ 142
+V+VFV ++K ED L + H H +
Sbjct: 238 QVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSN 297
Query: 143 QDRDYVLNDFRQGKAPILVATDVAARGLD-------VEDVNTVNIGSLQLSANHNISQVI 195
+ R ++ FR ++VAT A G++ V D+ G ++ +N I Q+I
Sbjct: 298 EQRRFIEEMFRNRYIKVIVATPTLAAGVNLPARLVIVRDITRYGNGGIRYLSNMEIKQMI 357
>gnl|CDD|100035 cd02204, PurL_repeat2, PurL subunit of the formylglycinamide
ribonucleotide amidotransferase (FGAR-AT), second
repeat. FGAR-AT catalyzes the ATP-dependent conversion
of formylglycinamide ribonucleotide (FGAR) and glutamine
to formylglycinamidine ribonucleotide (FGAM), ADP,
phosphate, and glutamate in the fourth step of the
purine biosynthetic pathway. In eukaryotes and
Gram-negative bacteria, FGAR-AT is encoded by the purL
gene as a multidomain protein with a molecular mass of
about 140 kDa. In Gram-positive bacteria and archaea
FGAR-AT is a complex of three proteins: PurS, PurL, and
PurQ. PurL itself contains two tandem N- and C-terminal
domains (four domains altogether). The N-terminal
domains bind ATP and are related to the ATP-binding
domains of HypE, ThiL, SelD and PurM.
Length = 264
Score = 29.8 bits (68), Expect = 1.2
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 181 GSLQLSANHNISQVIEVVQDYEKEKRLFSLIRELGKYTLITQESSSTLSE 230
GS A H + + D E+EK LF ++EL K L+ S+ +S+
Sbjct: 150 GSEYALAYHGLGGGAPPLVDLEREKALFDAVQELIKEGLVL--SAHDVSD 197
>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain. This domain
is the second of two tandem AAA domains found in a wide
variety of helicase enzymes.
Length = 165
Score = 29.1 bits (66), Expect = 1.2
Identities = 15/70 (21%), Positives = 28/70 (40%), Gaps = 6/70 (8%)
Query: 108 KVIVFVETKKKVEDITRALRR---ERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVATD 164
V+V + +E + L E+ + + G+ R+ +L F++GK IL
Sbjct: 11 GVLVLFPSYSLLEQVAELLASELLEKGIELLVQGEG---SREKLLERFKKGKGAILFGVG 67
Query: 165 VAARGLDVED 174
G+D
Sbjct: 68 SFWEGIDFPG 77
>gnl|CDD|226581 COG4096, HsdR, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 875
Score = 29.3 bits (66), Expect = 1.9
Identities = 21/78 (26%), Positives = 31/78 (39%), Gaps = 7/78 (8%)
Query: 108 KVIVFVETKKKVEDITRALRRE----RHSAICIHGDKTQQDRDYVLNDFRQGKAP-ILVA 162
K IVF + E I AL E +Q + + N + K P I +
Sbjct: 428 KTIVFAKNHDHAERIREALVNEYPEYNGRYAMKITGDAEQAQALIDNFIDKEKYPRIAIT 487
Query: 163 TDVAARGLDVEDVNTVNI 180
D+ G+DV +V VN+
Sbjct: 488 VDLLTTGVDVPEV--VNL 503
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 29.3 bits (66), Expect = 2.1
Identities = 16/54 (29%), Positives = 24/54 (44%)
Query: 110 IVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPILVAT 163
I++ ++ KVED L+ SA H R V F++ I+VAT
Sbjct: 240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVAT 293
>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3. 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; DEAD/DEAH box helicase DNA
helicase cas3'; Often but not always is fused to HD
nuclease domain; signature gene for Type I.
Length = 353
Score = 28.5 bits (64), Expect = 2.8
Identities = 17/71 (23%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSA--ICIHGDKTQQDR----DYVLNDFRQGKAPILV 161
V + V T + ++ + L+ + + IH T++DR +L +F++ + ++V
Sbjct: 220 SVAIIVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFTEKDRAKKEAELLLEFKKSEKFVIV 279
Query: 162 ATDVAARGLDV 172
AT V LD+
Sbjct: 280 ATQVIEASLDI 290
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 28.4 bits (64), Expect = 3.5
Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 108 KVIVFVETKKKVEDITRALRRERHSAICIH-GDKTQQDRDYVLNDFRQGKAPILVATDVA 166
++F T+ E + L++ I +H G +++ R V ++G+ +VAT
Sbjct: 255 TTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGELKAVVATSSL 314
Query: 167 ARGLDVEDVNTV 178
G+D+ D++ V
Sbjct: 315 ELGIDIGDIDLV 326
>gnl|CDD|99744 cd06451, AGAT_like, Alanine-glyoxylate aminotransferase (AGAT)
family. This family belongs to pyridoxal phosphate
(PLP)-dependent aspartate aminotransferase superfamily
(fold I). The major groups in this CD correspond to
alanine-glyoxylate aminotransferase (AGAT),
serine-glyoxylate aminotransferase (SGAT), and
3-hydroxykynurenine transaminase (HKT). AGAT is a
homodimeric protein, which catalyses the transamination
of glyoxylate to glycine, and SGAT converts serine and
glyoxylate to hydroxypyruvate and glycine. HKT catalyzes
the PLP-dependent transamination of 3-hydroxykynurenine,
a potentially toxic metabolite of the kynurenine
pathway.
Length = 356
Score = 28.0 bits (63), Expect = 4.5
Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 11/54 (20%)
Query: 91 HRFVFNCQYEMAKNPAFKVIVFVETKK----KVEDITRALRRERHSAICI-HGD 139
R+ +MA+ V V VE E+I AL + A+ + H +
Sbjct: 87 DRWA-----DMAERYGADVDV-VEKPWGEAVSPEEIAEALEQHDIKAVTLTHNE 134
>gnl|CDD|130260 TIGR01192, chvA, glucan exporter ATP-binding protein. This model
describes glucan exporter ATP binding protein in
bacteria. It belongs to the larger ABC transporter
superfamily with the characteristic ATP binding motif.
The In general, this protein is in some ways implicated
in osmoregulation and suggested to participate in the
export of glucan from the cytoplasm to periplasm. The
cyclic beta-1,2-glucan in the bactrerial periplasmic
space is suggested to confer the property of high
osmolority. It has also been demonstrated that mutants
in this loci have lost functions of virulence and
motility. It is unclear as to how virulence and
osmoadaptaion are related [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 585
Score = 27.9 bits (62), Expect = 4.9
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 113 VETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVL 149
VET+ +V++ ALR+ R + I H T ++ D VL
Sbjct: 504 VETEARVKNAIDALRKNRTTFIIAHRLSTVRNADLVL 540
>gnl|CDD|215770 pfam00176, SNF2_N, SNF2 family N-terminal domain. This domain is
found in proteins involved in a variety of processes
including transcription regulation (e.g., SNF2, STH1,
brahma, MOT1), DNA repair (e.g. ERCC6, RAD16, RAD5), DNA
recombination (e.g. RAD54), and chromatin unwinding
(e.g. ISWI) as well as a variety of other proteins with
little functional information (e.g. lodestar, ETL1).
Length = 301
Score = 27.7 bits (62), Expect = 5.2
Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 6/81 (7%)
Query: 133 AICIHGDKTQQDRDYVLNDFRQGKAPILVAT-DVAAR-GLDVEDVNTVNIGSLQLSANHN 190
+ HGD ++ + R +++ T +V + + +N V + L H
Sbjct: 76 VVVYHGDGRERSKLRQSMAKRLDTYDVVITTYEVLRKDKKLLSLLNKVEWDRVVLDEAHR 135
Query: 191 I----SQVIEVVQDYEKEKRL 207
+ S++ + ++ + RL
Sbjct: 136 LKNSKSKLYKALKKLKTRNRL 156
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 27.7 bits (62), Expect = 5.3
Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 11/64 (17%)
Query: 110 IVFVET---KKKVEDITRALRRERHSAI--------CIHGDKTQQDRDYVLNDFRQGKAP 158
I+F++T +K + R + +E SAI + D+ D ++VL + K P
Sbjct: 50 IIFIDTPGFHEKKHSLNRLMMKEARSAIGGVDLILFVVDSDQWNGDGEFVLTKLQNLKRP 109
Query: 159 ILVA 162
+++
Sbjct: 110 VVLT 113
>gnl|CDD|218722 pfam05732, RepL, Firmicute plasmid replication protein (RepL).
This family consists of Firmicute RepL proteins which
are involved in plasmid replication.
Length = 165
Score = 27.2 bits (60), Expect = 5.6
Identities = 13/61 (21%), Positives = 25/61 (40%), Gaps = 5/61 (8%)
Query: 98 QYEMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGD----KTQQDRDYVLNDFR 153
Q E+A+ + +T K +E+ L+++ I+ D R +L FR
Sbjct: 78 QREIAEETGISLETVRQTMKALEE-GNFLKKKTSGVYMINPDLLFKGDDTKRLNLLLQFR 136
Query: 154 Q 154
+
Sbjct: 137 K 137
>gnl|CDD|214971 smart01008, Ald_Xan_dh_C, Aldehyde oxidase and xanthine
dehydrogenase, a/b hammerhead domain. Aldehyde oxidase
catalyses the conversion of an aldehyde in the presence
of oxygen and water to an acid and hydrogen peroxide.
The enzyme is a homodimer, and requires FAD, molybdenum
and two 2FE-2S clusters as cofactors. Xanthine
dehydrogenase catalyses the hydrogenation of xanthine
to urate, and also requires FAD, molybdenum and two
2FE-2S clusters as cofactors. This activity is often
found in a bifunctional enzyme with xanthine oxidase
activity too. The enzyme can be converted from the
dehydrogenase form to the oxidase form irreversibly by
proteolysis or reversibly through oxidation of
sulphydryl groups.
Length = 107
Score = 26.3 bits (59), Expect = 6.0
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 45 PIALVLAPTRELAQQ 59
P+A V+A T E A+
Sbjct: 80 PVAAVVAETEEAARD 94
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 27.7 bits (62), Expect = 6.1
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 137 HGDKTQQDRDYVLNDFRQGKAPILVATDVAARGLDVEDVNT 177
H ++DR V + FR+GK +LV+T A G VN
Sbjct: 321 HAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAG-----VNL 356
>gnl|CDD|239993 cd04621, CBS_pair_8, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa (IMP
dehydrogenase-1), and homocystinuria (cystathionine
beta-synthase).
Length = 135
Score = 26.6 bits (59), Expect = 7.5
Identities = 23/103 (22%), Positives = 37/103 (35%), Gaps = 9/103 (8%)
Query: 100 EMAKNPAFKVIVFVETKKKVEDITRALRRERHSAICIHGDKTQQDRDYVLNDFRQGKAPI 159
EM KN +VIV + K V IT R A D + + R+
Sbjct: 18 EMEKNGVGRVIVVDDNGKPVGVIT-----YRDLAFAEFEDNERGLPKKSIKMKRKAGQKR 72
Query: 160 LVATDVAARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQDYE 202
V L ED+ T I + +S N ++ +++ +
Sbjct: 73 --YRYVKEVPLVAEDIMTEEIIT--VSPNDDVVDAAKLMLEAN 111
>gnl|CDD|202102 pfam02056, Glyco_hydro_4, Family 4 glycosyl hydrolase.
Length = 183
Score = 26.6 bits (59), Expect = 10.0
Identities = 20/109 (18%), Positives = 40/109 (36%), Gaps = 12/109 (11%)
Query: 105 PAFKVIVFVETKKKVEDITRALRRERHSA---ICIHG----DKTQQDRDYVLNDFRQGKA 157
P ++ ++ +++++ I A ++ A I + D D+V+N R G
Sbjct: 27 PGRELALYDIDEERLDAIQTACKKLVDEAGPDIKFEKTTDRKEALTDADFVINAIRVGLL 86
Query: 158 PILVATDVA---ARGLDVEDVNTVNIGSLQLSANHNISQVIEVVQDYEK 203
P D G+ TV G + I ++ +D E+
Sbjct: 87 PARE-LDEKIPLRHGVVGTIQETVGPGGI-FRGLRTIPVFFDIAKDIEE 133
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
0.319 0.134 0.384
Gapped
Lambda K H
0.267 0.0825 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,626,155
Number of extensions: 1083228
Number of successful extensions: 1254
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1244
Number of HSP's successfully gapped: 81
Length of query: 233
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 139
Effective length of database: 6,768,326
Effective search space: 940797314
Effective search space used: 940797314
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 (21.8 bits)
S2: 57 (25.6 bits)