RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12726
(558 letters)
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 155 bits (395), Expect = 3e-40
Identities = 71/313 (22%), Positives = 110/313 (35%), Gaps = 60/313 (19%)
Query: 7 TPIS-QMAEFPLEPNLSKMLIMSVHLQCSDEVLTIVSMLSVQNV---FYRP-KDKQALAD 61
TP+ QM+ PL+P L++ML+ + C E TI SMLS Q+ F R K ++
Sbjct: 455 TPLGKQMSLLPLDPRLARMLLTAPEGGCLGEAATIASMLSEQDRESDFSRDVKLRKQRTA 514
Query: 62 QKKAKFNQME------GDHITLLAVYNSWRNNK------FSNAWCYENFVQIRTLKRAQD 109
Q K + GDH+ LL + K C + L RA
Sbjct: 515 QDLLKRLKRRNAADPRGDHLLLLEAFPDRIARKRAKGEYLRANGCRAMLFPTKALSRAPW 574
Query: 110 VRKQLLGIMDRHKLDVVSAGK-------------------NTVRVQKAVCSGFFRNAAKK 150
+ LL +++A + ++ A+ +G N A+
Sbjct: 575 IIAALLVQTSALAGRILAAAEIDEDEWAAQHLPEHCYSEPIWDDIRGALAAGRKLNIAQL 634
Query: 151 DP-QEGYRTLVDSQVVYIHPSS-ALFNRQPEWVIYHELVQTTKEYMRE-----------V 197
Y TL D+ V+ HPSS L EW+ Y E ++T K Y+RE +
Sbjct: 635 QLDGRPYVTLSDNTPVFAHPSSVRLGLVLLEWIKYAEFLRTRKGYLREGRGERWPDVQTL 694
Query: 198 TSIDPKWLVEFAP---AFFKFSDPT------KLSKFKKNQRLEPLQRTNRISFPPGL-LK 247
+ WL E + L + Q L+ + P G ++
Sbjct: 695 IELLKLWLKEQVKGLRGLDGLTKAAMKQALPDLLPWDLTQLLDERA-PTELELPTGSQIR 753
Query: 248 QAVKKRPEIKLIV 260
+ P L V
Sbjct: 754 LRYSREPGPTLAV 766
Score = 120 bits (303), Expect = 2e-28
Identities = 44/106 (41%), Positives = 66/106 (62%), Gaps = 2/106 (1%)
Query: 244 GLLKQAVKKRPE-IKLIVTSATLDAVKFSSYFFEAPIFTIPGRTFPVEVLYTKEPETDY- 301
GLLK + +R + +KLI+ SATLDA +FS+YF AP+ I GRT+PVE+ Y E E DY
Sbjct: 183 GLLKDLLARRRDDLKLIIMSATLDAERFSAYFGNAPVIEIEGRTYPVEIRYLPEAEADYI 242
Query: 302 LDASLITVMQIHLREPPGDVLLFLTGKLDVRKQLLGIMDRHKLDVV 347
L +++ + IHLRE G +L+FL G+ ++ + + D +
Sbjct: 243 LLDAIVAAVDIHLREGSGSILVFLPGQREIERTAEWLEKAELGDDL 288
Score = 104 bits (262), Expect = 2e-23
Identities = 39/75 (52%), Positives = 48/75 (64%), Gaps = 5/75 (6%)
Query: 468 REEIDTACEILYERMKSLGPDVPELIILPVYSALPSEMQTRIFEAAPPGSRKVVIATNIA 527
+ EI+ E L + +L ILP+Y AL +E Q R+FE AP G RKVV+ATNIA
Sbjct: 269 QREIERTAEWLEKAEL-----GDDLEILPLYGALSAEEQVRVFEPAPGGKRKVVLATNIA 323
Query: 528 ETSLTIDGIFYVVDP 542
ETSLTI GI YV+D
Sbjct: 324 ETSLTIPGIRYVIDS 338
Score = 69.7 bits (171), Expect = 2e-12
Identities = 36/181 (19%), Positives = 58/181 (32%), Gaps = 42/181 (23%)
Query: 324 FLTGKLDVRKQLLGIMDRHKLDVVSAGK-------------------NTVRVQKAVCSGF 364
L+ + LL +++A + ++ A+ +G
Sbjct: 568 ALSRAPWIIAALLVQTSALAGRILAAAEIDEDEWAAQHLPEHCYSEPIWDDIRGALAAGR 627
Query: 365 FRNAAKKDP-QEGYRTLVDSQVVYIHPSS-ALFNRQPEWVIYHELVQTTKEYMRE----- 417
N A+ Y TL D+ V+ HPSS L EW+ Y E ++T K Y+RE
Sbjct: 628 KLNIAQLQLDGRPYVTLSDNTPVFAHPSSVRLGLVLLEWIKYAEFLRTRKGYLREGRGER 687
Query: 418 ------VTSIDPKWLVEFAP---AFFKFSDPT------KLSKFKKNQRL-EPLYNKYEEP 461
+ + WL E + L + Q L E + E P
Sbjct: 688 WPDVQTLIELLKLWLKEQVKGLRGLDGLTKAAMKQALPDLLPWDLTQLLDERAPTELELP 747
Query: 462 N 462
Sbjct: 748 T 748
>gnl|CDD|219532 pfam07717, OB_NTP_bind, Oligonucleotide/oligosaccharide-binding
(OB)-fold. This family is found towards the C-terminus
of the DEAD-box helicases (pfam00270). In these
helicases it is apparently always found in association
with pfam04408. There do seem to be a couple of
instances where it occurs by itself - . The structure
PDB:3i4u adopts an OB-fold. helicases (pfam00270). In
these helicases it is apparently always found in
association with pfam04408. This C-terminal domain of
the yeast helicase contains an
oligonucleotide/oligosaccharide-binding (OB)-fold which
seems to be placed at the entrance of the putative
nucleic acid cavity. It also constitutes the binding
site for the G-patch-containing domain of Pfa1p. When
found on DEAH/RHA helicases, this domain is central to
the regulation of the helicase activity through its
binding of both RNA and G-patch domain proteins.
Length = 109
Score = 129 bits (327), Expect = 6e-36
Identities = 53/109 (48%), Positives = 76/109 (69%), Gaps = 8/109 (7%)
Query: 112 KQLLGIMDRHKLDVV------SAGKNTVRVQKAVCSGFFRNAAKKDPQEGY-RTLVDSQV 164
KQLL I++R L S+ + ++KA+C+G F N A+ ++G +TL + Q
Sbjct: 1 KQLLEILERLGLPEEPSSLLNSSSNDYELIRKALCAGLFPNVARLVDEKGEYKTLKEGQP 60
Query: 165 VYIHPSSALFNRQP-EWVIYHELVQTTKEYMREVTSIDPKWLVEFAPAF 212
V+IHPSS LF ++P EWV+YHELV+TTKEYMR+VT+IDP+WL+E AP +
Sbjct: 61 VFIHPSSVLFGKKPPEWVVYHELVETTKEYMRDVTAIDPEWLLELAPHY 109
Score = 129 bits (327), Expect = 6e-36
Identities = 53/109 (48%), Positives = 76/109 (69%), Gaps = 8/109 (7%)
Query: 333 KQLLGIMDRHKLDVV------SAGKNTVRVQKAVCSGFFRNAAKKDPQEGY-RTLVDSQV 385
KQLL I++R L S+ + ++KA+C+G F N A+ ++G +TL + Q
Sbjct: 1 KQLLEILERLGLPEEPSSLLNSSSNDYELIRKALCAGLFPNVARLVDEKGEYKTLKEGQP 60
Query: 386 VYIHPSSALFNRQP-EWVIYHELVQTTKEYMREVTSIDPKWLVEFAPAF 433
V+IHPSS LF ++P EWV+YHELV+TTKEYMR+VT+IDP+WL+E AP +
Sbjct: 61 VFIHPSSVLFGKKPPEWVVYHELVETTKEYMRDVTAIDPEWLLELAPHY 109
>gnl|CDD|218070 pfam04408, HA2, Helicase associated domain (HA2). This presumed
domain is about 90 amino acid residues in length. It is
found is a diverse set of RNA helicases. Its function
is unknown, however it seems likely to be involved in
nucleic acid binding.
Length = 91
Score = 113 bits (286), Expect = 2e-30
Identities = 40/74 (54%), Positives = 52/74 (70%), Gaps = 1/74 (1%)
Query: 6 VTPIS-QMAEFPLEPNLSKMLIMSVHLQCSDEVLTIVSMLSVQNVFYRPKDKQALADQKK 64
+TP+ QMAE PL+P L KML++S C DE+LTI +MLSV + FYRPK+K+ AD +
Sbjct: 18 LTPLGRQMAELPLDPRLGKMLLLSAEFGCLDEILTIAAMLSVPSPFYRPKEKEEEADAAR 77
Query: 65 AKFNQMEGDHITLL 78
KF E DH+TLL
Sbjct: 78 RKFASAESDHLTLL 91
>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model
represents HrpA, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria
and a few high-GC Gram-positive bacteria. HrpA is about
1300 amino acids long, while its paralog HrpB, also
uncharacterized, is about 800 amino acids long. Related
characterized eukarotic proteins are RNA helicases
associated with pre-mRNA processing [Unknown function,
Enzymes of unknown specificity].
Length = 1283
Score = 122 bits (308), Expect = 5e-29
Identities = 71/227 (31%), Positives = 115/227 (50%), Gaps = 18/227 (7%)
Query: 5 VVTPIS-QMAEFPLEPNLSKMLIMSVHLQCSDEVLTIVSMLSVQNVFYRPKDKQALADQK 63
+TPI Q+A+ P++P L++ML+ + L C EVL I S LS+Q+ RP +KQ ADQ
Sbjct: 472 QLTPIGRQLAQLPVDPRLARMLLEAHRLGCLQEVLIIASALSIQDPRERPMEKQQAADQA 531
Query: 64 KAKFNQMEGDHITLLAVYNSWRN----------NKFSNAWCYENFVQIRTLKRAQDVRKQ 113
A+F D ++ + N WR+ N+F N C + ++ ++ QD+ +Q
Sbjct: 532 HARFKDPRSDFLSRV---NLWRHIEEQRQALSANQFRN-ACRKQYLNYLRVREWQDIYRQ 587
Query: 114 LLGIMDRHKLDVVSAGKNTVRVQKAVCSGFFRNAAKKDPQEGYRTLVDSQVVYIHPSSAL 173
L ++ L + + + KA+ SG KD + Y + +I P S L
Sbjct: 588 LTQVVKELGLKLNEEPADYDAIHKALLSGLLSQIGMKDEKHEY-DGARGRKFHIFPGSPL 646
Query: 174 FNRQPEWVIYHELVQTTKEYMREVTSIDPKWLVEFAPAFFK--FSDP 218
F + P+WV+ ELV+T+K Y R V I+P+W+ A K + +P
Sbjct: 647 FKKPPKWVMAAELVETSKLYARLVAKIEPEWVEPVAGHLIKKNYFEP 693
Score = 93.3 bits (232), Expect = 1e-19
Identities = 45/108 (41%), Positives = 69/108 (63%), Gaps = 7/108 (6%)
Query: 231 EPLQRTNRISFPPGLLKQAVKKRPEIKLIVTSATLDAVKFSSYFFEAPIFTIPGRTFPVE 290
E +R+ I F G LKQ + +RP++K+I+TSAT+D +FS +F API + GRT+PVE
Sbjct: 187 EAHERSLNIDFLLGYLKQLLPRRPDLKIIITSATIDPERFSRHFNNAPIIEVSGRTYPVE 246
Query: 291 VLY------TKEPETDYLDASLITVMQIHLREPPGDVLLFLTGKLDVR 332
V Y ++ + D L+A L V ++ E PGD+L+FL G+ ++R
Sbjct: 247 VRYRPLVEEQEDDDLDQLEAILDAVDEL-FAEGPGDILIFLPGEREIR 293
Score = 60.9 bits (148), Expect = 1e-09
Identities = 25/49 (51%), Positives = 37/49 (75%), Gaps = 2/49 (4%)
Query: 494 ILPVYSALPSEMQTRIFEAAPPGSRKVVIATNIAETSLTIDGIFYVVDP 542
ILP+Y+ L ++ Q R+F+ P R++V+ATN+AETSLT+ GI YV+D
Sbjct: 309 ILPLYARLSNKEQQRVFQ--PHSGRRIVLATNVAETSLTVPGIHYVIDT 355
Score = 60.6 bits (147), Expect = 2e-09
Identities = 33/112 (29%), Positives = 54/112 (48%), Gaps = 3/112 (2%)
Query: 330 DVRKQLLGIMDRHKLDVVSAGKNTVRVQKAVCSGFFRNAAKKDPQEGYRTLVDSQVVYIH 389
D+ +QL ++ L + + + KA+ SG KD + Y + +I
Sbjct: 583 DIYRQLTQVVKELGLKLNEEPADYDAIHKALLSGLLSQIGMKDEKHEY-DGARGRKFHIF 641
Query: 390 PSSALFNRQPEWVIYHELVQTTKEYMREVTSIDPKWLVEFAPAFFK--FSDP 439
P S LF + P+WV+ ELV+T+K Y R V I+P+W+ A K + +P
Sbjct: 642 PGSPLFKKPPKWVMAAELVETSKLYARLVAKIEPEWVEPVAGHLIKKNYFEP 693
>gnl|CDD|214852 smart00847, HA2, Helicase associated domain (HA2) Add an
annotation. This presumed domain is about 90 amino
acid residues in length. It is found is a diverse set
of RNA helicases. Its function is unknown, however it
seems likely to be involved in nucleic acid binding.
Length = 82
Score = 95.0 bits (237), Expect = 8e-24
Identities = 37/78 (47%), Positives = 52/78 (66%), Gaps = 3/78 (3%)
Query: 2 DSLVVTPI-SQMAEFPLEPNLSKMLIMSVHLQCSDEVLTIVSMLSVQNVFYRPKDKQALA 60
D +TP+ +MAE PL+P L+KML+ + C DE+LTIV+MLSV + RPK+K+ A
Sbjct: 7 DDGRLTPLGRKMAELPLDPRLAKMLLAAAEFGCLDEILTIVAMLSVGD--PRPKEKREDA 64
Query: 61 DQKKAKFNQMEGDHITLL 78
D + +F E DH+TLL
Sbjct: 65 DAARRRFADPESDHLTLL 82
>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional.
Length = 1294
Score = 101 bits (254), Expect = 2e-22
Identities = 61/222 (27%), Positives = 112/222 (50%), Gaps = 11/222 (4%)
Query: 7 TPIS-QMAEFPLEPNLSKMLIMSVHLQCSDEVLTIVSMLSVQNVFYRPKDKQALADQKKA 65
TP+ Q+A+ P++P L++M++ + C EV+ I S LS+Q+ RP DKQ +D+K
Sbjct: 483 TPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITSALSIQDPRERPMDKQQASDEKHR 542
Query: 66 KFNQMEGDHITLLAVYNSWR-------NNKFSNAWCYENFVQIRTLKRAQDVRKQLLGIM 118
+F E D + + ++N + +N+F C +++ ++ QD+ QL ++
Sbjct: 543 RFADKESDFLAFVNLWNYLQEQQKALSSNQFRRL-CRTDYLNYLRVREWQDIYTQLRQVV 601
Query: 119 DRHKLDVVSAGKNTVRVQKAVCSGFFRNAAKKDPQEGYRTLVDSQVVYIHPSSALFNRQP 178
+ V S + A+ +G + KD ++ T + I P S LF + P
Sbjct: 602 KELGIPVNSEPAEYREIHTALLTGLLSHIGMKDAEKQEYTGARNARFSIFPGSGLFKKPP 661
Query: 179 EWVIYHELVQTTKEYMREVTSIDPKWLVEFAPAFFK--FSDP 218
+WV+ ELV+T++ + R I+P+W+ A K +S+P
Sbjct: 662 KWVMVAELVETSRLWGRIAARIEPEWIEPLAQHLIKRSYSEP 703
Score = 84.3 bits (209), Expect = 6e-17
Identities = 44/108 (40%), Positives = 68/108 (62%), Gaps = 7/108 (6%)
Query: 231 EPLQRTNRISFPPGLLKQAVKKRPEIKLIVTSATLDAVKFSSYFFEAPIFTIPGRTFPVE 290
E +R+ I F G LK+ + +RP++K+I+TSAT+D +FS +F API + GRT+PVE
Sbjct: 194 EAHERSLNIDFILGYLKELLPRRPDLKVIITSATIDPERFSRHFNNAPIIEVSGRTYPVE 253
Query: 291 VLY------TKEPETDYLDASLITVMQIHLREPPGDVLLFLTGKLDVR 332
V Y + E D L A V ++ RE PGD+L+F++G+ ++R
Sbjct: 254 VRYRPIVEEADDTERDQLQAIFDAVDELG-REGPGDILIFMSGEREIR 300
Score = 65.1 bits (159), Expect = 6e-11
Identities = 31/75 (41%), Positives = 46/75 (61%), Gaps = 9/75 (12%)
Query: 468 REEIDTACEILYERMKSLGPDVPELIILPVYSALPSEMQTRIFEAAPPGSRKVVIATNIA 527
RE DTA + L + ++ ILP+Y+ L + Q R+F+ R++V+ATN+A
Sbjct: 297 REIRDTA-DALNKL------NLRHTEILPLYARLSNSEQNRVFQ--SHSGRRIVLATNVA 347
Query: 528 ETSLTIDGIFYVVDP 542
ETSLT+ GI YV+DP
Sbjct: 348 ETSLTVPGIKYVIDP 362
Score = 51.6 bits (124), Expect = 1e-06
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 387 YIHPSSALFNRQPEWVIYHELVQTTKEYMREVTSIDPKWLVEFAPAFFK--FSDP 439
I P S LF + P+WV+ ELV+T++ + R I+P+W+ A K +S+P
Sbjct: 649 SIFPGSGLFKKPPKWVMVAELVETSRLWGRIAARIEPEWIEPLAQHLIKRSYSEP 703
>gnl|CDD|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional.
Length = 812
Score = 74.6 bits (184), Expect = 5e-14
Identities = 35/72 (48%), Positives = 42/72 (58%), Gaps = 6/72 (8%)
Query: 470 EIDTACEILYERMKSLGPDVPELIILPVYSALPSEMQTRIFEAAPPGSRKVVIATNIAET 529
EI E L R + DV ++ P+Y AL Q + AP G RKVV+ATNIAET
Sbjct: 224 EIQRVQEQLASR---VASDV---LLCPLYGALSLAEQQKAILPAPAGRRKVVLATNIAET 277
Query: 530 SLTIDGIFYVVD 541
SLTI+GI VVD
Sbjct: 278 SLTIEGIRLVVD 289
Score = 54.5 bits (132), Expect = 9e-08
Identities = 27/75 (36%), Positives = 39/75 (52%)
Query: 253 RPEIKLIVTSATLDAVKFSSYFFEAPIFTIPGRTFPVEVLYTKEPETDYLDASLITVMQI 312
R ++KL++ SATLD + +AP+ GR+FPVE Y P D ++
Sbjct: 147 RDDLKLLIMSATLDNDRLQQLLPDAPVIVSEGRSFPVERRYQPLPAHQRFDEAVARATAE 206
Query: 313 HLREPPGDVLLFLTG 327
LR+ G +LLFL G
Sbjct: 207 LLRQESGSLLLFLPG 221
>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model
represents HrpB, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria,
but also in a few species of other lineages. The member
from Rhizobium meliloti has been designated HelO. HrpB
is typically about 800 residues in length, while its
paralog HrpA (TIGR01967), also uncharacterized, is about
1300 amino acids long. Related characterized eukarotic
proteins are RNA helicases associated with pre-mRNA
processing [Unknown function, Enzymes of unknown
specificity].
Length = 819
Score = 72.9 bits (179), Expect = 2e-13
Identities = 36/72 (50%), Positives = 42/72 (58%), Gaps = 6/72 (8%)
Query: 470 EIDTACEILYERMKSLGPDVPELIILPVYSALPSEMQTRIFEAAPPGSRKVVIATNIAET 529
EI E L ER L DV +I P+Y L Q R + P G RKVV+ATNIAET
Sbjct: 221 EIRRVQEQLAER---LDSDV---LICPLYGELSLAAQDRAIKPDPQGRRKVVLATNIAET 274
Query: 530 SLTIDGIFYVVD 541
SLTI+GI V+D
Sbjct: 275 SLTIEGIRVVID 286
Score = 59.8 bits (145), Expect = 2e-09
Identities = 26/81 (32%), Positives = 46/81 (56%)
Query: 253 RPEIKLIVTSATLDAVKFSSYFFEAPIFTIPGRTFPVEVLYTKEPETDYLDASLITVMQI 312
R ++K++ SATLD + SS +AP+ GR+FPVE+ Y L+ ++ ++
Sbjct: 144 REDLKILAMSATLDGERLSSLLPDAPVVESEGRSFPVEIRYLPLRGDQRLEDAVSRAVEH 203
Query: 313 HLREPPGDVLLFLTGKLDVRK 333
L G +L+FL G+ ++R+
Sbjct: 204 ALASETGSILVFLPGQAEIRR 224
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 53.4 bits (129), Expect = 4e-09
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 476 EILYERMKSLGPDVPELIILPVYSALPSEMQTRIFEAAPPGSRKVVIATNIAETSLTIDG 535
E L E +K LG + + ++ L E + I + G KV++AT++AE L + G
Sbjct: 1 EELAELLKELG-----IKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPG 55
Query: 536 IFYVVD---PFDIE 546
+ V+ P+
Sbjct: 56 VDLVIIYDLPWSPA 69
>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 = 42.1 bits (100), Expect = 3e-05
Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 6/68 (8%)
Query: 490 PELIILPVYSALPSEMQTRIFEAAPPGSRKVVIATNIAETSLTIDGIFYVVD---PFDIE 546
P + + ++ L E + I E G KV++AT++A + + + V++ P++
Sbjct: 6 PGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWNPA 65
Query: 547 VRQAKYHR 554
R
Sbjct: 66 SY---IQR 70
>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 = 31.1 bits (71), Expect = 0.58
Identities = 11/83 (13%), Positives = 31/83 (37%), Gaps = 11/83 (13%)
Query: 475 CEILYERMKSLGPDVPELIILPVYSALPSEMQTRIFEAAPPGSRKVVIATNIAETSLTID 534
+ L E ++ G + + ++ E + + + G V++AT++ + +
Sbjct: 41 LDELAELLRKPG-----IKVAALHGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLP 95
Query: 535 GIFYVVD---PFDIEVRQAKYHR 554
+ V++ P+ R
Sbjct: 96 NVSVVINYDLPWSPSSY---LQR 115
>gnl|CDD|176480 cd08643, DNA_pol_A_pol_I_B, Polymerase I functions primarily to
fill DNA gaps that arise during DNA repair,
recombination and replication. Family A polymerase
functions primarily to fill DNA gaps that arise during
DNA repair, recombination and replication. DNA-dependent
DNA polymerases can be classified in six main groups
based upon phylogenetic relationships with E. coli
polymerase I (classA), E. coli polymerase II (class B),
E.coli polymerase III (class C), euryarchaaeota
polymerase II (class D), human polymerase beta (class
x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma
pigmentosum variant (class Y). Family A polymerase are
found primarily in organisms related to prokaryotes and
include prokaryotic DNA polymerase I ,mitochondrial
polymerase delta, and several bacteriphage polymerases
including those from odd-numbered phage (T3, T5, and
T7). Prokaryotic Pol Is have two functional domains
located on the same polypeptide; a 5'-3' polymerase and
5'-3' exonuclease. Pol I uses its 5' nuclease activity
to remove the ribonucleotide portion of newly
synthesized Okazaki fragments and DNA polymerase
activity to fill in the resulting gap. A combination of
phylogenomic and signature sequence-based (or phonetic)
approaches is used to understand the evolutionary
relationships among bacteria. DNA polymerase I is one of
the conserved proteins that is used to search for
protein signatures. The structure of these polymerases
resembles in overall morphology a cupped human right
hand, with fingers (which bind an incoming nucleotide
and interact with the single-stranded template), palm
(which harbors the catalytic amino acid residues and
also binds an incoming dNTP) and thumb (which binds
double-stranded DNA) subdomains.
Length = 429
Score = 31.6 bits (72), Expect = 1.2
Identities = 15/79 (18%), Positives = 30/79 (37%), Gaps = 3/79 (3%)
Query: 174 FNRQPEWVIYHELVQTTKEYMREVTSIDPKWLVEFAPAFFKFSDPTKLSKFKKNQRLEPL 233
FN++ +Y +L ++ E+ + P W V F T + + + P
Sbjct: 1 FNQEKAAKLYAQLAGRREDLENELQEVFPPWYV---SDGFVPKKRTTNNSVRGYVKGAPY 57
Query: 234 QRTNRISFPPGLLKQAVKK 252
+ ++F P K K+
Sbjct: 58 TKIKLVTFNPSSRKHIAKR 76
>gnl|CDD|227885 COG5598, COG5598, Trimethylamine:corrinoid methyltransferase
[Coenzyme metabolism].
Length = 526
Score = 31.2 bits (71), Expect = 1.7
Identities = 11/43 (25%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 213 FKFSDPTKLSKFKKN-QRLEPLQRTNRISFPPGLLKQAVKKRP 254
+ D L +K+ ++ +R+ FP GL+++A+K P
Sbjct: 74 IEVRDDEALELWKEAGAIVDE--DGDRVRFPRGLVREALKSAP 114
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 30.3 bits (68), Expect = 3.1
Identities = 14/34 (41%), Positives = 22/34 (64%), Gaps = 3/34 (8%)
Query: 516 GSRKVVIATNIAETSLTIDGIFYVVD---PFDIE 546
G ++++AT++A L IDG+ YV + PFD E
Sbjct: 306 GQLEILVATDVAARGLHIDGVKYVYNYDLPFDAE 339
>gnl|CDD|213344 cd12205, RasGAP_plexin, Ras-GTPase Activating Domain of plexins.
Plexins form a conserved family of transmembrane
receptors for semaphorins and may be the ancestors of
semaphorins. Ligand binding activates signal
transduction pathways controlling axon guidance in the
nervous system and other developmental processes,
including cell migration and morphogenesis, immune
function, and tumor progression. Plexins are divided
into four types (A-D) according to sequence similarity.
In vertebrates, type A Plexins serve as the co-receptors
for neuropilins to mediate the signaling of class 3
semaphorins except Sema3E, which signals through Plexin
D1. Plexins serve as direct receptors for several other
members of the semaphorin family: class 6 semaphorins
signal through type A plexins and class 4 semaphorins
through type B. Plexin C1 serves as the receptor of
Sema7A and plays regulation roles in both immune and
nervous systems. Plexins contain a C-terminal RasGAP
domain, which functions as an enhancer of the hydrolysis
of GTP that is bound to Ras-GTPases. Plexins display GAP
activity towards the Ras homolog Rap. Other proteins
having a RasGAP domain include p120GAP, IQGAP,
Rab5-activating protein 6, and Neurofibromin. Although
the Rho (Ras homolog) GTPases are most closely related
to members of the Ras family, RhoGAP and RasGAP show no
sequence homology at their amino acid level. RasGTPases
function as molecular switches in a large number of of
signaling pathways. When bound to GTP they are in the on
state and when bound to GDP they are in the off state.
The RasGAP domain speeds up the hydrolysis of GTP in
Ras-like proteins acting as a negative regulator.
Length = 382
Score = 29.5 bits (67), Expect = 5.4
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 6/48 (12%)
Query: 249 AVKKRPEI---KLIVTSATLDAVKFSSYFFEAPIFTIPGRTFPVEVLY 293
A+K PEI +L+ T TL KF FE+ I ++P R+ P + Y
Sbjct: 165 AIKLIPEIFLTRLLSTKGTLQ--KFVDDLFES-ILSVPQRSLPPAIKY 209
>gnl|CDD|218935 pfam06199, Phage_tail_2, Phage major tail protein 2. characterized
members are major tail proteins from various phage,
including lactococcal temperate bacteriophage TP901-1.
Length = 134
Score = 28.0 bits (63), Expect = 6.2
Identities = 11/40 (27%), Positives = 17/40 (42%)
Query: 515 PGSRKVVIATNIAETSLTIDGIFYVVDPFDIEVRQAKYHR 554
G R +V E S++ +GIF D D + A +
Sbjct: 46 AGWRGLVAGAGSKEASISGEGIFARDDASDDALEDAFFDG 85
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.135 0.398
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,564,921
Number of extensions: 2794125
Number of successful extensions: 2294
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2267
Number of HSP's successfully gapped: 35
Length of query: 558
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 456
Effective length of database: 6,413,494
Effective search space: 2924553264
Effective search space used: 2924553264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 62 (27.6 bits)