RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15610
(237 letters)
>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 = 151 bits (382), Expect = 8e-43
Identities = 65/156 (41%), Positives = 90/156 (57%), Gaps = 11/156 (7%)
Query: 49 SQEELGDEALTLVFVETKKGA-DQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCD 107
++ L D V VE + +++ F +++E+ E L D
Sbjct: 223 ARRYLNDPVEIEVSVEKLERTLKKIKQFYLEV----------ESEEEKLELLLKLLKDED 272
Query: 108 EALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
E +VFV TK+ ++L + L G+ V ++HGD Q+ER+ AL +F+ GE +LVAT V
Sbjct: 273 EGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKDGELRVLVATDV 332
Query: 168 AARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
AARGLDIP V HVIN+DLP D E+YVHRIGRTGR G
Sbjct: 333 AARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAG 368
>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 = 131 bits (332), Expect = 4e-39
Identities = 47/94 (50%), Positives = 62/94 (65%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
L+F +KK D+L + L G V ++HGD +Q+EREE L+ FR GE +LVAT V AR
Sbjct: 31 VLIFCPSKKMLDELAELLRKPGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIAR 90
Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
G+D+P+V VIN+DLP Y+ RIGR GR G
Sbjct: 91 GIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQ 124
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 134 bits (340), Expect = 1e-36
Identities = 55/103 (53%), Positives = 74/103 (71%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
L+FVETKKGAD L L G+P IHGD+ Q+ER L F++G++PI++AT VA+RG
Sbjct: 381 LIFVETKKGADFLTKELRLDGWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATDVASRG 440
Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFPFSYNQP 214
LD+ VK+VINFD P+ +E+YVHRIGRTGR G +++ P
Sbjct: 441 LDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTP 483
>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 = 121 bits (305), Expect = 1e-35
Identities = 39/78 (50%), Positives = 51/78 (65%)
Query: 126 DFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL 185
L G V +HG +Q+EREE L FR+G++ +LVAT VA RG+D+P V VIN+DL
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60
Query: 186 PSDVEEYVHRIGRTGRMG 203
P + Y+ RIGR GR G
Sbjct: 61 PWNPASYIQRIGRAGRAG 78
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 120 bits (304), Expect = 1e-35
Identities = 39/82 (47%), Positives = 52/82 (63%)
Query: 122 DQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI 181
++L + L G V +HG +Q+EREE L +F +G+ +LVAT VA RGLD+P V VI
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 182 NFDLPSDVEEYVHRIGRTGRMG 203
+DLP Y+ RIGR GR G
Sbjct: 61 IYDLPWSPASYIQRIGRAGRAG 82
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 122 bits (308), Expect = 2e-32
Identities = 44/94 (46%), Positives = 63/94 (67%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
+VF TKK ++ D L+ G+ ++HGD Q++R++ L RF + +LVAT VAAR
Sbjct: 245 CVVFCNTKKECQEVADALNAQGFSALALHGDLEQRDRDQVLVRFANRSCSVLVATDVAAR 304
Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
GLDI ++ VIN++L D E +VHRIGRTGR G+
Sbjct: 305 GLDIKALEAVINYELARDPEVHVHRIGRTGRAGS 338
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 121 bits (305), Expect = 4e-32
Identities = 43/94 (45%), Positives = 59/94 (62%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
++VFV T++ +L +L G + G+ Q +R EA++R G +LVAT VAAR
Sbjct: 248 SIVFVRTRERVHELAGWLRKAGINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATDVAAR 307
Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
G+DI V HVINFD+P + Y+HRIGRTGR G
Sbjct: 308 GIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGR 341
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 109 bits (274), Expect = 6e-28
Identities = 47/93 (50%), Positives = 58/93 (62%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
++F TK +++ L G+ V + GD QK+R L F G+ ILVAT VAARG
Sbjct: 259 IIFANTKHRCEEIWGHLAADGHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATDVAARG 318
Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
L IP V HV N+DLP D E+YVHRIGRTGR G
Sbjct: 319 LHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGA 351
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 107 bits (269), Expect = 2e-27
Identities = 48/114 (42%), Positives = 70/114 (61%), Gaps = 4/114 (3%)
Query: 94 EREEAQQYTLISCDEALTLV----FVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREE 149
E+EE + TL E LT+ + T++ D L +H + V+ +HGD QK+R+
Sbjct: 249 EKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDL 308
Query: 150 ALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
+R FRSG T +L+ T + ARG+D+ V VIN+DLP+ E Y+HRIGR+GR G
Sbjct: 309 IMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFG 362
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 107 bits (268), Expect = 1e-26
Identities = 53/95 (55%), Positives = 65/95 (68%)
Query: 109 ALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVA 168
A T+VFV TK +++ L HGY V + GD QK+RE L RF+ G+ ILVAT VA
Sbjct: 258 ARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATDVA 317
Query: 169 ARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
ARGL I VK+V N+DLP D E+YVHRIGRT R+G
Sbjct: 318 ARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLG 352
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 106 bits (265), Expect = 2e-26
Identities = 47/90 (52%), Positives = 64/90 (71%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
LVF TK GA+ L + L+ G +IHG+++Q R AL F+SG+ +LVAT +AARG
Sbjct: 249 LVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKSGDIRVLVATDIAARG 308
Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGR 201
LDI + HV+N++LP+ E+YVHRIGRTGR
Sbjct: 309 LDIEELPHVVNYELPNVPEDYVHRIGRTGR 338
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 102 bits (255), Expect = 4e-25
Identities = 42/94 (44%), Positives = 63/94 (67%), Gaps = 1/94 (1%)
Query: 112 LVFVETKKGADQLEDFLH-HHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
+VFV ++ GAD L + + G SIHG+++ KER E ++ F GE P++VAT V R
Sbjct: 371 VVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATGVLGR 430
Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMGN 204
G+D+ V+ VI FD+P+ ++EY+H+IGR RMG
Sbjct: 431 GVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGE 464
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 98.4 bits (245), Expect = 1e-23
Identities = 43/93 (46%), Positives = 60/93 (64%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
++FV TK ++ + L +GY +++GD Q RE+ L R + G IL+AT VAAR
Sbjct: 248 AIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLDILIATDVAAR 307
Query: 171 GLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
GLD+ + V+N+D+P D E YVHRIGRTGR G
Sbjct: 308 GLDVERISLVVNYDIPMDSESYVHRIGRTGRAG 340
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 90.4 bits (224), Expect = 6e-21
Identities = 42/92 (45%), Positives = 55/92 (59%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
+VF K ++E+ L G + GD Q +R + L FR G+ +LVAT VA RG
Sbjct: 339 MVFANRKDEVRRIEERLVKDGINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATDVAGRG 398
Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
+ I + HVINF LP D ++YVHRIGRTGR G
Sbjct: 399 IHIDGISHVINFTLPEDPDDYVHRIGRTGRAG 430
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 75.8 bits (187), Expect = 7e-16
Identities = 30/92 (32%), Positives = 51/92 (55%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
+++ T+K ++L ++L +G + H + +ERE + F + E ++VAT G
Sbjct: 234 IIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAFGMG 293
Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
+D P V+ VI++DLP +E Y GR GR G
Sbjct: 294 IDKPDVRFVIHYDLPGSIESYYQETGRAGRDG 325
>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 = 69.3 bits (170), Expect = 1e-13
Identities = 33/141 (23%), Positives = 59/141 (41%), Gaps = 27/141 (19%)
Query: 63 VETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKGAD 122
V+ L D+L +K R ++ +++ ++K +
Sbjct: 206 VKKNNKQKFLLDYL---------------KKHRGQS------------GIIYASSRKKVE 238
Query: 123 QLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVIN 182
+L + L G + H + K R E F + ++VAT G+D P+V+ VI+
Sbjct: 239 ELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKPNVRFVIH 298
Query: 183 FDLPSDVEEYVHRIGRTGRMG 203
+D+P ++E Y GR GR G
Sbjct: 299 YDMPGNLESYYQEAGRAGRDG 319
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 67.8 bits (166), Expect = 3e-13
Identities = 37/105 (35%), Positives = 58/105 (55%), Gaps = 11/105 (10%)
Query: 107 DEALTLVFVETKKGADQLEDFLHHHGYPVTSI---HGDR------TQKEREEALRRFRSG 157
++ +VF E + A+++ +FL G R +QKE++E + +FR G
Sbjct: 365 GDSRVIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKG 424
Query: 158 ETPILVATAVAARGLDIPHVKHVINFD-LPSDVEEYVHRIGRTGR 201
E +LVAT+V GLDIP V VI ++ +PS++ + R GRTGR
Sbjct: 425 EYNVLVATSVGEEGLDIPEVDLVIFYEPVPSEI-RSIQRKGRTGR 468
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 66.4 bits (163), Expect = 1e-12
Identities = 39/99 (39%), Positives = 59/99 (59%), Gaps = 10/99 (10%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPV------TSIHGDR--TQKEREEALRRFRSGETPILV 163
+VF + + A+++ D L G S GD+ +QKE+ E L +FR+GE +LV
Sbjct: 369 IVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLV 428
Query: 164 ATAVAARGLDIPHVKHVINFD-LPSDVEEYVHRIGRTGR 201
+T+VA GLDIP V VI ++ +PS++ + R GRTGR
Sbjct: 429 STSVAEEGLDIPSVDLVIFYEPVPSEI-RSIQRKGRTGR 466
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 56.1 bits (136), Expect = 4e-09
Identities = 34/98 (34%), Positives = 45/98 (45%), Gaps = 9/98 (9%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
LV TKK A+ L ++L G V +H D ER E +R R GE +LV +
Sbjct: 449 VLVTTLTKKMAEDLTEYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLRE 508
Query: 171 GLDIPHVKHVINFDLPSDVEEY-------VHRIGRTGR 201
GLD+P V V D +D E + + IGR R
Sbjct: 509 GLDLPEVSLVAILD--ADKEGFLRSERSLIQTIGRAAR 544
>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 = 54.8 bits (132), Expect = 1e-08
Identities = 25/92 (27%), Positives = 47/92 (51%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
+++ ++K ++Q+ L + G + H R++ +F+ E ++VAT G
Sbjct: 230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMG 289
Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
++ P V+ VI++ LP +E Y GR GR G
Sbjct: 290 INKPDVRFVIHYSLPKSMESYYQESGRAGRDG 321
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 53.8 bits (130), Expect = 2e-08
Identities = 32/100 (32%), Positives = 45/100 (45%), Gaps = 17/100 (17%)
Query: 111 TLVFVETKKGADQL---------EDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPI 161
TL+F T+ GA++L + HHG S+ R R E R + GE
Sbjct: 256 TLIFTNTRSGAERLAFRLKKLGPDIIEVHHG----SL--SREL--RLEVEERLKEGELKA 307
Query: 162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGR 201
+VAT+ G+DI + VI P V ++ RIGR G
Sbjct: 308 VVATSSLELGIDIGDIDLVIQLGSPKSVNRFLQRIGRAGH 347
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 53.2 bits (128), Expect = 3e-08
Identities = 31/108 (28%), Positives = 48/108 (44%), Gaps = 3/108 (2%)
Query: 93 KEREEAQQYTLI--SCDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEA 150
ER+ A L+ TL+F + A ++ G V +I G+ ++ERE
Sbjct: 266 SERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEEREAI 324
Query: 151 LRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGR 198
L RFR+G +LV V G+DIP +I ++ R+GR
Sbjct: 325 LERFRTGGIKVLVTVKVLDEGVDIPDADVLIILRPTGSRRLFIQRLGR 372
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 53.2 bits (128), Expect = 4e-08
Identities = 32/98 (32%), Positives = 48/98 (48%), Gaps = 18/98 (18%)
Query: 111 TLVFVETKKG---ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA- 166
L+FV G A++L ++L HG IH E+EEAL F GE +LV A
Sbjct: 338 GLIFVPIDYGREKAEELAEYLRSHGINAELIH-----AEKEEALEDFEEGEVDVLVGVAS 392
Query: 167 ---VAARGLDIPH-VKHVINFDLPS-----DVEEYVHR 195
V RGLD+PH +++ + + +P +EE +
Sbjct: 393 YYGVLVRGLDLPHRIRYAVFYGVPKFRFRLTLEESDPK 430
Score = 32.4 bits (74), Expect = 0.20
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 138 IHGDRTQKEREEALRRFRSGETPILVATA 166
H KE+EEAL R SG+ IL+ T+
Sbjct: 161 YHSALPTKEKEEALERIESGDFDILITTS 189
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 51.1 bits (123), Expect = 2e-07
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 13/84 (15%)
Query: 112 LVFVETKKG---ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA-- 166
L+FV + KG A++L ++L G E +F GE +LV A
Sbjct: 332 LIFVPSDKGKEYAEELAEYLEDLGINAELAISGF-----ERKFEKFEEGEVDVLVGVASY 386
Query: 167 --VAARGLDIPH-VKHVINFDLPS 187
V RG+D+P +++ I + +P
Sbjct: 387 YGVLVRGIDLPERIRYAIFYGVPK 410
Score = 31.8 bits (73), Expect = 0.33
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 139 HGDRTQKEREEALRRFRSGETPILVAT 165
H +KE+EE L R + G+ ILV T
Sbjct: 160 HSSLKKKEKEEFLERLKEGDFDILVTT 186
>gnl|CDD|223627 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
[Transcription / DNA replication, recombination, and
repair].
Length = 866
Score = 50.9 bits (121), Expect = 2e-07
Identities = 23/96 (23%), Positives = 39/96 (40%), Gaps = 5/96 (5%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
L+F + D LED+L G + G K R+E + RF + E + ++ A
Sbjct: 714 VLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRRQELIDRFNADEEEKVFLLSLKAG 773
Query: 171 GLDIP-----HVKHVINFDLPSDVEEYVHRIGRTGR 201
GL + V + P+ + + R R G+
Sbjct: 774 GLGLNLTGADTVILFDPWWNPAVELQAIDRAHRIGQ 809
Score = 36.3 bits (83), Expect = 0.012
Identities = 18/63 (28%), Positives = 24/63 (38%), Gaps = 1/63 (1%)
Query: 36 DKRSCLLDLLSSPSQEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKER 95
K L +LL E G L+F + D LED+L G + G K R
Sbjct: 692 GKLQALDELLL-DKLLEEGHYHKVLIFSQFTPVLDLLEDYLKALGIKYVRLDGSTPAKRR 750
Query: 96 EEA 98
+E
Sbjct: 751 QEL 753
>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 = 50.0 bits (120), Expect = 4e-07
Identities = 32/96 (33%), Positives = 41/96 (42%), Gaps = 5/96 (5%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
LV TKK A+ L D+L G V +H + ER E +R R GE +LV +
Sbjct: 445 VLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLRE 504
Query: 171 GLDIPHVKHVINFD-----LPSDVEEYVHRIGRTGR 201
GLD+P V V D + IGR R
Sbjct: 505 GLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAAR 540
Score = 30.3 bits (69), Expect = 0.81
Identities = 15/39 (38%), Positives = 19/39 (48%)
Query: 59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREE 97
LV TKK A+ L D+L G V +H + ER E
Sbjct: 445 VLVTTLTKKMAEDLTDYLKELGIKVRYLHSEIDTLERVE 483
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 48.6 bits (116), Expect = 1e-06
Identities = 35/120 (29%), Positives = 46/120 (38%), Gaps = 6/120 (5%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
T+VF +++ +L D L G H KER+ R F + E +V TA A
Sbjct: 443 TIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQELAAVVTTAALAA 502
Query: 171 GLDIPHVKHVINFDLPS-----DVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSYGGSSS 225
G+D P VI L V E+ +GR GR D Y G Y S
Sbjct: 503 GVDFP-ASQVIFESLAMGIEWLSVREFQQMLGRAGRPDYHDRGKVYLLVEPGKKYHASME 561
Score = 28.2 bits (63), Expect = 5.1
Identities = 11/37 (29%), Positives = 16/37 (43%)
Query: 59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKER 95
T+VF +++ +L D L G H KER
Sbjct: 443 TIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKER 479
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 47.6 bits (114), Expect = 2e-06
Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 101 YTLISCDEALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGDRTQKEREEALRRFRSGE 158
LI E L L + A++L + L V +HG E++ + F+ GE
Sbjct: 480 CPLIEESEKLEL------QAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGE 533
Query: 159 TPILVATAVAARGLDIP 175
ILVAT V G+D+P
Sbjct: 534 IDILVATTVIEVGVDVP 550
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 46.7 bits (112), Expect = 5e-06
Identities = 28/109 (25%), Positives = 48/109 (44%), Gaps = 21/109 (19%)
Query: 82 PVTSIHGDRTQKE------REEAQQ-------YTLISCDEALTLVFVETKKGADQLEDFL 128
P+T++ ++++ REE + LI E L L + A++ + L
Sbjct: 446 PITTVVIPDSRRDEVYERIREEIAKGRQAYVVCPLIEESEKLDL------QSAEETYEEL 499
Query: 129 HHH--GYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIP 175
V +HG E++ + F++GE ILVAT V G+D+P
Sbjct: 500 QEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATTVIEVGVDVP 548
Score = 29.3 bits (67), Expect = 2.0
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 121 ADQ----LEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVAT 165
A+Q L+ L G V + G KER E L SGE I++ T
Sbjct: 323 AEQHYENLKKLLEPLGIRVALLTGSLKGKERREILEAIASGEADIVIGT 371
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 45.5 bits (108), Expect = 1e-05
Identities = 23/92 (25%), Positives = 43/92 (46%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
+++ ++ + L G + H R + F+ + I+VAT G
Sbjct: 240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMG 299
Query: 172 LDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
++ P+V+ V++FD+P ++E Y GR GR G
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQETGRAGRDG 331
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 45.4 bits (108), Expect = 1e-05
Identities = 19/43 (44%), Positives = 24/43 (55%)
Query: 133 YPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIP 175
Y V +HG E+E + FR GE ILVAT V G+D+P
Sbjct: 483 YNVGLLHGRMKSDEKEAVMEEFREGEVDILVATTVIEVGVDVP 525
Score = 30.8 bits (70), Expect = 0.75
Identities = 13/45 (28%), Positives = 20/45 (44%)
Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVAT 165
+ L + L G V + G K R+E L SG+ ++V T
Sbjct: 301 YNSLRNLLAPLGIEVALLTGSLKGKRRKELLETIASGQIHLVVGT 345
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 44.6 bits (106), Expect = 2e-05
Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 4/81 (4%)
Query: 104 ISCDEALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGD--RTQKEREEALRRFRSGET 159
SC E + G +++E+ L G + I D R + E+ L +F +GE
Sbjct: 476 QSCPECGSEHLRAVGPGTERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLDQFANGEA 535
Query: 160 PILVATAVAARGLDIPHVKHV 180
IL+ T + A+G D P+V V
Sbjct: 536 DILIGTQMIAKGHDFPNVTLV 556
Score = 27.3 bits (61), Expect = 8.2
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 122 DQLEDFLH-HHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVA 168
QL G V +H + ER RR R GE +++ T A
Sbjct: 259 PQLLARFKARFGAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSA 306
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse
gyrase, found in both archaeal and bacterial
thermophiles. This enzyme, a fusion of a type I
topoisomerase domain and a helicase domain, introduces
positive supercoiling to increase the melting
temperature of DNA double strands. Generally, these
gyrases are encoded as a single polypeptide. An
exception was found in Methanopyrus kandleri, where
enzyme is split within the topoisomerase domain,
yielding a heterodimer of gene products designated RgyB
and RgyA [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1171
Score = 44.4 bits (105), Expect = 3e-05
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 12/84 (14%)
Query: 112 LVFVETKKG---ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA-- 166
+V+V G A+++ +FL +HG + H + +E +F GE +L+ A
Sbjct: 330 IVYVSIDYGKEKAEEIAEFLENHGVKAVAYHA----TKPKEDYEKFAEGEIDVLIGVASY 385
Query: 167 --VAARGLDIPH-VKHVINFDLPS 187
RGLD+P V++ + +P
Sbjct: 386 YGTLVRGLDLPERVRYAVFLGVPK 409
Score = 30.6 bits (69), Expect = 0.75
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 138 IHGDRTQKEREEALRRFRSGETPILVATA 166
H KE++E + R +G+ IL+ T
Sbjct: 158 YHSRLPTKEKKEFMERIENGDFDILITTT 186
>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 = 43.9 bits (104), Expect = 4e-05
Identities = 27/103 (26%), Positives = 41/103 (39%), Gaps = 9/103 (8%)
Query: 111 TLVFVETKKGADQLEDFL--------HHHGYPVTSIHGDRTQKEREEALRRFRSGETPIL 162
TLVF ++K + L V++ ++ER F+ GE +
Sbjct: 309 TLVFFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGV 368
Query: 163 VATAVAARGLDIPHVKHVINFDLPSD-VEEYVHRIGRTGRMGN 204
+AT G+DI + VI + P V + R GR GR G
Sbjct: 369 IATNALELGIDIGSLDAVIAYGYPGVSVLSFRQRAGRAGRRGQ 411
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 39.9 bits (93), Expect = 0.001
Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 4/86 (4%)
Query: 118 KKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHV 177
+K A++L++F H + HG +R +++ E I+ AT G++ P V
Sbjct: 694 EKVAERLQEFGHKAAF----YHGSMDPAQRAFVQKQWSKDEINIICATVAFGMGINKPDV 749
Query: 178 KHVINFDLPSDVEEYVHRIGRTGRMG 203
+ VI+ LP +E Y GR GR G
Sbjct: 750 RFVIHHSLPKSIEGYHQECGRAGRDG 775
>gnl|CDD|234468 TIGR04095, dnd_restrict_1, DNA phosphorothioation system
restriction enzyme. The DNA phosphorothioate
modification system dnd (DNA instability during
electrophoresis) recently has been shown to provide a
modification essential to a restriction system. This
protein family was detected by Partial Phylogenetic
Profiling as linked to dnd, and its members usually are
clustered with the dndABCDE genes.
Length = 451
Score = 39.2 bits (92), Expect = 0.001
Identities = 30/103 (29%), Positives = 47/103 (45%), Gaps = 2/103 (1%)
Query: 101 YTLISC-DEALTLVFVETKKGADQLEDFL-HHHGYPVTSIHGDRTQKEREEALRRFRSGE 158
+TL C D + E + D + L + G V + + +++EREE LR+F SG
Sbjct: 280 HTLFYCGDGSTEDGSDEEDRQIDAVVRLLGNELGMRVNTFTAEESKEEREELLRQFESGL 339
Query: 159 TPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGR 201
LVA G+DIP + S+ +++ R GR R
Sbjct: 340 LQGLVAIRCLDEGVDIPATRTAYILASSSNPRQFIQRRGRVLR 382
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 39.5 bits (92), Expect = 0.001
Identities = 22/64 (34%), Positives = 33/64 (51%)
Query: 137 SIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRI 196
S HG ++++R + +SGE +VAT+ G+D+ V VI P V + RI
Sbjct: 306 SHHGSVSKEQRAITEQALKSGELRCVVATSSLELGIDMGAVDLVIQVATPLSVASGLQRI 365
Query: 197 GRTG 200
GR G
Sbjct: 366 GRAG 369
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 38.7 bits (90), Expect = 0.002
Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 13/83 (15%)
Query: 112 LVFVETKKG---ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATA-- 166
L+FV +G A+++E +L G+ + + + ++ F GE L+ A
Sbjct: 334 LIFVPIDEGAEKAEEIEKYLLEDGFKIELVSA-----KNKKGFDLFEEGEIDYLIGVATY 388
Query: 167 --VAARGLDIPH-VKHVINFDLP 186
RGLD+P ++ + + +P
Sbjct: 389 YGTLVRGLDLPERIRFAVFYGVP 411
Score = 32.6 bits (74), Expect = 0.19
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 139 HGDRTQKEREEALRRFRSGETPILVATA 166
H + +KE+EE L R +G+ ILV TA
Sbjct: 159 HSNLRKKEKEEFLERIENGDFDILVTTA 186
>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 = 37.2 bits (87), Expect = 0.002
Identities = 15/65 (23%), Positives = 25/65 (38%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
LV + +Q+ + L + + RE+ L RF+ G+ IL
Sbjct: 12 VLVLFPSYSLLEQVAELLASELLEKGIELLVQGEGSREKLLERFKKGKGAILFGVGSFWE 71
Query: 171 GLDIP 175
G+D P
Sbjct: 72 GIDFP 76
>gnl|CDD|235395 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional.
Length = 652
Score = 38.5 bits (91), Expect = 0.002
Identities = 27/67 (40%), Positives = 34/67 (50%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAAR 170
LV TK+ A+ L D+L G V +H D ER E +R R GE +LV +
Sbjct: 449 VLVTTLTKRMAEDLTDYLKELGIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGINLLRE 508
Query: 171 GLDIPHV 177
GLDIP V
Sbjct: 509 GLDIPEV 515
>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 = 38.5 bits (90), Expect = 0.003
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 138 IHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI-----NFDLPSDVEEY 192
HG T+ E EE + F GE +LV T + G+DIP+ +I F L + + +
Sbjct: 692 AHGQMTENELEEVMLEFYKGEFQVLVCTTIIETGIDIPNANTIIIERADKFGL-AQLYQL 750
Query: 193 VHRIGRTGRMG 203
R+GR+ +
Sbjct: 751 RGRVGRSKKKA 761
>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 = 36.8 bits (86), Expect = 0.008
Identities = 31/108 (28%), Positives = 43/108 (39%), Gaps = 25/108 (23%)
Query: 111 TLVFVETKKGA--------DQLEDF-----LHHHGYPVTSIHGDRTQKER-EEALRRFRS 156
TLVF T+ A + +F LHH S+ DR Q+ E A+ +
Sbjct: 250 TLVFTNTRSQAELWFQALWEANPEFALPIALHH-----GSL--DREQRRWVEAAMA---A 299
Query: 157 GETPILVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTG-RMG 203
G +V T+ G+D V VI P V + R GR+ R G
Sbjct: 300 GRLRAVVCTSSLDLGVDFGPVDLVIQIGSPKGVARLLQRAGRSNHRPG 347
>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 = 35.9 bits (83), Expect = 0.013
Identities = 25/96 (26%), Positives = 44/96 (45%), Gaps = 8/96 (8%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYP---VTSIHGDRTQKEREEALRRFRSGETPILVATAV 167
L+F + +Q+ L P + S+H + R+E + FR G+ +L+ T +
Sbjct: 308 VLIFFPEIETMEQVAAALKK-KLPKETIASVHS--EDQHRKEKVEAFRDGKITLLITTTI 364
Query: 168 AARGLDIPHVK-HVINFDLPSDVEEYVHRI-GRTGR 201
RG+ P+V V+ + E + +I GR GR
Sbjct: 365 LERGVTFPNVDVFVLGAEHRVFTESALVQIAGRVGR 400
>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 = 35.4 bits (82), Expect = 0.020
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 4/86 (4%)
Query: 99 QQYTLISCDEALTLVFVETKKGADQLEDFLHHH--GYPVTSIHGD--RTQKEREEALRRF 154
Q+ +C + + V G +Q+E+ L G + I D + E L +F
Sbjct: 249 QEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDSDTTSRKGAHEALLNQF 308
Query: 155 RSGETPILVATAVAARGLDIPHVKHV 180
+G+ IL+ T + A+G P+V V
Sbjct: 309 ANGKADILIGTQMIAKGHHFPNVTLV 334
>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 = 34.2 bits (79), Expect = 0.023
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVAT 165
++L+ G V + G + KE+ L++ G+ ILV T
Sbjct: 62 YEELKKLFKILGLRVALLTGGTSLKEQARKLKK---GKADILVGT 103
>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 = 35.1 bits (81), Expect = 0.031
Identities = 25/101 (24%), Positives = 38/101 (37%), Gaps = 8/101 (7%)
Query: 111 TLVFVETKKGADQ--------LEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPIL 162
TL FV +++GA+ L + V + ++R E R R GE +
Sbjct: 274 TLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGV 333
Query: 163 VATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTGRMG 203
T G+DI + V+ P + GR GR G
Sbjct: 334 ATTNALELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRG 374
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 34.9 bits (80), Expect = 0.036
Identities = 42/188 (22%), Positives = 66/188 (35%), Gaps = 46/188 (24%)
Query: 50 QEELGDEALTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEA 109
+E + D LVFV ++K A+ + L H +S +
Sbjct: 230 KETVNDGGQVLVFVSSRKNAEDYAEMLIQHFPEFNDFK----------------VSSENN 273
Query: 110 LTLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAA 169
D + + HG V H + ++R FR+ ++VAT A
Sbjct: 274 ---------NVYDDSLNEMLPHG--VAFHHAGLSNEQRRFIEEMFRNRYIKVIVATPTLA 322
Query: 170 RGLDIPHVKHVINFDL---------PSDVEEYVHRIGRTGRMGNLDFPFSYNQPGYGGSY 220
G+++P + VI D+ E IGR GR G Y+Q G G Y
Sbjct: 323 AGVNLP-ARLVIVRDITRYGNGGIRYLSNMEIKQMIGRAGRPG-------YDQYGIGYIY 374
Query: 221 GGSSSQNS 228
++S S
Sbjct: 375 --AASPAS 380
>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 = 34.3 bits (79), Expect = 0.039
Identities = 22/96 (22%), Positives = 36/96 (37%), Gaps = 20/96 (20%)
Query: 138 IHGDRTQKERE----EALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL----PSDV 189
+H T+K+R E L + E ++VAT V LD I+ D+ + +
Sbjct: 254 LHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQVIEASLD-------ISADVMITELAPI 306
Query: 190 EEYVHRIGRTGRMG-----NLDFPFSYNQPGYGGSY 220
+ + R+GR R G N + P
Sbjct: 307 DSLIQRLGRLHRYGRKNGENFEVYIITIAPEGKLFP 342
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 34.5 bits (80), Expect = 0.049
Identities = 21/71 (29%), Positives = 36/71 (50%), Gaps = 6/71 (8%)
Query: 138 IHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVI-----NFDLPSDVEEY 192
HG ++E EE + F +GE +LV T + G+DIP+ +I F L + + +
Sbjct: 835 AHGQMRERELEEVMLDFYNGEYDVLVCTTIIETGIDIPNANTIIIERADKFGL-AQLYQL 893
Query: 193 VHRIGRTGRMG 203
R+GR+ +
Sbjct: 894 RGRVGRSNKQA 904
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 33.6 bits (77), Expect = 0.055
Identities = 23/87 (26%), Positives = 35/87 (40%), Gaps = 17/87 (19%)
Query: 121 ADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVAT------AVAARGLDI 174
A++L+ G V ++G + E LR+ SG+T ILV T + L +
Sbjct: 71 AEELKKLGPSLGLKVVGLYGG---DSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSL 127
Query: 175 PHVKHVINFDLPSDVEEYVHRIGRTGR 201
+V VI D HR+ G
Sbjct: 128 SNVDLVI-LD-------EAHRLLDGGF 146
>gnl|CDD|217600 pfam03529, TF_Otx, Otx1 transcription factor.
Length = 86
Score = 31.7 bits (72), Expect = 0.075
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 207 FPFSYNQ-PGYGGSYGGSSS 225
+P +Y Q PGY Y GSSS
Sbjct: 26 YPMTYTQAPGYSQGYPGSSS 45
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 33.6 bits (78), Expect = 0.088
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 123 QLEDFLHHH--GYPVTSIHGD--RTQKEREEALRRFRSGETPILVATAVAARGLDIPHV 177
+LE+ L + I D R + E+ L +F GE IL+ T + A+G D P+V
Sbjct: 441 RLEEELAELFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQMLAKGHDFPNV 499
Score = 27.4 bits (62), Expect = 7.2
Identities = 10/44 (22%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 123 QLEDFLHHH-GYPVTSIHGDRTQKEREEALRRFRSGETPILVAT 165
Q+ G PV +H + ER + R+ + GE +++
Sbjct: 205 QMLARFRARFGAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGA 248
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 33.6 bits (77), Expect = 0.090
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 144 QKEREEALRRFR-SGETPILVATAVAARGLDIPH 176
+ EREE L +F+ SGE ILV G+D P
Sbjct: 513 EDEREELLEKFKASGEGLILVGGGSFWEGVDFPG 546
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 33.1 bits (76), Expect = 0.12
Identities = 19/74 (25%), Positives = 33/74 (44%), Gaps = 9/74 (12%)
Query: 139 HGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPH----VKHVINFDL-----PSDV 189
H +++R+ FR G+ +LV+T A G+++P +K +D V
Sbjct: 321 HAGLPREDRQLVEDAFRKGKIKVLVSTPTLAAGVNLPARTVIIKDTRRYDPKGGIVDIPV 380
Query: 190 EEYVHRIGRTGRMG 203
+ + GR GR G
Sbjct: 381 LDVLQMAGRAGRPG 394
>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 = 32.8 bits (75), Expect = 0.14
Identities = 23/82 (28%), Positives = 35/82 (42%), Gaps = 17/82 (20%)
Query: 131 HGYPVTSIHG-----DRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKHVINFDL 185
+ IH DR +KE E L F+ E ++VAT V LD I+ D+
Sbjct: 243 PEEEIMLIHSRFTEKDRAKKE-AELLLEFKKSEKFVIVATQVIEASLD-------ISVDV 294
Query: 186 ----PSDVEEYVHRIGRTGRMG 203
+ ++ + R+GR R G
Sbjct: 295 MITELAPIDSLIQRLGRLHRYG 316
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 32.8 bits (75), Expect = 0.15
Identities = 32/104 (30%), Positives = 46/104 (44%), Gaps = 15/104 (14%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRS----GETPILVATA 166
LV V T A +L + L G V +H T K+REE R + E I+VAT
Sbjct: 443 VLVIVNTVDRAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFKQNEGFIVVATQ 502
Query: 167 VAARGLDIPHVKHVINFDL----PSDVEEYVHRIGRTGRMGNLD 206
V G+D I+FD+ + ++ + R GR R G +
Sbjct: 503 VIEAGVD-------IDFDVLITELAPIDSLIQRAGRVNRHGKKE 539
>gnl|CDD|239825 cd04333, ProX_deacylase, This CD, composed mainly of bacterial
single-domain proteins, includes the Thermus
thermophilus (Tt) YbaK-like protein, a homolog of the
trans-acting Escherichia coli YbaK Cys-tRNA(Pro)
deacylase and the Agrobacterium tumefaciens ProX
Ala-tRNA(Pro) deacylase and also the cis-acting
prolyl-tRNA synthetase-editing domain (ProRS-INS). While
ProX and ProRS-INS hydrolyze misacylated Ala-tRNA(Pro),
the E. coli YbaK hydrolyzes misacylated Cys-tRNA(Pro). A
few CD members are N-terminal, YbaK-ProX-like domains of
an uncharacterized protein with a C-terminal, predicted
Fe-S protein domain.
Length = 148
Score = 30.9 bits (71), Expect = 0.27
Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 6/49 (12%)
Query: 154 FRSGETPILVATAVAARGLDIPHVKHVINFDL----PSDVEEYV-HRIG 197
FR + P+LV T+ AR +D K + L +V E IG
Sbjct: 47 FRVDDEPVLVVTSGDAR-VDNKKFKALFGEKLKMADAEEVRELTGFAIG 94
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 31.8 bits (73), Expect = 0.37
Identities = 27/99 (27%), Positives = 46/99 (46%), Gaps = 12/99 (12%)
Query: 111 TLVFVETKKGADQLEDFLHH------HGYPVTSI---HGDRTQKEREEALRRFRSGETPI 161
TL+F T+ GA E L++ Y +I H +++ R E + + GE +
Sbjct: 287 TLIFTNTRSGA---ERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKV 343
Query: 162 LVATAVAARGLDIPHVKHVINFDLPSDVEEYVHRIGRTG 200
+V++ G+DI ++ V+ P V + RIGR G
Sbjct: 344 VVSSTSLELGIDIGYIDLVVLLGSPKSVSRLLQRIGRAG 382
>gnl|CDD|225202 COG2320, GrpB, Uncharacterized conserved protein [Function
unknown].
Length = 185
Score = 30.5 bits (69), Expect = 0.51
Identities = 26/86 (30%), Positives = 33/86 (38%), Gaps = 8/86 (9%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARG 171
LV VE+ AD+L + L GYP + G RT + R R S P V V RG
Sbjct: 69 LVVVESLDAADELAEPLSAAGYPHVTNDG-RTLRFRLWLKRVHASAREPTHV--HVVTRG 125
Query: 172 LDIPHVKHVINFDL----PSDVEEYV 193
++ D P E Y
Sbjct: 126 SPE-IEFALLFRDWLRANPEIREAYA 150
>gnl|CDD|181458 PRK08527, PRK08527, acetolactate synthase 3 catalytic subunit;
Validated.
Length = 563
Score = 30.8 bits (70), Expect = 0.63
Identities = 27/96 (28%), Positives = 42/96 (43%), Gaps = 27/96 (28%)
Query: 156 SGETPI-LVAT----AVAARGLDIPHVKHVINF------DLPSDVEE--YVHRIGR---- 198
SG+ P L+ T + A G+ P VKH N+ +LP ++E Y+ R GR
Sbjct: 99 SGQVPNSLIGTDAFQEIDAVGISRPCVKH--NYLVKSIEELPRILKEAFYIARSGRPGPV 156
Query: 199 --------TGRMGNLDFPFSYNQPGYGGSYGGSSSQ 226
T +G ++P + Y +Y G+S Q
Sbjct: 157 HIDIPKDVTATLGEFEYPKEISLKTYKPTYKGNSRQ 192
>gnl|CDD|181929 PRK09526, lacI, lac repressor; Reviewed.
Length = 342
Score = 30.3 bits (69), Expect = 0.79
Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 13/72 (18%)
Query: 126 DFLHHHGY-PVTSIHGD-RTQKEREEALRRFRSGETP--ILVA---------TAVAARGL 172
++L + P+ GD ++ L+ R G P ILVA A+ GL
Sbjct: 205 EYLTDYQLQPIAVREGDWSAMSGYQQTLQMLREGPVPSAILVANDQMALGVLRALHESGL 264
Query: 173 DIPHVKHVINFD 184
+P VI +D
Sbjct: 265 RVPGQISVIGYD 276
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 30.2 bits (68), Expect = 1.1
Identities = 26/99 (26%), Positives = 47/99 (47%), Gaps = 13/99 (13%)
Query: 112 LVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFR---SGETPILVATAVA 168
L+F + + D LED+L + GY I G+ ++R+ ++ F S + L++T
Sbjct: 491 LIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPGSEKFVFLLSTRAG 550
Query: 169 ARGLDIPHVKHVINFDLPSD--------VEEYVHRIGRT 199
G+++ VI +D SD ++ HRIG+
Sbjct: 551 GLGINLATADIVILYD--SDWNPQVDLQAQDRAHRIGQK 587
>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 = 29.8 bits (67), Expect = 1.3
Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 11/81 (13%)
Query: 122 DQLEDFLHH--HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKH 179
++L D L G + I G +K+RE A++ IL+ T+ G+D
Sbjct: 282 NRLSDLLQQQGLGDDIGRITGFAPKKDRERAMQ------FDILLGTSTVDVGVDF-KRDW 334
Query: 180 VINFDLPSDVEEYVHRIGRTG 200
+I F D + R+GR G
Sbjct: 335 LI-FS-ARDAAAFWQRLGRLG 353
>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 = 29.9 bits (67), Expect = 1.3
Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 11/81 (13%)
Query: 122 DQLEDFLHH--HGYPVTSIHGDRTQKEREEALRRFRSGETPILVATAVAARGLDIPHVKH 179
++L D L G + I G +K+RE A++ IL+ T+ G+D
Sbjct: 286 NRLSDLLQQQGLGDDIGRITGFAPKKDRERAMQ------FDILLGTSTVDVGVDF-KRDW 338
Query: 180 VINFDLPSDVEEYVHRIGRTG 200
+I F D + R+GR G
Sbjct: 339 LI-FS-ARDAAAFWQRLGRLG 357
>gnl|CDD|204349 pfam09949, DUF2183, Uncharacterized conserved protein (DUF2183).
This domain, found in various hypothetical bacterial
proteins, has no known function.
Length = 99
Score = 27.9 bits (63), Expect = 1.8
Identities = 5/18 (27%), Positives = 8/18 (44%)
Query: 70 DQLEDFLHHHGYPVTSIH 87
L FL +G+P +
Sbjct: 14 PFLTRFLERNGFPKGPLL 31
Score = 27.9 bits (63), Expect = 1.8
Identities = 5/18 (27%), Positives = 8/18 (44%)
Query: 122 DQLEDFLHHHGYPVTSIH 139
L FL +G+P +
Sbjct: 14 PFLTRFLERNGFPKGPLL 31
>gnl|CDD|173947 cd08188, Fe-ADH4, Iron-containing alcohol dehydrogenases-like.
Iron-containing alcohol dehydrogenase-like. Alcohol
dehydrogenase catalyzes the reduction of acetaldehyde to
alcohol with NADP as cofactor. Its activity requires
iron ions. The protein structure represents a
dehydroquinate synthase-like fold and is belonged to the
alcohol dehydrogenase-like superfamily. They are
distinct from other alcohol dehydrogenases which contain
different protein domains. Proteins of this family have
not been characterized. Their specific function is
unknown.
Length = 377
Score = 29.1 bits (66), Expect = 2.0
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 8/35 (22%)
Query: 172 LDIPH-------VKHVINFDLPSDVEEYVHRIGRT 199
LD+PH + HV+ F+ P+ E Y RI
Sbjct: 270 LDLPHGECNAILLPHVMEFNYPAAPERYA-RIAEA 303
>gnl|CDD|226032 COG3501, VgrG, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 550
Score = 28.8 bits (65), Expect = 2.4
Identities = 14/50 (28%), Positives = 18/50 (36%), Gaps = 5/50 (10%)
Query: 109 ALTLVFVETKKGAD----QLEDFLHHHGYPVTSIHGDRTQKEREEALRRF 154
LV V+TK G D E + + G G R + R EA
Sbjct: 241 RADLVAVDTKAGQDLARLDTEAY-DYPGRFKDREDGQRLARLRMEAHEAR 289
>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 = 28.8 bits (64), Expect = 3.3
Identities = 9/44 (20%), Positives = 16/44 (36%), Gaps = 1/44 (2%)
Query: 134 PVTSIHGDRTQKEREEALRRFR-SGETPILVATAVAARGLDIPH 176
+ E+ +G P+L+A A G+D+ H
Sbjct: 497 EIVIQSEKNRLASAEQQFLALYANGIQPVLIAAGGAWTGIDLTH 540
>gnl|CDD|222252 pfam13596, PAS_10, PAS domain.
Length = 106
Score = 26.7 bits (60), Expect = 4.9
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 132 GYPVTSIHGDRTQKEREEALRRFRSGETP 160
G P+ IH + + EE + R+GE
Sbjct: 40 GRPLADIHPPLSVPDVEEIIHALRTGERD 68
>gnl|CDD|204432 pfam10281, Ish1, Putative stress-responsive nuclear envelope
protein. This family of proteins found in fungi is a
putative stress-responsive nuclear envelope protein
Ish1.
Length = 38
Score = 25.2 bits (56), Expect = 5.3
Identities = 10/35 (28%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 122 DQLEDFLHHHGYPVTSIHGDRTQKEREEALRRFRS 156
L+++L HG PV + R+E L R
Sbjct: 7 SDLKEWLDSHGIPV-----PKKAATRDELLALARK 36
>gnl|CDD|223973 COG1043, LpxA, Acyl-[acyl carrier protein].
Length = 260
Score = 27.6 bits (62), Expect = 6.0
Identities = 19/49 (38%), Positives = 22/49 (44%), Gaps = 7/49 (14%)
Query: 142 RTQKEREE--ALRR-----FRSGETPILVATAVAARGLDIPHVKHVINF 183
R REE ALR+ FRSG T +A D P VK I+F
Sbjct: 202 RRGFSREEIHALRKAYKLLFRSGLTLREALEEIAEEYADNPEVKEFIDF 250
>gnl|CDD|235234 PRK04164, PRK04164, hypothetical protein; Provisional.
Length = 181
Score = 27.1 bits (61), Expect = 6.0
Identities = 11/38 (28%), Positives = 15/38 (39%)
Query: 59 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKERE 96
V V TK+ +L + L GY VT + R
Sbjct: 93 ITVRVITKEYELELANELRELGYGVTVFDAEGRDGPRM 130
Score = 27.1 bits (61), Expect = 6.0
Identities = 11/38 (28%), Positives = 15/38 (39%)
Query: 111 TLVFVETKKGADQLEDFLHHHGYPVTSIHGDRTQKERE 148
V V TK+ +L + L GY VT + R
Sbjct: 93 ITVRVITKEYELELANELRELGYGVTVFDAEGRDGPRM 130
>gnl|CDD|153325 cd07641, BAR_ASAP1, The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP
with SH3 domain, ANK repeat and PH domain containing
protein 1. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. ASAP1 (ArfGAP with SH3
domain, ANK repeat and PH domain containing protein 1)
is also known as DDEF1 (Development and Differentiation
Enhancing Factor 1), AMAP1, centaurin beta-4, or PAG2.
ASAP1 is an Arf GTPase activating protein (GAP) with
activity towards Arf1 and Arf5 but not Arf6 However, it
has been shown to bind GTP-Arf6 stably without GAP
activity. It has been implicated in cell growth,
migration, and survival, as well as in tumor invasion
and malignancy. It binds paxillin and cortactin, two
components of invadopodia which are essential for tumor
invasiveness. It also binds focal adhesion kinase (FAK)
and the SH2/SH3 adaptor CrkL. ASAP1 contains an
N-terminal BAR domain, followed by a Pleckstrin homology
(PH) domain, an Arf GAP domain, ankyrin (ANK) repeats,
and a C-terminal SH3 domain. BAR domains form dimers
that bind to membranes, induce membrane bending and
curvature, and may also be involved in protein-protein
interactions. The BAR domain of ASAP1 mediates membrane
bending, is essential for function, and autoinhibits GAP
activity by interacting with the PH and/or Arf GAP
domains.
Length = 215
Score = 27.3 bits (60), Expect = 6.1
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 78 HHGYPVTSIHGDRTQKERE-EAQQYTLISCDEALTLVFVETKKGADQLEDFLHHH 131
HG T I G +E E E + + L C+ + + ++TKKG D L++ + ++
Sbjct: 137 QHGMIRTEITGAEIAEEMEKERRLFQLQMCEYLIKVNEIKTKKGVDLLQNLIKYY 191
>gnl|CDD|240651 cd12174, PGDH_like_3, Putative D-3-Phosphoglycerate Dehydrogenases,
NAD-binding and catalytic domains. Phosphoglycerate
dehydrogenases (PGDHs) catalyze the initial step in the
biosynthesis of L-serine from D-3-phosphoglycerate.
PGDHs come in 3 distinct structural forms, with this
first group being related to 2-hydroxy acid
dehydrogenases, sharing structural similarity to formate
and glycerate dehydrogenases of the D-specific
2-hydroxyacid dehydrogenase superfamily, which also
include groups such as L-alanine dehydrogenase and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. Many, not all, members of this family are
dimeric.
Length = 305
Score = 27.5 bits (62), Expect = 6.2
Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 161 ILVATAVAARGLD-IPHVKHVINFDLPSDVEEYVHRIGRTGRMGNLDFP 208
IL A ++ +GL+ K+ + D D + I R+ ++ ++DF
Sbjct: 3 ILTANKISKKGLERFKKDKYEVKEDALEDPDAL---IVRSDKLHDMDFA 48
>gnl|CDD|146741 pfam04260, DUF436, Protein of unknown function (DUF436). Family of
bacterial proteins with undetermined function.
Length = 172
Score = 27.1 bits (61), Expect = 6.6
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 150 ALRRFRSGETPILVATAVAARGLDIP------HVKHV 180
A ++ + P+ V VA G+DI H+KHV
Sbjct: 106 AYQQMKD---PVEVEHIVAHAGIDIGDTLIGMHLKHV 139
>gnl|CDD|239093 cd02410, archeal_CPSF_KH, The archaeal cleavage and polyadenylation
specificity factor (CPSF) contains an N-terminal K
homology RNA-binding domain (KH). The archeal CPSFs are
predicted to be metal-dependent RNases belonging to the
beta-CASP family, a subgroup enzymes within the
metallo-beta-lactamase fold. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In general, KH
domains are known to bind single-stranded RNA or DNA and
are found in a wide variety of proteins including
ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA.
Length = 145
Score = 26.5 bits (59), Expect = 8.1
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 13 LAIGRVGSTSENITQRIAWVDE 34
L IG+ GST IT+ W +
Sbjct: 89 LVIGKGGSTLREITRETGWAPK 110
>gnl|CDD|149922 pfam09015, NgoMIV_restric, NgoMIV restriction enzyme. Members of
this family are prokaryotic DNA restriction enzymes,
exhibiting an alpha/beta structure, with a central
region comprising a mixed six-stranded beta-sheet with
alpha-helices on each side. A long 'arm' protrudes out
of the core of the domain between strands beta2 and
beta3 and is mainly involved in the tetramerisation
interface of the protein. These restriction enzymes
recognise the double-stranded sequence GCCGGC and cleave
after G-1.
Length = 277
Score = 27.1 bits (60), Expect = 8.3
Identities = 16/33 (48%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 137 SIHGDRTQKEREEALR--RFRSGETP-ILVATA 166
+I DR Q R EAL R R G P I+V TA
Sbjct: 180 TIRSDRAQNTRTEALNLIRNRKGRLPHIVVVTA 212
>gnl|CDD|176451 cd08769, DAP_dppA_2, Peptidase M55, D-aminopeptidase
dipeptide-binding protein family. M55 Peptidase,
D-Aminopeptidase dipeptide-binding protein (dppA; DAP
dppA; EC 3.4.11.-) domain: Peptide transport systems are
found in many bacterial species and generally function
to accumulate intact peptides in the cell, where they
are hydrolyzed. The dipeptide-binding protein (dppA) of
Bacillus subtilis belongs to the dipeptide ABC transport
(dpp) operon expressed early during sporulation. It is a
binuclear zinc-dependent, D-specific aminopeptidase. The
biologically active enzyme is a homodecamer with active
sites buried in its channel. These
self-compartmentalizing proteases are characterized by a
SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the
preferred substrates. Bacillus subtilis dppA is thought
to function as an adaptation to nutrient deficiency;
hydrolysis of its substrate releases D-Ala which can be
used subsequently as metabolic fuel. This family also
contains a number of uncharacterized putative
peptidases.
Length = 270
Score = 27.2 bits (61), Expect = 8.4
Identities = 13/46 (28%), Positives = 19/46 (41%), Gaps = 9/46 (19%)
Query: 75 FLHHHGYPVTSIHGDRTQKEREEAQQYTLISCDEALTLVFVETKKG 120
+ G PV + GD E E+ + +E VFV TK+
Sbjct: 142 YAGEFGVPVVLVAGDS---ELEKEVK------EETPWAVFVPTKES 178
>gnl|CDD|237472 PRK13690, PRK13690, hypothetical protein; Provisional.
Length = 184
Score = 26.7 bits (60), Expect = 9.5
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 9/37 (24%)
Query: 150 ALRRFRSGETPILVATAVAARGLDIP------HVKHV 180
A + + P++V A G+DI H+KHV
Sbjct: 113 AYQHMKD---PVVVEHIKAHAGIDIGDTLIGMHLKHV 146
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.135 0.404
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,436,904
Number of extensions: 1181662
Number of successful extensions: 1540
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1521
Number of HSP's successfully gapped: 130
Length of query: 237
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 143
Effective length of database: 6,768,326
Effective search space: 967870618
Effective search space used: 967870618
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.6 bits)