RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12659
(1051 letters)
>gnl|CDD|185399 PTZ00017, PTZ00017, histone H2A; Provisional.
Length = 134
Score = 75.2 bits (185), Expect = 6e-16
Identities = 28/50 (56%), Positives = 37/50 (74%)
Query: 892 HKKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKTLKT 941
+KK RITPR++ LAI+ND EL++LL+ VTIA GGV+PNI + K K
Sbjct: 76 NKKKRITPRHIQLAIRNDEELNKLLAGVTIASGGVLPNIHKVLLPKKSKP 125
>gnl|CDD|238029 cd00074, H2A, Histone 2A; H2A is a subunit of the nucleosome. The
nucleosome is an octamer containing two H2A, H2B, H3,
and H4 subunits. The H2A subunit performs essential
roles in maintaining structural integrity of the
nucleosome, chromatin condensation, and binding of
specific chromatin-associated proteins.
Length = 115
Score = 74.3 bits (183), Expect = 7e-16
Identities = 26/42 (61%), Positives = 34/42 (80%)
Query: 892 HKKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSM 933
+KK RITPR+L LA++ND EL++LL VTIA GGV+PNI +
Sbjct: 69 NKKKRITPRHLQLAVRNDEELNKLLKGVTIASGGVLPNIHKV 110
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 220
Score = 75.1 bits (185), Expect = 4e-15
Identities = 36/121 (29%), Positives = 63/121 (52%), Gaps = 4/121 (3%)
Query: 177 PFTPTQIEAIRAGM-QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQAL 235
+Q EAI+ + +TL+ GPPGTGKT V+II L N P ++ L+ SN A+
Sbjct: 1 ELNDSQREAIKKALSSSDITLIQGPPGTGKTTTIVEIIKQLLSNAPGKKVLVCAPSNSAV 60
Query: 236 NQLFEKIISLDVDERHLLRLGHGEEALETEKDFSRYGRVNYVLAKRLDLLQEVERLQKSL 295
+ + E+++ + ++R+G E +D +Y + AK LL+ + +L+ L
Sbjct: 61 DNILERLLEQKFGLK-IVRIGSPAR--EIHEDVLQYSLEYLLEAKFEQLLKRIRKLKSLL 117
Query: 296 D 296
+
Sbjct: 118 E 118
Score = 62.4 bits (152), Expect = 1e-10
Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 821 IEAIRAGM-QPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEK 879
EAI+ + +TL+ GPPGTGKT V+II L N P ++ L+ SN A++ + E+
Sbjct: 7 REAIKKALSSSDITLIQGPPGTGKTTTIVEIIKQLLSNAPGKKVLVCAPSNSAVDNILER 66
Query: 880 IIS 882
++
Sbjct: 67 LLE 69
>gnl|CDD|197711 smart00414, H2A, Histone 2A.
Length = 106
Score = 68.5 bits (168), Expect = 6e-14
Identities = 28/41 (68%), Positives = 34/41 (82%)
Query: 893 KKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSM 933
KK RITPR+L LAI+ND EL++LL VTIAQGGV+PNI +
Sbjct: 59 KKRRITPRHLQLAIRNDEELNKLLKGVTIAQGGVLPNIHKV 99
>gnl|CDD|177758 PLN00157, PLN00157, histone H2A; Provisional.
Length = 132
Score = 69.1 bits (169), Expect = 7e-14
Identities = 30/62 (48%), Positives = 38/62 (61%), Gaps = 9/62 (14%)
Query: 892 HKKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKTLKTLLSPWKSEDG 951
+KK RI PR++ LA++ND ELS+LL VTIA GGV+PNI S +L P KS
Sbjct: 75 NKKSRIVPRHIQLAVRNDEELSKLLGGVTIAAGGVLPNIHS---------VLLPKKSGKS 125
Query: 952 SP 953
Sbjct: 126 KG 127
>gnl|CDD|215080 PLN00156, PLN00156, histone H2AX; Provisional.
Length = 139
Score = 61.9 bits (150), Expect = 3e-11
Identities = 26/46 (56%), Positives = 33/46 (71%)
Query: 892 HKKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDK 937
+KK RI PR++ LA++ND ELS+LL VTIA GGV+PNI K
Sbjct: 78 NKKNRIVPRHIQLAVRNDEELSKLLGSVTIAAGGVLPNIHQTLLPK 123
>gnl|CDD|227587 COG5262, HTA1, Histone H2A [Chromatin structure and dynamics].
Length = 132
Score = 60.6 bits (147), Expect = 7e-11
Identities = 30/48 (62%), Positives = 36/48 (75%)
Query: 893 KKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKTLK 940
KK RI PR+L LAI+ND EL++LL DVTIAQGGV+PNI K+ K
Sbjct: 76 KKKRIIPRHLQLAIRNDEELNKLLGDVTIAQGGVLPNINPGLLPKSSK 123
>gnl|CDD|165721 PLN00153, PLN00153, histone H2A; Provisional.
Length = 129
Score = 58.6 bits (141), Expect = 3e-10
Identities = 27/49 (55%), Positives = 36/49 (73%)
Query: 892 HKKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKTLK 940
+KK RI PR++ LAI+ND EL +LL +VTIA GGV+PNI ++ K K
Sbjct: 73 NKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLPKKTK 121
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 55.1 bits (133), Expect = 1e-09
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 822 EAIRAGMQP-GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKI 880
EA+ A L +V G PGTGKT A II+ L + L+V + +A +L E++
Sbjct: 1 EAVEAAASGRSLFVVDGGPGTGKTATAAAIIARLLAA--GRSVLVVAPTGRAARRLRERL 58
Query: 881 ISLDVDERHLLHK 893
+LD+ + LH
Sbjct: 59 AALDLADASTLHA 71
Score = 52.7 bits (127), Expect = 9e-09
Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 3/67 (4%)
Query: 184 EAIRAGMQP-GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKI 242
EA+ A L +V G PGTGKT A II+ L + L+V + +A +L E++
Sbjct: 1 EAVEAAASGRSLFVVDGGPGTGKTATAAAIIARLLAA--GRSVLVVAPTGRAARRLRERL 58
Query: 243 ISLDVDE 249
+LD+ +
Sbjct: 59 AALDLAD 65
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may
represent a DNA helicase. Eukaryotic members of this
family have been characterized as binding certain
single-stranded G-rich DNA sequences (GGGGT and GGGCT).
A number of related proteins are characterized as
helicases [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 56.7 bits (137), Expect = 5e-08
Identities = 37/139 (26%), Positives = 60/139 (43%), Gaps = 18/139 (12%)
Query: 166 YLFNEPRKNTIPFTP-------TQIEAIR-AGMQPGLTLVVGPPGTGKTDVAVQIISNLY 217
F +Q EA+ A L L+ GPPGTGKT V++I L
Sbjct: 139 REAPSKASEIHDFQFFDPNLNESQKEAVLFALSSKDLFLIHGPPGTGKTRTLVELIRQLV 198
Query: 218 HNFPHQRTLIVTHSNQALNQLFEKIISLDVDERHLLRLGHGEEALETEKDFSRYGRVNYV 277
R L+ SN A++ L E++ D ++RLGH L++ K S ++Y+
Sbjct: 199 KRGL--RVLVTAPSNIAVDNLLERLALCDQ---KIVRLGHPARLLKSNKQHS----LDYL 249
Query: 278 LAKRLDLLQEVERLQKSLD 296
+ + Q V +++ +D
Sbjct: 250 I-ENHPKYQIVADIREKID 267
Score = 40.2 bits (94), Expect = 0.007
Identities = 28/102 (27%), Positives = 42/102 (41%), Gaps = 10/102 (9%)
Query: 792 RSSFPQAEIRVKTDNPTKLVPPFKLTFH-------EIEAIR-AGMQPGLTLVVGPPGTGK 843
+ E + + P+K F + EA+ A L L+ GPPGTGK
Sbjct: 127 ENHSRLLEFILGREAPSKASEIHDFQFFDPNLNESQKEAVLFALSSKDLFLIHGPPGTGK 186
Query: 844 TDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDV 885
T V++I L R L+ SN A++ L E++ D
Sbjct: 187 TRTLVELIRQLVKRGL--RVLVTAPSNIAVDNLLERLALCDQ 226
>gnl|CDD|240330 PTZ00252, PTZ00252, histone H2A; Provisional.
Length = 134
Score = 50.0 bits (119), Expect = 3e-07
Identities = 18/38 (47%), Positives = 30/38 (78%)
Query: 893 KKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNI 930
K R+TPR + LA+++D +L LL +VT+++GGVMP++
Sbjct: 77 KPKRLTPRTVTLAVRHDDDLGSLLKNVTLSRGGVMPSL 114
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 49.8 bits (119), Expect = 1e-06
Identities = 26/133 (19%), Positives = 47/133 (35%), Gaps = 13/133 (9%)
Query: 171 PRKNTIPFTPTQIEAIRAGMQ-PGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 229
+ P P Q EAI A + ++ P G+GKT A+ R L++
Sbjct: 2 EKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLV 61
Query: 230 HSNQALNQLFEKIISL--DVDERHLLRLGHGEEALETEKDFSR---------YGRVNYVL 278
+ + Q E++ L + + + G G+ E + GR+ +L
Sbjct: 62 PTRELAEQWAEELKKLGPSLGLKVVGLYG-GDSKREQLRKLESGKTDILVTTPGRLLDLL 120
Query: 279 AKRLDLLQEVERL 291
L V+ +
Sbjct: 121 ENDKLSLSNVDLV 133
Score = 43.2 bits (102), Expect = 2e-04
Identities = 25/109 (22%), Positives = 41/109 (37%), Gaps = 22/109 (20%)
Query: 821 IEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKI 880
IEA+ +G++ + + P G+GKT A+ R L++ + + Q E++
Sbjct: 17 IEALLSGLRDVI--LAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEEL 74
Query: 881 -----------------ISLDVDERHLLHKKYRI---TPRYLLLAIKND 909
S R L K I TP LL ++ND
Sbjct: 75 KKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLEND 123
>gnl|CDD|177756 PLN00154, PLN00154, histone H2A; Provisional.
Length = 136
Score = 47.6 bits (113), Expect = 3e-06
Identities = 24/48 (50%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 893 KKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKTLK 940
K RITPR+L LAI+ D EL L+ TIA GGV+P+I +K+ K
Sbjct: 89 KVKRITPRHLQLAIRGDEELDTLIK-GTIAGGGVIPHIHKSLINKSTK 135
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 45.7 bits (109), Expect = 6e-06
Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 6/76 (7%)
Query: 176 IPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQAL 235
+ P Q EAI ++ L+V G+GKT A +I+ L ++ L V L
Sbjct: 2 LELRPYQEEAIERLLEKKRGLIVMATGSGKTLTAAALIARLAKGK--KKVLFVVPRKDLL 59
Query: 236 NQLFEKIISLDVDERH 251
Q II +DE H
Sbjct: 60 EQA-LVII---IDEAH 71
Score = 43.4 bits (103), Expect = 4e-05
Identities = 22/76 (28%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 814 FKLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQAL 873
+L ++ EAI ++ L+V G+GKT A +I+ L ++ L V L
Sbjct: 2 LELRPYQEEAIERLLEKKRGLIVMATGSGKTLTAAALIARLAKGK--KKVLFVVPRKDLL 59
Query: 874 NQLFEKIISLDVDERH 889
Q II +DE H
Sbjct: 60 EQA-LVII---IDEAH 71
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 41.7 bits (98), Expect = 0.002
Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 13/81 (16%)
Query: 170 EPRKNTIPFTPT----QIEAIRA----GMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFP 221
P K + F Q EA+ A ++V P G GKT VA + I+ L
Sbjct: 25 LPLKLIVAFEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELK---- 80
Query: 222 HQRTLIVTHSNQALNQLFEKI 242
+ TL++ + + L+Q E +
Sbjct: 81 -RSTLVLVPTKELLDQWAEAL 100
Score = 40.5 bits (95), Expect = 0.004
Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 11/89 (12%)
Query: 798 AEIRVKTDNPTKLVPPF--KLTFHEIEAIRA----GMQPGLTLVVGPPGTGKTDVAVQII 851
A+ + P KL+ F +L ++ EA+ A ++V P G GKT VA + I
Sbjct: 17 ADYVLDEGLPLKLIVAFEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAI 76
Query: 852 SNLYHNFPHQRTLIVTHSNQALNQLFEKI 880
+ L + TL++ + + L+Q E +
Sbjct: 77 AELK-----RSTLVLVPTKELLDQWAEAL 100
>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 = 39.2 bits (92), Expect = 0.002
Identities = 13/46 (28%), Positives = 23/46 (50%)
Query: 195 TLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFE 240
L+ P G+GKT A+ I L + + L++ + + NQ+ E
Sbjct: 3 VLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAE 48
Score = 39.2 bits (92), Expect = 0.002
Identities = 13/46 (28%), Positives = 23/46 (50%)
Query: 833 TLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFE 878
L+ P G+GKT A+ I L + + L++ + + NQ+ E
Sbjct: 3 VLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAE 48
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 36.4 bits (84), Expect = 0.025
Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 4/76 (5%)
Query: 183 IEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN---QALNQLF 239
+ R+G P L+ GP GTGKT + +++ L QAL +L
Sbjct: 16 LRRARSG-GPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRELL 74
Query: 240 EKIISLDVDERHLLRL 255
+++ E LLR
Sbjct: 75 RQLLRELAAELLLLRE 90
Score = 35.6 bits (82), Expect = 0.040
Identities = 24/103 (23%), Positives = 40/103 (38%), Gaps = 6/103 (5%)
Query: 821 IEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN---QALNQLF 877
+ R+G P L+ GP GTGKT + +++ L QAL +L
Sbjct: 16 LRRARSG-GPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRELL 74
Query: 878 EKIISLDVDERHLLHKKYRITPRYLLLAIKNDV--ELSQLLSD 918
+++ E LL + L+ D+ L +LL+
Sbjct: 75 RQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLAR 117
>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 = 36.5 bits (85), Expect = 0.028
Identities = 27/118 (22%), Positives = 43/118 (36%), Gaps = 22/118 (18%)
Query: 822 EAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHNFPHQRTLIVTHS----NQALNQL 876
+AI A + LV P G+GKT + I+ L + L++ + Q +L
Sbjct: 6 QAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQIYEEL 65
Query: 877 FEKI-------------ISLDVDERHLLHKKYRI---TPRYLLLAIKN-DVELSQLLS 917
+ SL R L K I TP LL ++ ++L + L
Sbjct: 66 KKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLKNLK 123
Score = 36.5 bits (85), Expect = 0.030
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 179 TPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQ-IISNLYHNFPHQRTLIVT 229
TP Q +AI A + LV P G+GKT + I+ L + L++
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLA 52
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 35.7 bits (83), Expect = 0.028
Identities = 29/107 (27%), Positives = 44/107 (41%), Gaps = 18/107 (16%)
Query: 834 LVVGPPGTGKTDVAVQIISNLYHNF-----PHQRTLIVTHSNQALNQLFE--KIISLDV- 885
L+ GPPGTGKT +A + L F + V S + L +LFE K ++ V
Sbjct: 2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVI 61
Query: 886 --DERHLLHKKYRITPRYLLLAIKNDVELSQLLS---DVTIAQGGVM 927
DE L R ++ ++QLL+ T + V+
Sbjct: 62 FIDEIDALAGS-----RGSGGDSESRRVVNQLLTELDGFTSSLSKVI 103
Score = 34.5 bits (80), Expect = 0.084
Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 196 LVVGPPGTGKTDVAVQIISNLYHNF-----PHQRTLIVTHSNQALNQLFEKI 242
L+ GPPGTGKT +A + L F + V S + L +LFE
Sbjct: 2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAA 53
>gnl|CDD|190347 pfam02562, PhoH, PhoH-like protein. PhoH is a cytoplasmic protein
and predicted ATPase that is induced by phosphate
starvation.
Length = 205
Score = 35.9 bits (84), Expect = 0.052
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 177 PFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAV 210
P T Q + A + + +GP GTGKT +AV
Sbjct: 4 PKTLGQKRYVEAIRKNDIVFGIGPAGTGKTYLAV 37
Score = 30.9 bits (71), Expect = 2.7
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 816 LTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVAV 848
T + + A + + +GP GTGKT +AV
Sbjct: 5 KTLGQKRYVEAIRKNDIVFGIGPAGTGKTYLAV 37
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 34.6 bits (80), Expect = 0.11
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 176 IPFTPTQIEAIRAGMQP--GLTLVVGPPGTGKTDVAVQII 213
+ P + + G+ P GLTL+ G PGTGK+ +A+ +
Sbjct: 15 LDAPPPPLRWLVKGLLPRGGLTLLAGAPGTGKSTLALDLA 54
Score = 33.4 bits (77), Expect = 0.22
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 831 GLTLVVGPPGTGKTDVAVQII 851
GLTL+ G PGTGK+ +A+ +
Sbjct: 34 GLTLLAGAPGTGKSTLALDLA 54
>gnl|CDD|216004 pfam00580, UvrD-helicase, UvrD/REP helicase N-terminal domain. The
Rep family helicases are composed of four structural
domains. The Rep family function as dimers. REP
helicases catalyze ATP dependent unwinding of double
stranded DNA to single stranded DNA. Some members have
large insertions near to the carboxy-terminus relative
to other members of the family.
Length = 267
Score = 35.3 bits (82), Expect = 0.12
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 179 TPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNL--YHNFPHQRTLIVTHSNQALN 236
P Q +A+ P LV+ G+GKT V + I+ L + L VT +N+A
Sbjct: 2 NPEQRKAVTHLGGP--LLVLAGAGSGKTRVLTERIAYLILEGGIDPEEILAVTFTNKAAR 59
Query: 237 QLFEKIISL 245
++ E+I+ L
Sbjct: 60 EMKERILKL 68
Score = 33.0 bits (76), Expect = 0.63
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 4/64 (6%)
Query: 822 EAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNL--YHNFPHQRTLIVTHSNQALNQLFEK 879
+A+ P LV+ G+GKT V + I+ L + L VT +N+A ++ E+
Sbjct: 7 KAVTHLGGP--LLVLAGAGSGKTRVLTERIAYLILEGGIDPEEILAVTFTNKAAREMKER 64
Query: 880 IISL 883
I+ L
Sbjct: 65 ILKL 68
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 35.6 bits (82), Expect = 0.13
Identities = 13/43 (30%), Positives = 26/43 (60%), Gaps = 5/43 (11%)
Query: 195 TLVVGPPGTGKT----DVAVQIISNLYHNFPHQRTLIVTHSNQ 233
TL++GPP GKT D+A +++S+ + F ++ I+ ++
Sbjct: 140 TLIIGPPQVGKTTLLRDIA-RLLSDGINQFLPKKVGIIDERSE 181
Score = 35.6 bits (82), Expect = 0.13
Identities = 13/43 (30%), Positives = 26/43 (60%), Gaps = 5/43 (11%)
Query: 833 TLVVGPPGTGKT----DVAVQIISNLYHNFPHQRTLIVTHSNQ 871
TL++GPP GKT D+A +++S+ + F ++ I+ ++
Sbjct: 140 TLIIGPPQVGKTTLLRDIA-RLLSDGINQFLPKKVGIIDERSE 181
>gnl|CDD|233417 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit. This
family describes the exodeoxyribonuclease V alpha
subunit, RecD. RecD is part of a RecBCD complex. A
related family in the Gram-positive bacteria separates
in a phylogenetic tree, has an additional N-terminal
extension of about 200 residues, and is not supported as
a member of a RecBCD complex by neighboring genes. The
related family is consequently described by a different
model [DNA metabolism, DNA replication, recombination,
and repair].
Length = 586
Score = 35.1 bits (81), Expect = 0.19
Identities = 12/56 (21%), Positives = 21/56 (37%), Gaps = 4/56 (7%)
Query: 162 SRGPYLFNEPR-KNTIPFTPT---QIEAIRAGMQPGLTLVVGPPGTGKTDVAVQII 213
+N P Q A+ ++ +L+ G PGTGKT +++
Sbjct: 126 EARKRTAPSAILENLFPLLNEQNWQKVAVALALKSNFSLITGGPGTGKTTTVARLL 181
Score = 32.4 bits (74), Expect = 1.6
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 821 IEAIRAGMQPGLTLVVGPPGTGKTDVAVQII 851
A+ ++ +L+ G PGTGKT +++
Sbjct: 151 KVAVALALKSNFSLITGGPGTGKTTTVARLL 181
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 34.4 bits (79), Expect = 0.24
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 184 EAIRAGMQPG-LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 229
E + G+ G + L+ GPPGTGKT A+Q + + L V+
Sbjct: 14 EILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGAREG--EPVLYVS 58
Score = 34.4 bits (79), Expect = 0.24
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 822 EAIRAGMQPG-LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 867
E + G+ G + L+ GPPGTGKT A+Q + + L V+
Sbjct: 14 EILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGAREG--EPVLYVS 58
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 32.6 bits (75), Expect = 0.27
Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 8/70 (11%)
Query: 190 MQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN----QALNQLFEKIISL 245
G+ ++ G G+GKT + ++ L P++R + V + + L + + + L
Sbjct: 2 RGAGIGVLTGESGSGKTTLLRRLARQL----PNRRVVYVEAPSLGTPKDLLRKILRALGL 57
Query: 246 DVDERHLLRL 255
+ L
Sbjct: 58 PLSGGTTAEL 67
Score = 31.9 bits (73), Expect = 0.60
Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 8/75 (10%)
Query: 828 MQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSN----QALNQLFEKIISL 883
G+ ++ G G+GKT + ++ L P++R + V + + L + + + L
Sbjct: 2 RGAGIGVLTGESGSGKTTLLRRLARQL----PNRRVVYVEAPSLGTPKDLLRKILRALGL 57
Query: 884 DVDERHLLHKKYRIT 898
+ I
Sbjct: 58 PLSGGTTAELLEAIL 72
>gnl|CDD|238544 cd01124, KaiC, KaiC is a circadian clock protein primarily found in
cyanobacteria KaiC is a RecA-like ATPase, having both
Walker A and Walker B motifs. A related protein is found
in archaea.
Length = 187
Score = 33.5 bits (77), Expect = 0.34
Identities = 27/97 (27%), Positives = 40/97 (41%), Gaps = 8/97 (8%)
Query: 194 LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDERHLL 253
TL+ G PGTGKT A+Q + + L VT ++ +L E SL D L
Sbjct: 1 STLLSGGPGTGKTTFALQFLYAGLAR--GEPGLYVTLE-ESPEELIENAESLGWDLERLE 57
Query: 254 RLGHGEEALETEKDFSRYGRVNYVLAKRLDLLQEVER 290
G A+ D + RL+L+Q ++
Sbjct: 58 DE--GLLAIV---DADPDEIGPAESSLRLELIQRLKD 89
Score = 31.5 bits (72), Expect = 1.5
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 832 LTLVVGPPGTGKTDVAVQ 849
TL+ G PGTGKT A+Q
Sbjct: 1 STLLSGGPGTGKTTFALQ 18
>gnl|CDD|222258 pfam13604, AAA_30, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. There is a Walker A and
Walker B.
Length = 195
Score = 33.3 bits (77), Expect = 0.41
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 178 FTPTQIEAIRAGMQPG--LTLVVGPPGTGKT 206
+ Q EA+R + G + +V GP GTGKT
Sbjct: 2 LSAEQREAVRHVLTSGDRVAVVQGPAGTGKT 32
>gnl|CDD|182031 PRK09694, PRK09694, helicase Cas3; Provisional.
Length = 878
Score = 34.0 bits (78), Expect = 0.47
Identities = 28/110 (25%), Positives = 38/110 (34%), Gaps = 38/110 (34%)
Query: 166 YLFN--EPRKNTIPFTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHN---- 219
L N +PR Q +QPGLT++ P G+GKT+ A+ L
Sbjct: 280 LLDNGYQPR-------QLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQGLAD 332
Query: 220 -----FPHQRT--------------------LIVTHSNQALNQLFEKIIS 244
P Q T LI+ H N N LF+ + S
Sbjct: 333 SIIFALPTQATANAMLSRLEALASKLFPSPNLILAHGNSRFNHLFQSLKS 382
Score = 32.9 bits (75), Expect = 1.0
Identities = 23/83 (27%), Positives = 31/83 (37%), Gaps = 29/83 (34%)
Query: 829 QPGLTLVVGPPGTGKTDVAVQIISNLYHN---------FPHQRT---------------- 863
QPGLT++ P G+GKT+ A+ L P Q T
Sbjct: 300 QPGLTIIEAPTGSGKTEAALAYAWRLIDQGLADSIIFALPTQATANAMLSRLEALASKLF 359
Query: 864 ----LIVTHSNQALNQLFEKIIS 882
LI+ H N N LF+ + S
Sbjct: 360 PSPNLILAHGNSRFNHLFQSLKS 382
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 32.9 bits (75), Expect = 0.48
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 194 LTLVVGPPGTGKTDVAVQIISN 215
L LV GP G+GKT +A+Q+ N
Sbjct: 1 LILVFGPTGSGKTTLALQLALN 22
Score = 32.9 bits (75), Expect = 0.48
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 832 LTLVVGPPGTGKTDVAVQIISN 853
L LV GP G+GKT +A+Q+ N
Sbjct: 1 LILVFGPTGSGKTTLALQLALN 22
>gnl|CDD|232966 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes
for a probable ATP-dependent protease involved in both
DNA repair and degradation of proteins, peptides,
glycopeptides. Also known as sms. Residues 11-28 of the
SEED alignment contain a putative Zn binding domain.
Residues 110-117 of the seed contain a putative ATP
binding site both documented in Haemophilus and in
Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
178:5045-5048(1996)) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 454
Score = 34.0 bits (78), Expect = 0.50
Identities = 29/103 (28%), Positives = 51/103 (49%), Gaps = 6/103 (5%)
Query: 791 LRSSFPQAEIRVK-TDNPTKLVPPFKLTFHEIE-AIRAGMQPG-LTLVVGPPGTGKTDVA 847
++ PQA+ + + VP F F E++ + G+ PG L L+ G PG GK+ +
Sbjct: 52 GKAGIPQAQKSQTISAIELEEVPRFSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLL 111
Query: 848 VQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDERHL 890
+Q+ L N + L V+ ++L Q+ + I L + E +L
Sbjct: 112 LQVACQLAKNQM--KVLYVS-GEESLQQIKMRAIRLGLPEPNL 151
Score = 30.5 bits (69), Expect = 5.4
Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 7/86 (8%)
Query: 174 NTIPFTPTQIEAIR---AGMQPG-LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 229
F+ E R G+ PG L L+ G PG GK+ + +Q+ L N + L V+
Sbjct: 72 EVPRFSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQM--KVLYVS 129
Query: 230 HSNQALNQLFEKIISLDVDERHLLRL 255
++L Q+ + I L + E +L L
Sbjct: 130 -GEESLQQIKMRAIRLGLPEPNLYVL 154
>gnl|CDD|184377 PRK13894, PRK13894, conjugal transfer ATPase TrbB; Provisional.
Length = 319
Score = 32.8 bits (75), Expect = 0.80
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 179 TPTQIEAIRAGMQPGLT-LVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV 228
T Q EAI A ++ LV+G G+GKT + II+ + P +R I+
Sbjct: 134 TAAQREAIIAAVRAHRNILVIGGTGSGKTTLVNAIINEMVIQDPTERVFII 184
Score = 31.6 bits (72), Expect = 2.1
Identities = 21/73 (28%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 834 LVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQ---ALNQLFEKIISLDVDERHL 890
LV+G G+GKT + II+ + P +R I+ + + A + S+DV+ L
Sbjct: 152 LVIGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTGEIQCAAENYVQYHTSIDVNMTAL 211
Query: 891 LHKKYRITPRYLL 903
L R+ P +L
Sbjct: 212 LKTTLRMRPDRIL 224
>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510). This
family consists of several hypothetical bacterial
proteins of around 200 residues in length. The function
of this family is unknown.
Length = 214
Score = 32.4 bits (74), Expect = 0.84
Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 25/76 (32%)
Query: 86 KKRTEEEENEDEDVEMENKDANVLTTTPPRQAIIIGFLLIQVLKKRTEEEENEDEDVEME 145
+ EEENE+ED E +++ TEE+ + + E+
Sbjct: 87 EDEESEEENEEEDEESSDENEKE-----------------------TEEKTESNVEKEIT 123
Query: 146 NKDGKPIITV--EPHV 159
N KP+ T PH
Sbjct: 124 NPSWKPVGTEQTGPHA 139
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 32.9 bits (76), Expect = 0.89
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 183 IEAIRA-GMQPGLTLVVGPPGTGKTDVAVQIISN 215
I+A + G L+ GPPG GKT +A II+N
Sbjct: 42 IKAAKKRGEALDHVLLFGPPGLGKTTLA-HIIAN 74
Score = 32.9 bits (76), Expect = 0.89
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 821 IEAIRA-GMQPGLTLVVGPPGTGKTDVAVQIISN 853
I+A + G L+ GPPG GKT +A II+N
Sbjct: 42 IKAAKKRGEALDHVLLFGPPGLGKTTLA-HIIAN 74
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 31.6 bits (71), Expect = 0.97
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 191 QPGLTLVVGPPGTGKTDVAVQIISNL 216
+ L+VGPPG+GKT +A + L
Sbjct: 1 PGEVILIVGPPGSGKTTLARALAREL 26
Score = 31.6 bits (71), Expect = 0.97
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 829 QPGLTLVVGPPGTGKTDVAVQIISNL 854
+ L+VGPPG+GKT +A + L
Sbjct: 1 PGEVILIVGPPGSGKTTLARALAREL 26
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 32.7 bits (75), Expect = 1.0
Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 814 FKLTFHEIEAIRAGMQPGLTLVVGPPGTGKTDVA 847
K TF I ++ G P + L PGTGKT VA
Sbjct: 29 DKETFKSI--VKKGRIPNMLLHSPSPGTGKTTVA 60
Score = 30.0 bits (68), Expect = 7.4
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 192 PGLTLVVGPPGTGKTDVA 209
P + L PGTGKT VA
Sbjct: 43 PNMLLHSPSPGTGKTTVA 60
>gnl|CDD|223288 COG0210, UvrD, Superfamily I DNA and RNA helicases [DNA
replication, recombination, and repair].
Length = 655
Score = 32.9 bits (75), Expect = 1.2
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 179 TPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLY--HNFPHQRTLIVTHSNQALN 236
P Q EA+ P LV+ G+GKT V + I+ L ++ L +T +N+A
Sbjct: 4 NPEQREAVLHPDGP--LLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAA 61
Query: 237 QLFEKIISL 245
++ E+++ L
Sbjct: 62 EMRERLLKL 70
Score = 30.2 bits (68), Expect = 6.9
Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 830 PGLTLVVGPPGTGKTDVAVQIISNLY--HNFPHQRTLIVTHSNQALNQLFEKIISL 883
G LV+ G+GKT V + I+ L ++ L +T +N+A ++ E+++ L
Sbjct: 15 DGPLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEMRERLLKL 70
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 32.7 bits (75), Expect = 1.3
Identities = 15/31 (48%), Positives = 22/31 (70%), Gaps = 2/31 (6%)
Query: 185 AIRAGMQPGLTLVVGPPGTGKTDVAVQIISN 215
AI+A + G ++ GPPG GKT +A +II+N
Sbjct: 46 AIKAD-RVGSLILYGPPGVGKTTLA-RIIAN 74
Score = 32.7 bits (75), Expect = 1.3
Identities = 15/31 (48%), Positives = 22/31 (70%), Gaps = 2/31 (6%)
Query: 823 AIRAGMQPGLTLVVGPPGTGKTDVAVQIISN 853
AI+A + G ++ GPPG GKT +A +II+N
Sbjct: 46 AIKAD-RVGSLILYGPPGVGKTTLA-RIIAN 74
>gnl|CDD|238551 cd01131, PilT, Pilus retraction ATPase PilT. PilT is a nucleotide
binding protein responsible for the retraction of type
IV pili, likely by pili disassembly. This retraction
provides the force required for travel of bacteria in
low water environments by a mechanism known as twitching
motility.
Length = 198
Score = 31.5 bits (72), Expect = 1.3
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 193 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 229
GL LV GP G+GK+ +I + N H I+T
Sbjct: 2 GLVLVTGPTGSGKSTTLAAMIDYINKNKTHH---ILT 35
Score = 31.5 bits (72), Expect = 1.3
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 831 GLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVT 867
GL LV GP G+GK+ +I + N H I+T
Sbjct: 2 GLVLVTGPTGSGKSTTLAAMIDYINKNKTHH---ILT 35
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 32.1 bits (74), Expect = 1.4
Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 185 AIRAGMQPGLTLVVGPPGTGKTDVAVQ 211
A+R G +P L+ GPPGTGKT V+
Sbjct: 49 ALR-GSRPLNVLIYGPPGTGKT-TTVK 73
Score = 32.1 bits (74), Expect = 1.4
Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 823 AIRAGMQPGLTLVVGPPGTGKTDVAVQ 849
A+R G +P L+ GPPGTGKT V+
Sbjct: 49 ALR-GSRPLNVLIYGPPGTGKT-TTVK 73
>gnl|CDD|236436 PRK09263, PRK09263, anaerobic ribonucleoside triphosphate reductase;
Provisional.
Length = 711
Score = 32.5 bits (75), Expect = 1.4
Identities = 25/85 (29%), Positives = 37/85 (43%), Gaps = 20/85 (23%)
Query: 943 LSPWKSEDGSPFFGGWARMAQPIVNFAVVEVAKPNIEEALETEKDFSRYGRVNYVLAKRL 1002
L WK E+G G R N VV + P I ALE + D ++ +L +RL
Sbjct: 389 LQGWKDENGEEVHDG--RN-----NLGVVTLNLPRI--ALEAKGDEDKFWE---ILDERL 436
Query: 1003 DLLQE-----VERLQKSLDVSGDVA 1022
+L ++ +ERL+ VA
Sbjct: 437 ELAKKALMTRIERLK---GAKPRVA 458
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 32.5 bits (74), Expect = 1.4
Identities = 26/120 (21%), Positives = 44/120 (36%), Gaps = 15/120 (12%)
Query: 183 IEAIR-AGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV-THSNQALNQLFE 240
EA+ A L+ P GTGKT +A + + L + + +I+ T + QL E
Sbjct: 24 AEAVAEALKGGEGLLIEAPTGTGKT-LAYLLPA-LAYAREEGKKVIISTRTKALQEQLLE 81
Query: 241 KIISLDVDERHLLRLGHGEEALETEKDFSRYGRVNYVLAKRLDLLQEVERLQKSLDVSGD 300
+ + + + L GR NY+ RL+ L ++ S
Sbjct: 82 EDLPIHKLLKKLGGKFAL-----------LKGRSNYLCLSRLERLAQLGGDDDDYLQSLA 130
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 32.6 bits (75), Expect = 1.5
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 5/40 (12%)
Query: 183 IEAIRAGMQ-----PGLTLVVGPPGTGKTDVAVQIISNLY 217
I RAG++ G+ L+VGP G GKT+ A+ + LY
Sbjct: 582 IRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLY 621
Score = 32.6 bits (75), Expect = 1.5
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 5/40 (12%)
Query: 821 IEAIRAGMQ-----PGLTLVVGPPGTGKTDVAVQIISNLY 855
I RAG++ G+ L+VGP G GKT+ A+ + LY
Sbjct: 582 IRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLY 621
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 32.3 bits (74), Expect = 1.5
Identities = 25/94 (26%), Positives = 43/94 (45%), Gaps = 21/94 (22%)
Query: 833 TLVVGPPGTGKTDVAVQIISNLYHNFPHQ-------RTLIVTHSN---QALNQLFEKIIS 882
TLVV P G GKT +A +I+N F + + L++ H+ + ++I +
Sbjct: 32 TLVVLPTGLGKTFIAAMVIANRLRWFGGKVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAA 91
Query: 883 L----DVDERHLLHKKYRI---TPRYLLLAIKND 909
L +ER L K ++ TP+ ++ND
Sbjct: 92 LTGEVRPEEREELWAKKKVFVATPQ----VVEND 121
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 32.3 bits (74), Expect = 1.6
Identities = 12/17 (70%), Positives = 15/17 (88%)
Query: 196 LVVGPPGTGKTDVAVQI 212
L+VGPPGTGKT +A+ I
Sbjct: 69 LIVGPPGTGKTALAMGI 85
Score = 32.3 bits (74), Expect = 1.6
Identities = 12/17 (70%), Positives = 15/17 (88%)
Query: 834 LVVGPPGTGKTDVAVQI 850
L+VGPPGTGKT +A+ I
Sbjct: 69 LIVGPPGTGKTALAMGI 85
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 32.1 bits (73), Expect = 1.9
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 11/45 (24%)
Query: 181 TQIEAIRAGMQPGL--------TLVVGPPGTGKTDVAVQIISNLY 217
T + RA GL L GPPGTGKT +A ++++ +Y
Sbjct: 295 TAMALARAER--GLPVAQTSNHMLFAGPPGTGKTTIA-RVVAKIY 336
Score = 31.0 bits (70), Expect = 4.0
Identities = 11/23 (47%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 833 TLVVGPPGTGKTDVAVQIISNLY 855
L GPPGTGKT +A ++++ +Y
Sbjct: 315 MLFAGPPGTGKTTIA-RVVAKIY 336
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 32.1 bits (73), Expect = 2.1
Identities = 34/101 (33%), Positives = 47/101 (46%), Gaps = 16/101 (15%)
Query: 117 AIIIGFLLIQVLK-----KRTEEEENEDEDVEMENKDGKPIITVEPHVIPSRGPYLFNEP 171
IIIG LK K T ++E++ E +E NK + I EP +R P F+E
Sbjct: 11 LIIIGLYFFNALKNQQTNKITIDKESKKE-LEKLNK-MRAIRLTEPLSEKTR-PKSFDE- 66
Query: 172 RKNTIPFTPTQIEAIRA---GMQPGLTLVVGPPGTGKTDVA 209
I I+A++A G P ++ GPPG GKT A
Sbjct: 67 ----IIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAA 103
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 31.9 bits (73), Expect = 2.1
Identities = 45/144 (31%), Positives = 62/144 (43%), Gaps = 27/144 (18%)
Query: 183 IEAIRAGMQPG-LTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIV---THSN-----Q 233
+E I+ G G L+ GPPGTGKT +A+ I L + P I +S +
Sbjct: 40 VEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPF--CPISGSEVYSLEMKKTE 97
Query: 234 ALNQLFEKIISLDVDERHLLRLGHGE----EALETEKDFSRYG-RVNYVL--------AK 280
AL Q F K I + + E + GE E E E S YG + + K
Sbjct: 98 ALTQAFRKAIGVRIKEEKEVY--EGEVVELEIEEAENPLSGYGKTIKHGKITLKTTKMEK 155
Query: 281 RLDLLQEV-ERLQKSLDVSGDVAY 303
L L ++ E+LQK +GDV Y
Sbjct: 156 TLKLGPKIYEQLQKEKVQAGDVIY 179
Score = 30.7 bits (70), Expect = 4.1
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 821 IEAIRAGMQPG-LTLVVGPPGTGKTDVAVQI 850
+E I+ G G L+ GPPGTGKT +A+ I
Sbjct: 40 VEMIKEGKIAGRAVLIAGPPGTGKTALAIAI 70
>gnl|CDD|219284 pfam07064, RIC1, RIC1. RIC1 has been identified in yeast as a
Golgi protein involved in retrograde transport to the
cis-Golgi network. It forms a heterodimer with Rgp1 and
functions as a guanyl-nucleotide exchange factor.
Length = 251
Score = 31.2 bits (71), Expect = 2.2
Identities = 45/208 (21%), Positives = 69/208 (33%), Gaps = 39/208 (18%)
Query: 208 VAVQIISNLYHNFPHQRTLIVTHSNQALNQLFEKIISLDVDERHLLRLGHGEEALETEKD 267
+ + +FP R I TH LF L RHLL+ GE+AL +
Sbjct: 58 AESESVQRRDSSFPFLRFEIRTH-------LF-----LPYILRHLLKRNWGEQALYLAQH 105
Query: 268 FSRYGRVNYVLAKRLD--LLQEVERLQKSLDVSGDVAYTCETAGHFFLYQVLARWEKFLA 325
+VL L L +EV+ ++ + L + +FL
Sbjct: 106 MRHLPYFPHVLELLLHTVLDEEVDSSEQDSPRDSLLPAVIS---------FLQEFPEFLD 156
Query: 326 TVRPSDGKTVPVK-TIKTEFP-FHGFFENAPKP--LFKEKSYETDMEIAEGCFRYIEKMF 381
V V+ T KTE + F+ P LF+E ++ A ++
Sbjct: 157 IV---------VQCTRKTELRLWRTLFDYLGPPKDLFEECLELGRLKTAASYLLVLQN-L 206
Query: 382 TQLEEFR--AFELLRSGLDRSKYLLVKE 407
A LL L+ + L KE
Sbjct: 207 EGSASSSDCAVRLLVLALEEKNWELCKE 234
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 31.5 bits (72), Expect = 2.2
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 173 KNTIPFTPTQIEAIRAGMQPGLTLVVGPPGTGKT 206
+ +P P + + + G+ +VGP G GKT
Sbjct: 179 EGMLPVKPEEDPILE---RGGVIALVGPTGVGKT 209
>gnl|CDD|147845 pfam05914, RIB43A, RIB43A. This family consists of several
RIB43A-like eukaryotic proteins. Ciliary and flagellar
microtubules contain a specialised set of
protofilaments, termed ribbons, that are composed of
tubulin and several associated proteins. RIB43A was
first characterized in the unicellular biflagellate,
Chlamydomonas reinhardtii although highly related
sequences are present in several higher eukaryotes
including humans. The function of this protein is
unknown although the structure of RIB43A and its
association with the specialised protofilament ribbons
and with basal bodies is relevant to the proposed role
of ribbons in forming and stabilising doublet and
triplet microtubules and in organising their
three-dimensional structure. Human RIB43A homologues
could represent a structural requirement in centriole
replication in dividing cells.
Length = 379
Score = 31.6 bits (72), Expect = 2.5
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 11/71 (15%)
Query: 126 QVLKKRTEEEENEDEDVEMENKDGKPIITVEPHVIPSRGPYLFNEPRKNTIPF-----TP 180
+ ++R ++EE ED E+ N+ ++T P V S F R IP +P
Sbjct: 226 RERERREKQEEQEDNLAEIYNQLTSDLLTENPDVAQSS----FGPHRV--IPDRWKGMSP 279
Query: 181 TQIEAIRAGMQ 191
Q+ AIR G +
Sbjct: 280 EQLAAIRKGQE 290
>gnl|CDD|236093 PRK07773, PRK07773, replicative DNA helicase; Validated.
Length = 886
Score = 31.6 bits (72), Expect = 2.7
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 818 FHEIEAIRAGMQPG-LTLVVGPPGTGKTDVAVQIISN--LYHNFP 859
F E++A+ G+ PG L +V P GKT + N + H
Sbjct: 204 FTELDAMTNGLHPGQLIIVAARPSMGKTTFGLDFARNCAIRHRLA 248
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 31.2 bits (72), Expect = 2.9
Identities = 11/17 (64%), Positives = 14/17 (82%), Gaps = 1/17 (5%)
Query: 199 GPPGTGKTDVAVQIISN 215
GPPGTGKT +A +II+
Sbjct: 43 GPPGTGKTTLA-RIIAG 58
Score = 31.2 bits (72), Expect = 2.9
Identities = 11/17 (64%), Positives = 14/17 (82%), Gaps = 1/17 (5%)
Query: 837 GPPGTGKTDVAVQIISN 853
GPPGTGKT +A +II+
Sbjct: 43 GPPGTGKTTLA-RIIAG 58
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 31.3 bits (72), Expect = 3.0
Identities = 12/21 (57%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 195 TLVVGPPGTGKTDVAVQIISN 215
L+ GPPG GKT +A II+N
Sbjct: 54 VLLYGPPGLGKTTLA-NIIAN 73
Score = 31.3 bits (72), Expect = 3.0
Identities = 12/21 (57%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 833 TLVVGPPGTGKTDVAVQIISN 853
L+ GPPG GKT +A II+N
Sbjct: 54 VLLYGPPGLGKTTLA-NIIAN 73
>gnl|CDD|153040 pfam12606, RELT, Tumour necrosis factor receptor superfamily member
19. This family of proteins is found in bacteria and
eukaryotes. Proteins in this family are typically
between 49 and 288 amino acids in length. There are two
completely conserved residues (K and Y) that may be
functionally important. The members of tumor necrosis
factor receptor (TNFR) superfamily have been designated
as the "guardians of the immune system" due to their
roles in immune cell proliferation, differentiation,
activation, and death (apoptosis). The messenger RNA of
RELT is especially abundant in hematologic tissues such
as spleen, lymph node, and peripheral blood leukocytes
as well as in leukemias and lymphomas. RELT is able to
activate the NF-kappaB pathway and selectively binds
tumor necrosis factor receptor-associated factor 1.
Length = 50
Score = 28.0 bits (63), Expect = 3.3
Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 117 AIIIGFLLIQVLKK-----RTEEEENEDEDVEMENKD 148
++G L+ +LKK + E+E E+ + E K+
Sbjct: 13 MGLLGLLICTLLKKKGYRCTVDPLEDEPEEKKEEEKE 49
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 31.1 bits (71), Expect = 3.4
Identities = 34/148 (22%), Positives = 57/148 (38%), Gaps = 29/148 (19%)
Query: 715 DVYETFNV--LMRRKPKENNFKAVLETIRDLMNTECVVPDWLHDII-LGYGDPGAAHYTE 771
D+ + N ++R ++ K V+ DL V D+L D + + YG+PG
Sbjct: 245 DIRQRLNAARVIRELAEDG--KYVIVVEHDL-----AVLDYLSDFVHILYGEPGVYGVVS 297
Query: 772 MPNEI--ATMDFNDTFLNMDHLR-------------SSFPQAEIRVKTDNPTKLVPPFKL 816
P + ++ +L +++R + V+ + K FKL
Sbjct: 298 KPKSVRVGINEYLKGYLPEENVRFRPEEIEFEEKPPRDDKARDTLVEYPDLKKTYGDFKL 357
Query: 817 TFHEIEAIRAGMQPGLTLVVGPPGTGKT 844
E E I G G ++GP G GKT
Sbjct: 358 EVEEGE-IYDGEVIG---ILGPNGIGKT 381
>gnl|CDD|233261 TIGR01073, pcrA, ATP-dependent DNA helicase PcrA. Designed to
identify pcrA members of the uvrD/rep subfamily [DNA
metabolism, DNA replication, recombination, and repair].
Length = 726
Score = 31.3 bits (71), Expect = 3.5
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 180 PTQIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHN---FPHQRTLIVTHSNQALN 236
P Q EA++ P L++ G+GKT V I++L P L +T +N+A
Sbjct: 7 PEQREAVKTTEGP--LLIMAGAGSGKTRVLTHRIAHLIAEKNVAPWN-ILAITFTNKAAR 63
Query: 237 QLFEKIISL 245
++ E++ L
Sbjct: 64 EMKERVEKL 72
Score = 29.7 bits (67), Expect = 9.5
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 834 LVVGPPGTGKTDVAVQIISNLYHN---FPHQRTLIVTHSNQALNQLFEKIISL 883
L++ G+GKT V I++L P L +T +N+A ++ E++ L
Sbjct: 21 LIMAGAGSGKTRVLTHRIAHLIAEKNVAPWN-ILAITFTNKAAREMKERVEKL 72
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 31.2 bits (71), Expect = 3.5
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 190 MQPG-LTLVVGPPGTGKTDVAVQIISNLYH 218
++PG LT+V+G PG+G + + I SN
Sbjct: 84 IKPGELTVVLGRPGSGCSTLLKTIASNTDG 113
Score = 31.2 bits (71), Expect = 3.5
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 828 MQPG-LTLVVGPPGTGKTDVAVQIISNLYH 856
++PG LT+V+G PG+G + + I SN
Sbjct: 84 IKPGELTVVLGRPGSGCSTLLKTIASNTDG 113
>gnl|CDD|234011 TIGR02782, TrbB_P, P-type conjugative transfer ATPase TrbB. The
TrbB protein is found in the trb locus of Agrobacterium
Ti plasmids where it is involved in the type IV
secretion system for plasmid conjugative transfer. TrbB
is a homolog of the vir system VirB11 ATPase , and the
Flp pilus sytem ATPase TadA [Cellular processes,
Conjugation].
Length = 299
Score = 30.9 bits (70), Expect = 3.9
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 819 HEIEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQ 871
EA+ A LVVG G+GKT +A +++ + N P R +I+ + +
Sbjct: 124 VLREAVLARKN---ILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTRE 173
Score = 30.9 bits (70), Expect = 4.0
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 183 IEAIRAGMQPGLTLVVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHSNQ 233
EA+ A LVVG G+GKT +A +++ + N P R +I+ + +
Sbjct: 126 REAVLARKN---ILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTRE 173
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 30.7 bits (70), Expect = 3.9
Identities = 25/124 (20%), Positives = 46/124 (37%), Gaps = 18/124 (14%)
Query: 98 DVEMENKDANV-LTTTPPRQA----IIIGFLLIQVLKKRTEEEENED-----EDVEMENK 147
V + + V + P +++ L+ +++ ED E +
Sbjct: 45 GVSIVARGEAVRIIGARPLVDVATRVLLTLELLAEVRRGIASIYLEDVLSAFRGAESLQQ 104
Query: 148 DGKPIITVEPHVIPSRGPYLFNEPRKNTI-PFTPTQIEAIRAGMQPGLTLVVGPPGTGKT 206
+ + ++ H + R R +I P TP Q A + + +GP GTGKT
Sbjct: 105 LEESVEELDTHFLRGR-------TRDKSIIPKTPGQNMYPEAIEEHDIVFGIGPAGTGKT 157
Query: 207 DVAV 210
+AV
Sbjct: 158 YLAV 161
>gnl|CDD|172375 PRK13851, PRK13851, type IV secretion system protein VirB11;
Provisional.
Length = 344
Score = 30.6 bits (69), Expect = 4.5
Identities = 37/126 (29%), Positives = 51/126 (40%), Gaps = 16/126 (12%)
Query: 834 LVVGPPGTGKTDVAVQIISNLYHNFPHQRTLI---------VTHSNQALNQLFEKI-ISL 883
L+ GP G+GKT ++ +IS + P Q LI + H N + L+ K L
Sbjct: 166 LLCGPTGSGKTTMSKTLISAI----PPQERLITIEDTLELVIPHENH-VRLLYSKNGAGL 220
Query: 884 D-VDERHLLHKKYRITPRYLLLAIKNDVELSQLLSDVTIAQGGVMPNIQSMKFDKTLKTL 942
V HLL R+ P +LL D LS+V G + I + K L
Sbjct: 221 GAVTAEHLLQASLRMRPDRILLGEMRDDAAWAYLSEVVSGHPGSISTIHGANPVQGFKKL 280
Query: 943 LSPWKS 948
S KS
Sbjct: 281 FSLVKS 286
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 29.2 bits (66), Expect = 5.0
Identities = 12/26 (46%), Positives = 19/26 (73%), Gaps = 1/26 (3%)
Query: 196 LVVGPPGTGKTDVAVQIISNLYHNFP 221
L+VGPPGTGK+++A + ++ N P
Sbjct: 3 LLVGPPGTGKSELA-ERLAAALSNRP 27
Score = 29.2 bits (66), Expect = 5.0
Identities = 12/26 (46%), Positives = 19/26 (73%), Gaps = 1/26 (3%)
Query: 834 LVVGPPGTGKTDVAVQIISNLYHNFP 859
L+VGPPGTGK+++A + ++ N P
Sbjct: 3 LLVGPPGTGKSELA-ERLAAALSNRP 27
>gnl|CDD|110723 pfam01745, IPT, Isopentenyl transferase. Isopentenyl transferase /
dimethylallyl transferase synthesises
isopentenyladensosine 5'-monophosphate, a cytokinin that
induces shoot formation on host plants infected with the
Ti plasmid.
Length = 232
Score = 30.1 bits (68), Expect = 5.1
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 192 PGLTLVVGPPGTGKTDVAVQI 212
GL L+ G TGKT A+ +
Sbjct: 1 MGLYLIWGATCTGKTAEAIAL 21
Score = 30.1 bits (68), Expect = 5.1
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 830 PGLTLVVGPPGTGKTDVAVQI 850
GL L+ G TGKT A+ +
Sbjct: 1 MGLYLIWGATCTGKTAEAIAL 21
>gnl|CDD|114172 pfam05432, BSP_II, Bone sialoprotein II (BSP-II). Bone
sialoprotein (BSP) is a major structural protein of the
bone matrix that is specifically expressed by
fully-differentiated osteoblasts. The expression of bone
sialoprotein (BSP) is normally restricted to mineralised
connective tissues of bones and teeth where it has been
associated with mineral crystal formation. However, it
has been found that ectopic expression of BSP occurs in
various lesions, including oral and extraoral
carcinomas, in which it has been associated with the
formation of microcrystalline deposits and the
metastasis of cancer cells to bone.
Length = 291
Score = 30.4 bits (68), Expect = 5.1
Identities = 22/80 (27%), Positives = 33/80 (41%), Gaps = 21/80 (26%)
Query: 90 EEEENEDEDVEMENKDANVLTTTPPRQAII----IGFLLIQVLKK--------------- 130
+ + NEDE+ E EN + +T A IG +Q+ KK
Sbjct: 77 DSDGNEDEEAEAENTTLSTVTLGYGGDATPGTGNIGLAALQLPKKAGNAGKKATKEDESD 136
Query: 131 --RTEEEENEDEDVEMENKD 148
EEEE E+E+ E+E +
Sbjct: 137 EDEEEEEEEEEEEAEVEENE 156
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 30.7 bits (70), Expect = 5.2
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 178 FTPTQIEAIRAGMQPGLTLVVGPPGTGKTDVAV 210
TP Q AI L++ P G+GKT+ A
Sbjct: 23 LTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAF 55
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 30.6 bits (69), Expect = 5.2
Identities = 33/145 (22%), Positives = 58/145 (40%), Gaps = 29/145 (20%)
Query: 108 VLTTTPPRQAIIIGFLLIQVLKKRTEE-EENEDEDVEMENKDG--KPIITVEPHV-IPSR 163
V++T P + +++ +K E E + V E+ G + + V +P +
Sbjct: 140 VVSTQPAGFVYVTEATEVEIREKPVREEIERKVPKVTYEDIGGLKEAKEKIREMVELPMK 199
Query: 164 GPYLFNEPRKNTIPFTPTQIEAIRAGMQP--GLTLVVGPPGTGKT----DVAVQIISNLY 217
P LF G++P G+ L+ GPPGTGKT VA + +
Sbjct: 200 HPELFE-----------------HLGIEPPKGV-LLYGPPGTGKTLLAKAVANEAGAYFI 241
Query: 218 H-NFPHQRTLIVTHSNQALNQLFEK 241
N P + S + L ++F++
Sbjct: 242 SINGPEIMSKYYGESEERLREIFKE 266
Score = 30.3 bits (68), Expect = 6.6
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 192 PGLTLVVGPPGTGKTDVAVQIISNLYHNF-----PHQRTLIVTHSNQALNQLFEK 241
P L+ GPPGTGKT +A + + NF P + V S +A+ ++F K
Sbjct: 487 PKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKWVGESEKAIREIFRK 541
Score = 30.3 bits (68), Expect = 6.6
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 830 PGLTLVVGPPGTGKTDVAVQIISNLYHNF-----PHQRTLIVTHSNQALNQLFEK 879
P L+ GPPGTGKT +A + + NF P + V S +A+ ++F K
Sbjct: 487 PKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKWVGESEKAIREIFRK 541
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 30.1 bits (69), Expect = 5.2
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 196 LVVGPPGTGKTDVAVQIISNLYHNFP 221
+ G GTGKT + I N +
Sbjct: 19 GIFGGSGTGKTVLLGMIARNAKADVV 44
Score = 30.1 bits (69), Expect = 5.2
Identities = 8/26 (30%), Positives = 11/26 (42%)
Query: 834 LVVGPPGTGKTDVAVQIISNLYHNFP 859
+ G GTGKT + I N +
Sbjct: 19 GIFGGSGTGKTVLLGMIARNAKADVV 44
>gnl|CDD|225586 COG3044, COG3044, Predicted ATPase of the ABC class [General
function prediction only].
Length = 554
Score = 30.6 bits (69), Expect = 5.3
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 12/82 (14%)
Query: 160 IPSRGPYLFNEPRKNTIPF-----------TPTQIEAIRAGMQPGLTLVVGPPGTGKTDV 208
+ R + P + +PF P E + G+ G+TL+ G GKT +
Sbjct: 199 VLPRKAGICGPPMEEAVPFEAPESLPVEIELPNGKEVVGMGIPQGITLITGGNFHGKTTL 258
Query: 209 AVQIISNLYHNFPHQ-RTLIVT 229
I + ++ P R +VT
Sbjct: 259 LTAIERGVDNHIPGDGRERVVT 280
>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 30.3 bits (69), Expect = 5.4
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 197 VVGPPGTGKTDVAVQIISN 215
+ GP +GKT +A+Q+++N
Sbjct: 65 IYGPESSGKTTLALQLVAN 83
Score = 30.3 bits (69), Expect = 5.4
Identities = 8/19 (42%), Positives = 15/19 (78%)
Query: 835 VVGPPGTGKTDVAVQIISN 853
+ GP +GKT +A+Q+++N
Sbjct: 65 IYGPESSGKTTLALQLVAN 83
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 29.8 bits (68), Expect = 5.5
Identities = 11/25 (44%), Positives = 19/25 (76%), Gaps = 1/25 (4%)
Query: 189 GMQPG-LTLVVGPPGTGKTDVAVQI 212
G + G +T + GPPG+GKT++ +Q+
Sbjct: 19 GFERGTITQIYGPPGSGKTNICLQL 43
Score = 29.8 bits (68), Expect = 5.5
Identities = 11/25 (44%), Positives = 19/25 (76%), Gaps = 1/25 (4%)
Query: 827 GMQPG-LTLVVGPPGTGKTDVAVQI 850
G + G +T + GPPG+GKT++ +Q+
Sbjct: 19 GFERGTITQIYGPPGSGKTNICLQL 43
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 30.6 bits (70), Expect = 5.9
Identities = 31/113 (27%), Positives = 48/113 (42%), Gaps = 36/113 (31%)
Query: 833 TLVVGPPGTGKTDVAVQIISNLYHNFP---------------HQRTLIVTHSNQALNQLF 877
TLVV P G GKT +A+ +I+ H H + LN
Sbjct: 32 TLVVLPTGLGKTAIALLVIAERLHKKGGKVLILAPTKPLVEQHAEFF-----RKFLNIPE 86
Query: 878 EKIISL--DV--DERHLLHKKYRI---TPRYLLLAIKNDV---ELSQLLSDVT 920
EKI+ +V ++R L +K ++ TP+ I+ND+ +S L DV+
Sbjct: 87 EKIVVFTGEVSPEKRAELWEKAKVIVATPQ----VIENDLIAGRIS--LEDVS 133
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and host
eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 29.6 bits (67), Expect = 5.9
Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 178 FTPTQIEAIRAGMQPGLT-LVVGPPGTGKT 206
F+P Q + ++ L+ G G+GKT
Sbjct: 10 FSPLQAAYLWLAVEARKNILISGGTGSGKT 39
>gnl|CDD|185181 PRK15279, PRK15279, type III secretion protein SopE; Provisional.
Length = 240
Score = 29.7 bits (66), Expect = 6.3
Identities = 22/76 (28%), Positives = 28/76 (36%), Gaps = 4/76 (5%)
Query: 174 NTIPFTPTQIEAIRAGMQPGLTL--VVGPPGTGKTDVAVQIISNLYHNFPHQRTLIVTHS 231
N PF EA + PG T V P G G +IS+ +P I H
Sbjct: 136 NIAPFLQEIGEAAKNAGLPGTTKNDVFTPSGAGANPFITPLISSANSKYPRM--FINQHQ 193
Query: 232 NQALNQLFEKIISLDV 247
+ EKII +V
Sbjct: 194 QASFKIYAEKIIMTEV 209
>gnl|CDD|218709 pfam05707, Zot, Zonular occludens toxin (Zot). This family
consists of bacterial and viral proteins which are very
similar to the Zonular occludens toxin (Zot). Zot is
elaborated by bacteriophages present in toxigenic
strains of Vibrio cholerae. Zot is a single polypeptide
chain of 44.8 kDa, with the ability to reversibly alter
intestinal epithelial tight junctions, allowing the
passage of macromolecules through mucosal barriers.
Length = 183
Score = 29.6 bits (67), Expect = 6.5
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 194 LTLVVGPPGTGKTDVAVQ 211
+ L+ G PG+GKT AV
Sbjct: 2 IYLITGKPGSGKTLEAVS 19
Score = 29.6 bits (67), Expect = 6.5
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 832 LTLVVGPPGTGKTDVAVQ 849
+ L+ G PG+GKT AV
Sbjct: 2 IYLITGKPGSGKTLEAVS 19
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 30.4 bits (69), Expect = 6.6
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 192 PGLTLVVGPPGTGKTDVA 209
P L+VGPPGTGKT +A
Sbjct: 183 PKGVLLVGPPGTGKTLLA 200
Score = 30.4 bits (69), Expect = 6.6
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 830 PGLTLVVGPPGTGKTDVA 847
P L+VGPPGTGKT +A
Sbjct: 183 PKGVLLVGPPGTGKTLLA 200
>gnl|CDD|188267 TIGR03001, Sig-70_gmx1, RNA polymerase sigma-70 factor,
Myxococcales family 1. This group of sigma factors are
members of the sigma-70 family (TIGR02937) and are found
in multiple copies in the order Myxococcales. This model
supercedes TIGR02233, which has now been retired.
Length = 244
Score = 29.7 bits (67), Expect = 7.0
Identities = 20/83 (24%), Positives = 32/83 (38%), Gaps = 6/83 (7%)
Query: 223 QRTLIVTHSNQALNQLFEKII-SLDVDERHLLRLGHGE----EALETEKDFSRYGRVNYV 277
+ L+ Q Q + + +L ERHLLRL + + + R +V
Sbjct: 139 ELDLLRERYRQDFRQALREALAALSERERHLLRLHFVDGLSMDRIGAMYQVHRSTVSRWV 198
Query: 278 LAKRLDLLQEV-ERLQKSLDVSG 299
R LL+ RL + L +S
Sbjct: 199 AQARERLLERTRRRLAERLKLSS 221
>gnl|CDD|238713 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield adenosine
diphosphates (ADP). This enzyme is required for the
biosynthesis of ADP and is essential for homeostasis of
adenosine phosphates.
Length = 194
Score = 29.5 bits (67), Expect = 7.4
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 196 LVVGPPGTGKTDVAVQIISNLYHNFPH 222
L++GPPG+GK A + ++ Y PH
Sbjct: 3 LLLGPPGSGKGTQA-ERLAKKY-GLPH 27
Score = 29.5 bits (67), Expect = 7.4
Identities = 11/27 (40%), Positives = 17/27 (62%), Gaps = 2/27 (7%)
Query: 834 LVVGPPGTGKTDVAVQIISNLYHNFPH 860
L++GPPG+GK A + ++ Y PH
Sbjct: 3 LLLGPPGSGKGTQA-ERLAKKY-GLPH 27
>gnl|CDD|233193 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 30.0 bits (68), Expect = 7.7
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 813 PFKLTFHEIEAIRAGMQPGLTLVVGPPGTGKT 844
PF FH +A G TL+ GP G+GKT
Sbjct: 421 PFYFNFHVRDAKVLGH----TLIFGPTGSGKT 448
>gnl|CDD|213207 cd03240, ABC_Rad50, ATP-binding cassette domain of Rad50. The
catalytic domains of Rad50 are similar to the
ATP-binding cassette of ABC transporters, but are not
associated with membrane-spanning domains. The conserved
ATP-binding motifs common to Rad50 and the ABC
transporter family include the Walker A and Walker B
motifs, the Q loop, a histidine residue in the switch
region, a D-loop, and a conserved LSGG sequence. This
conserved sequence, LSGG, is the most specific and
characteristic motif of this family and is thus known as
the ABC signature sequence.
Length = 204
Score = 29.5 bits (67), Expect = 8.0
Identities = 13/27 (48%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 818 FHEIEAIRAGMQPGLTLVVGPPGTGKT 844
FHE I LTL+VG G GKT
Sbjct: 12 FHERSEIE--FFSPLTLIVGQNGAGKT 36
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 30.0 bits (68), Expect = 8.5
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 196 LVVGPPGTGKTDVAVQI 212
L+VGPPGTGKT +A I
Sbjct: 220 LLVGPPGTGKTLLAKAI 236
Score = 30.0 bits (68), Expect = 8.5
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 834 LVVGPPGTGKTDVAVQI 850
L+VGPPGTGKT +A I
Sbjct: 220 LLVGPPGTGKTLLAKAI 236
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH [Cellular processes, Cell
division, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 495
Score = 29.9 bits (68), Expect = 8.9
Identities = 11/14 (78%), Positives = 13/14 (92%)
Query: 196 LVVGPPGTGKTDVA 209
L+VGPPGTGKT +A
Sbjct: 92 LLVGPPGTGKTLLA 105
Score = 29.9 bits (68), Expect = 8.9
Identities = 11/14 (78%), Positives = 13/14 (92%)
Query: 834 LVVGPPGTGKTDVA 847
L+VGPPGTGKT +A
Sbjct: 92 LLVGPPGTGKTLLA 105
>gnl|CDD|172360 PRK13833, PRK13833, conjugal transfer protein TrbB; Provisional.
Length = 323
Score = 29.8 bits (67), Expect = 9.0
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 179 TPTQIEAIRAGMQPGLTLVV-GPPGTGKTDVAVQIISNLYHNFPHQRTLI 227
T Q IR+ + L +V+ G G+GKT +A +I+ + + P R +I
Sbjct: 130 TEAQASVIRSAIDSRLNIVISGGTGSGKTTLANAVIAEIVASAPEDRLVI 179
>gnl|CDD|235907 PRK07004, PRK07004, replicative DNA helicase; Provisional.
Length = 460
Score = 29.9 bits (67), Expect = 9.3
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 818 FHEIEAIRAGMQPG-LTLVVGPPGTGKTDVAVQI 850
F +++ + +GM G L +V G P GKT ++ I
Sbjct: 200 FVDLDRMTSGMHGGELIIVAGRPSMGKTAFSMNI 233
>gnl|CDD|226409 COG3893, COG3893, Inactivated superfamily I helicase [DNA
replication, recombination, and repair].
Length = 697
Score = 29.8 bits (67), Expect = 9.4
Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 3/73 (4%)
Query: 528 LAKRLDLLQEVERLQKSLD--VSGDVAYTCETAGHFFLYQVLARWEKFLATVRQRKQDRR 585
L++ DL LD +GD+A + F L V W K L + +
Sbjct: 139 LSELFDLFDTESSEWDKLDDLATGDLAAWWQVTLEF-LEIVYDAWPKRLEELGRSNPAAH 197
Query: 586 KPAVSRTNIIREK 598
+ A+ R +R K
Sbjct: 198 RNALFRAEAMRLK 210
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 28.7 bits (64), Expect = 9.6
Identities = 12/24 (50%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 183 IEAIRAGMQPGLTLVVGPPGTGKT 206
EA+ L L+ GPPGTGKT
Sbjct: 11 REALELPPPKNL-LLYGPPGTGKT 33
Score = 28.7 bits (64), Expect = 9.6
Identities = 12/24 (50%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 821 IEAIRAGMQPGLTLVVGPPGTGKT 844
EA+ L L+ GPPGTGKT
Sbjct: 11 REALELPPPKNL-LLYGPPGTGKT 33
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
0.320 0.137 0.402
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 54,922,756
Number of extensions: 5586937
Number of successful extensions: 6799
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6756
Number of HSP's successfully gapped: 222
Length of query: 1051
Length of database: 10,937,602
Length adjustment: 107
Effective length of query: 944
Effective length of database: 6,191,724
Effective search space: 5844987456
Effective search space used: 5844987456
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: 64 (28.4 bits)