RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13674
(315 letters)
>gnl|CDD|185407 PTZ00035, PTZ00035, Rad51 protein; Provisional.
Length = 337
Score = 230 bits (588), Expect = 8e-74
Identities = 88/161 (54%), Positives = 117/161 (72%), Gaps = 1/161 (0%)
Query: 60 AVEEEDEEDGEEFFQDVDILQNYNINVADIKKLKSVGLCTIKGVQMTTRRKMSQIKGFSE 119
+EE+EE+ E FQ+++ LQ+ IN ADIKKLK G+CT++ V T++ + IKG SE
Sbjct: 7 EQQEEEEEEEAEGFQEIEKLQSAGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISE 66
Query: 120 AKVDKIKEACMKICDNSFLTAAQVVEKRKQVFKITTGSTELDKILGGGIESMAITEAFGE 179
AKV+KIKEA K+ F++A + +E RK + +ITTGST+LDK+LGGGIE+ +ITE FGE
Sbjct: 67 AKVEKIKEAASKLVPMGFISATEYLEARKNIIRITTGSTQLDKLLGGGIETGSITELFGE 126
Query: 180 FRTGKTQLSHTLSITAQLPDETRGYTGGKVIYVDSENTLYP 220
FRTGKTQL HTL +T QLP E G GKV+Y+D+E T P
Sbjct: 127 FRTGKTQLCHTLCVTCQLPIEQGG-GEGKVLYIDTEGTFRP 166
Score = 116 bits (292), Expect = 4e-30
Identities = 46/59 (77%), Positives = 55/59 (93%)
Query: 257 ADPKKPVGGNIMAHASTTRISLRKGRGETRIAKIYDSPDMPEAEAMFAITNGGIADAKD 315
ADPKKP+GG+I+AHASTTR+SLRKGRGE RI KIYDSP++PE+EA+FAI+ GGI DAKD
Sbjct: 279 ADPKKPIGGHIIAHASTTRLSLRKGRGEQRICKIYDSPNLPESEAVFAISEGGIIDAKD 337
>gnl|CDD|131292 TIGR02238, recomb_DMC1, meiotic recombinase Dmc1. This model
describes DMC1, a subfamily of a larger family of DNA
repair and recombination proteins. It is eukaryotic only
and most closely related to eukaryotic RAD51. It also
resembles archaeal RadA (TIGR02236) and RadB (TIGR02237)
and bacterial RecA (TIGR02012). It has been
characterized for human as a recombinase active only in
meiosis.
Length = 313
Score = 221 bits (566), Expect = 8e-71
Identities = 95/145 (65%), Positives = 111/145 (76%), Gaps = 1/145 (0%)
Query: 76 VDILQNYNINVADIKKLKSVGLCTIKGVQMTTRRKMSQIKGFSEAKVDKIKEACMKICDN 135
+D LQ + IN ADIKKLKS G+CT+ GV MTTRR + +IKG SEAKVDKIKEA KI +
Sbjct: 1 IDKLQAHGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASKIINP 60
Query: 136 SFLTAAQVVEKRKQVFKITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITA 195
F+TA ++ +KRK+V KITTGS LD ILGGGIESM+ITE FGEFR GKTQLSHTL +TA
Sbjct: 61 GFITAFEISQKRKKVLKITTGSQALDGILGGGIESMSITEVFGEFRCGKTQLSHTLCVTA 120
Query: 196 QLPDETRGYTGGKVIYVDSENTLYP 220
QLP E G GKV Y+D+E T P
Sbjct: 121 QLPREM-GGGNGKVAYIDTEGTFRP 144
Score = 107 bits (269), Expect = 4e-27
Identities = 46/57 (80%), Positives = 52/57 (91%)
Query: 257 ADPKKPVGGNIMAHASTTRISLRKGRGETRIAKIYDSPDMPEAEAMFAITNGGIADA 313
ADPKKP+GG+++AHASTTRI LRKGRGE R+AK+YDSPDMPEAEA F IT GGIADA
Sbjct: 257 ADPKKPIGGHVLAHASTTRILLRKGRGEERVAKLYDSPDMPEAEASFQITEGGIADA 313
>gnl|CDD|215620 PLN03187, PLN03187, meiotic recombination protein DMC1 homolog;
Provisional.
Length = 344
Score = 186 bits (474), Expect = 1e-56
Identities = 85/170 (50%), Positives = 115/170 (67%), Gaps = 2/170 (1%)
Query: 59 AAVEEEDEEDGEEFFQDVDILQNYNINVADIKKLKSVGLCTIKGVQMTTRRKMSQIKGFS 118
VE E+ ++ E+ F+ +D L + IN D+KKL+ G+ T G+ M T++ ++ IKG S
Sbjct: 14 QLVEAEEVDEEEDLFESIDKLISQGINAGDVKKLQDAGIYTCNGLMMHTKKNLTGIKGLS 73
Query: 119 EAKVDKIKEACMKICDNSFLTAAQVVEKRKQVFKITTGSTELDKILGGGIESMAITEAFG 178
EAKVDKI EA K+ + F+T + + KRK V +ITTGS LD++LGGGIE+ ITEAFG
Sbjct: 74 EAKVDKICEAAEKLLNQGFITGSDALLKRKSVVRITTGSQALDELLGGGIETRCITEAFG 133
Query: 179 EFRTGKTQLSHTLSITAQLPDETRGYTGGKVIYVDSENTLYPLLNIIAIA 228
EFR+GKTQL+HTL +T QLP E G GKV Y+D+E T P I+ IA
Sbjct: 134 EFRSGKTQLAHTLCVTTQLPTEMGG-GNGKVAYIDTEGTFRPDR-IVPIA 181
Score = 97.5 bits (243), Expect = 3e-23
Identities = 37/58 (63%), Positives = 50/58 (86%)
Query: 258 DPKKPVGGNIMAHASTTRISLRKGRGETRIAKIYDSPDMPEAEAMFAITNGGIADAKD 315
DPKKP GG+++AHA+T R+ LRKG+GE R+ K++D+P++PEAEA F IT+GGI DAKD
Sbjct: 287 DPKKPAGGHVLAHAATIRLMLRKGKGEQRVCKVFDAPNLPEAEAEFQITSGGIMDAKD 344
>gnl|CDD|178728 PLN03186, PLN03186, DNA repair protein RAD51 homolog; Provisional.
Length = 342
Score = 182 bits (464), Expect = 2e-55
Identities = 81/170 (47%), Positives = 112/170 (65%), Gaps = 2/170 (1%)
Query: 59 AAVEEEDEEDGEEFFQDVDILQNYNINVADIKKLKSVGLCTIKGVQMTTRRKMSQIKGFS 118
A++EE+EE+ ++ LQ I DIKKLK G+ T++ + ++ + QIKG S
Sbjct: 11 QAMQEEEEEEAAHGPFPIEQLQASGIAALDIKKLKDAGIHTVESLAYAPKKDLLQIKGIS 70
Query: 119 EAKVDKIKEACMKICDNSFLTAAQVVEKRKQVFKITTGSTELDKILGGGIESMAITEAFG 178
EAKV+KI EA K+ F TA+Q+ +R+++ +ITTGS ELDKIL GGIE+ +ITE +G
Sbjct: 71 EAKVEKILEAASKLVPLGFTTASQLHAQRQEIIQITTGSRELDKILEGGIETGSITEIYG 130
Query: 179 EFRTGKTQLSHTLSITAQLPDETRGYTGGKVIYVDSENTLYPLLNIIAIA 228
EFRTGKTQL HTL +T QLP + G GK +Y+D+E T P +I IA
Sbjct: 131 EFRTGKTQLCHTLCVTCQLPLDQGGGE-GKAMYIDTEGTFRP-QRLIQIA 178
Score = 100 bits (251), Expect = 2e-24
Identities = 39/60 (65%), Positives = 49/60 (81%), Gaps = 1/60 (1%)
Query: 257 ADPK-KPVGGNIMAHASTTRISLRKGRGETRIAKIYDSPDMPEAEAMFAITNGGIADAKD 315
A P+ KP+GGNIMAHASTTR++LRKGRGE RI K+ SP +PEAEA F+I++ G+ D KD
Sbjct: 283 AGPQLKPIGGNIMAHASTTRLALRKGRGENRICKVISSPCLPEAEARFSISSEGVTDVKD 342
>gnl|CDD|233794 TIGR02239, recomb_RAD51, DNA repair protein RAD51. This eukaryotic
sequence family consists of RAD51, a protein involved in
DNA homologous recombination and repair. It is similar
in sequence the exclusively meiotic recombinase DMC1
(TIGR02238), to archaeal families RadA (TIGR02236) and
RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Length = 316
Score = 172 bits (439), Expect = 8e-52
Identities = 74/153 (48%), Positives = 105/153 (68%), Gaps = 2/153 (1%)
Query: 76 VDILQNYNINVADIKKLKSVGLCTIKGVQMTTRRKMSQIKGFSEAKVDKIKEACMKICDN 135
++ L+ I ADIKKL+ GL T++ V ++++ +IKG SEAK DKI K+
Sbjct: 1 IEKLEGNGITAADIKKLQEAGLHTVESVAYAPKKQLLEIKGISEAKADKILAEAAKLVPM 60
Query: 136 SFLTAAQVVEKRKQVFKITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITA 195
F TA + ++R++V ++TTGS ELDK+LGGGIE+ +ITE FGEFRTGKTQL HTL++T
Sbjct: 61 GFTTATEFHQRRQEVIQLTTGSKELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLAVTC 120
Query: 196 QLPDETRGYTGGKVIYVDSENTLYPLLNIIAIA 228
QLP + +G GK +Y+D+E T P ++AIA
Sbjct: 121 QLPID-QGGGEGKALYIDTEGTFRP-ERLLAIA 151
Score = 117 bits (295), Expect = 1e-30
Identities = 45/60 (75%), Positives = 50/60 (83%)
Query: 256 NADPKKPVGGNIMAHASTTRISLRKGRGETRIAKIYDSPDMPEAEAMFAITNGGIADAKD 315
DPKKP+GGNIMAHASTTR+SLRKGRGE RI KIYDSP +PE+EAMFAI GI D K+
Sbjct: 257 AGDPKKPIGGNIMAHASTTRLSLRKGRGEQRICKIYDSPCLPESEAMFAIYEDGIGDPKE 316
>gnl|CDD|235273 PRK04301, radA, DNA repair and recombination protein RadA;
Validated.
Length = 317
Score = 140 bits (355), Expect = 2e-39
Identities = 59/132 (44%), Positives = 89/132 (67%), Gaps = 2/132 (1%)
Query: 90 KKLKSVGLCTIKGVQMTTRRKMSQIKGFSEAKVDKIKEACMKICD-NSFLTAAQVVEKRK 148
+KL+ G T++ + + + +++S+ G E+ KI EA + D F TA +V+E+RK
Sbjct: 20 EKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAAREAADIGGFETALEVLERRK 79
Query: 149 QVFKITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGK 208
V KITTGS ELD++LGGGIE+ +ITE +GEF +GKTQ+ H L++ QLP+E +G GK
Sbjct: 80 NVGKITTGSKELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVQLPEE-KGGLEGK 138
Query: 209 VIYVDSENTLYP 220
+Y+D+E T P
Sbjct: 139 AVYIDTEGTFRP 150
Score = 94.9 bits (237), Expect = 2e-22
Identities = 33/63 (52%), Positives = 43/63 (68%), Gaps = 3/63 (4%)
Query: 251 VFFPLNADPKKPVGGNIMAHASTTRISLRKGRGETRIAKIYDSPDMPEAEAMFAITNGGI 310
FF DP +P+GG+I+ H +T RI LRK +G RIA++ DSP +PE EA+F IT GI
Sbjct: 258 AFFG---DPTQPIGGHILGHTATFRIYLRKSKGNKRIARLVDSPHLPEGEAVFRITEEGI 314
Query: 311 ADA 313
DA
Sbjct: 315 RDA 317
>gnl|CDD|117002 pfam08423, Rad51, Rad51. Rad51 is a DNA repair and recombination
protein and is a homologue of the bacterial ATPase RecA
protein.
Length = 261
Score = 138 bits (350), Expect = 3e-39
Identities = 55/100 (55%), Positives = 70/100 (70%), Gaps = 2/100 (2%)
Query: 129 CMKICDNSFLTAAQVVEKRKQVFKITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLS 188
K+ F TA ++ ++R +V +ITTGS ELDK+LGGGIE+ +ITE FGEFRTGKTQL
Sbjct: 1 ASKLVPMGFTTATELHQRRSEVIRITTGSKELDKLLGGGIETGSITEVFGEFRTGKTQLC 60
Query: 189 HTLSITAQLPDETRGYTGGKVIYVDSENTLYPLLNIIAIA 228
HTL +T QLP E G GK +Y+D+E T P I+AIA
Sbjct: 61 HTLCVTCQLPLEMGG-GEGKALYIDTEGTFRP-ERIVAIA 98
Score = 122 bits (308), Expect = 4e-33
Identities = 44/59 (74%), Positives = 52/59 (88%)
Query: 256 NADPKKPVGGNIMAHASTTRISLRKGRGETRIAKIYDSPDMPEAEAMFAITNGGIADAK 314
ADPKKP+GG+IMAHASTTR+ LRKGRGE R+ KIYDSP +PE+EA+FAI+ GGI DAK
Sbjct: 203 AADPKKPIGGHIMAHASTTRLYLRKGRGEQRVCKIYDSPCLPESEAVFAISEGGIGDAK 261
>gnl|CDD|131290 TIGR02236, recomb_radA, DNA repair and recombination protein RadA.
This family consists exclusively of archaeal RadA
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239), and archaeal RadB
(TIGR02237). This protein is involved in DNA repair and
recombination. The member from Pyrococcus horikoshii
contains an intein [DNA metabolism, DNA replication,
recombination, and repair].
Length = 310
Score = 134 bits (340), Expect = 2e-37
Identities = 64/132 (48%), Positives = 90/132 (68%), Gaps = 2/132 (1%)
Query: 90 KKLKSVGLCTIKGVQMTTRRKMSQIKGFSEAKVDKIKEACMKICD-NSFLTAAQVVEKRK 148
+KL+ G T + + + + +++S+I G SE KI +A K D F TA V+E+RK
Sbjct: 13 EKLREAGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAARKAADLGGFETADDVLERRK 72
Query: 149 QVFKITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGK 208
+ KITTGS ELD++LGGGIE+ AITE FGEF +GKTQ+ H L++ QLP+E +G GGK
Sbjct: 73 TIGKITTGSKELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNVQLPEE-KGGLGGK 131
Query: 209 VIYVDSENTLYP 220
+Y+D+ENT P
Sbjct: 132 AVYIDTENTFRP 143
Score = 86.0 bits (213), Expect = 3e-19
Identities = 33/62 (53%), Positives = 45/62 (72%), Gaps = 3/62 (4%)
Query: 251 VFFPLNADPKKPVGGNIMAHASTTRISLRKGRGETRIAKIYDSPDMPEAEAMFAITNGGI 310
FF DP +P+GG+I+ HA+T R+ LRKG+G+ RIA++ DSP +PE EA+F IT GI
Sbjct: 252 AFF---GDPTRPIGGHILGHAATFRVYLRKGKGDKRIARLVDSPHLPEGEAVFRITEKGI 308
Query: 311 AD 312
D
Sbjct: 309 ED 310
>gnl|CDD|238543 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. This group of
recombinases includes the eukaryotic proteins RAD51,
RAD55/57 and the meiosis-specific protein DMC1, and the
archaeal proteins radA and radB. They are closely
related to the bacterial RecA group. Rad51 proteins
catalyze a similiar recombination reaction as RecA,
using ATP-dependent DNA binding activity and a
DNA-dependent ATPase. However, this reaction is less
efficient and requires accessory proteins such as
RAD55/57 .
Length = 235
Score = 109 bits (274), Expect = 2e-28
Identities = 39/68 (57%), Positives = 50/68 (73%), Gaps = 1/68 (1%)
Query: 153 ITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKVIYV 212
+TTGS LD++LGGGIE+ +ITE FGEF +GKTQL H L++T QLP E G GK +Y+
Sbjct: 1 LTTGSKALDELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIE-LGGLEGKAVYI 59
Query: 213 DSENTLYP 220
D+E T P
Sbjct: 60 DTEGTFRP 67
Score = 103 bits (258), Expect = 4e-26
Identities = 41/60 (68%), Positives = 44/60 (73%)
Query: 251 VFFPLNADPKKPVGGNIMAHASTTRISLRKGRGETRIAKIYDSPDMPEAEAMFAITNGGI 310
DPKKP GGNI AHASTTR+ LRKGRGE RIAKI DSP +PE EA+FAIT GI
Sbjct: 175 GAAMFGGDPKKPAGGNIWAHASTTRLYLRKGRGEERIAKIVDSPHLPEGEAVFAITEEGI 234
>gnl|CDD|238687 cd01393, recA_like, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange. While prokaryotes have a single RecA
protein, eukaryotes have multiple RecA homologs such as
Rad51, DMC1 and Rad55/57. Archaea have the RecA-like
homologs radA and radB.
Length = 226
Score = 102 bits (256), Expect = 6e-26
Identities = 36/68 (52%), Positives = 46/68 (67%), Gaps = 1/68 (1%)
Query: 153 ITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKVIYV 212
I+TGS LD++LGGGI + ITE FGEF +GKTQL L++ AQLP G GKV+Y+
Sbjct: 1 ISTGSKALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLP-GELGGLEGKVVYI 59
Query: 213 DSENTLYP 220
D+E P
Sbjct: 60 DTEGAFRP 67
Score = 76.8 bits (190), Expect = 2e-16
Identities = 35/61 (57%), Positives = 41/61 (67%), Gaps = 6/61 (9%)
Query: 246 REDLIVFFPLNADPKKPVGGNIMAHASTTRISLRKGR---GETRIAKIYDSPDMPEAEAM 302
R + V F DP+ P GGN +AHASTTR+ LRKGR GE RIAK+ SP +PEAEA
Sbjct: 169 RAKVDVMFG---DPETPAGGNALAHASTTRLDLRKGRGIIGERRIAKVVKSPALPEAEAE 225
Query: 303 F 303
F
Sbjct: 226 F 226
>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 99.3 bits (248), Expect = 3e-24
Identities = 36/108 (33%), Positives = 54/108 (50%), Gaps = 8/108 (7%)
Query: 114 IKGFSEAKVDKIKEACMKICD-NSFLTAAQVVEKRKQVFKITTGSTELDKILGGGIESMA 172
+G E K + A ++ + A E+R+ + I+TGS LD+ LGGG+
Sbjct: 2 AQGIDEEKALEAALAQIEKAFGKGSIMALGGDERREDIEAISTGSLALDEALGGGLPRGR 61
Query: 173 ITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKVIYVDSENTLYP 220
ITE +G +GKT L+ L AQ P GGK ++D+E+ L P
Sbjct: 62 ITEIYGPESSGKTTLALQLVANAQKP-------GGKAAFIDTEHALDP 102
Score = 67.3 bits (165), Expect = 7e-13
Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 10/75 (13%)
Query: 246 REDLIVFFPLNADPKKPVGGNIMAHASTTRISLRKG------RGETRIAKIYDSPDMPEA 299
R + V F DP+ GGN + ++ R+ LR+ G R K+ + P
Sbjct: 196 RAKIGVMF---GDPETTTGGNALKFYASVRLDLRRIESLKEDVGNKRRVKVVKNKVAPPF 252
Query: 300 -EAMFAITNGGIADA 313
EA F IT GG D
Sbjct: 253 KEAEFDITYGGGIDR 267
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 60.6 bits (148), Expect = 8e-11
Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 7/64 (10%)
Query: 152 KITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKVIY 211
++ TG LD++LGGG E IT+ +G +GKT + L++ A G KVIY
Sbjct: 4 RLPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAK-------NGKKVIY 56
Query: 212 VDSE 215
+D+E
Sbjct: 57 IDTE 60
Score = 45.6 bits (109), Expect = 8e-06
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 251 VFFPLNADPKKPVGGNIMAHASTTRISLRKGRGETRIAKIYDSPDMPEAE-AMFAITNGG 309
V+ +++D +P+GG+ + H S T + L K R R A + PE E A F IT+ G
Sbjct: 161 VYSDIDSDGLRPLGGHTLEHWSKTILRLEKFRNGKRRATLEKHRSRPEGESAEFRITDRG 220
Query: 310 IADAK 314
I
Sbjct: 221 IEIID 225
>gnl|CDD|238688 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the bacterial
RecA. The precise function of radB is unclear.
Length = 218
Score = 52.9 bits (127), Expect = 3e-08
Identities = 27/63 (42%), Positives = 37/63 (58%), Gaps = 7/63 (11%)
Query: 153 ITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKVIYV 212
+ TG LD++LGGG+E +T+ +G TGKT +I QL ET G G KV Y+
Sbjct: 1 LPTGCKGLDELLGGGVERGTVTQVYGPPGTGKT------NIAIQLAVETAG-QGKKVAYI 53
Query: 213 DSE 215
D+E
Sbjct: 54 DTE 56
Score = 43.6 bits (103), Expect = 4e-05
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 251 VFFPLNADPKKPVGGNIMAHASTTRISLRKGRGETRIAKIYDSPDMPEAE-AMFAITNGG 309
V+ + + +P+GG+ + H S + L K R TR A + PE F IT+ G
Sbjct: 157 VYSDVGSGSVRPLGGHTLEHWSKVILRLEKLRVGTRRAVLEKHRFRPEGSSVYFRITDKG 216
Query: 310 I 310
I
Sbjct: 217 I 217
>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein RadB.
This family consists exclusively of archaeal RadB
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 50.5 bits (121), Expect = 2e-07
Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 7/56 (12%)
Query: 160 LDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKVIYVDSE 215
+D++LGGG+E IT+ +G +GKT + L++ A G KV+Y+D+E
Sbjct: 1 IDELLGGGVERGTITQIYGPPGSGKTNICMILAVNAA-------RQGKKVVYIDTE 49
Score = 35.1 bits (81), Expect = 0.029
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 251 VFFPLNADPKKPVGGNIMAHASTTRISLRKGRGETRIAKIYDSPDMPEAE-AMFAITNGG 309
V+ +N +P+GG+++ H S + L K RG R+A + PE E F IT+ G
Sbjct: 149 VYTDVNNGTLRPLGGHLLEHWSKVILRLEKFRGR-RLATLEKHRSRPEGESVYFRITDDG 207
Query: 310 I 310
I
Sbjct: 208 I 208
>gnl|CDD|225429 COG2874, FlaH, Predicted ATPases involved in biogenesis of archaeal
flagella [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 235
Score = 40.0 bits (94), Expect = 7e-04
Identities = 31/107 (28%), Positives = 48/107 (44%), Gaps = 16/107 (14%)
Query: 153 ITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKVIYV 212
I +G+ ELDK LGGGI ++ G+ TGK+ LS + L + R YV
Sbjct: 10 IKSGNDELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAYGF-LMNGYRVT------YV 62
Query: 213 DSENTLYPLLNIIAIASLVTLVGSRLPMSFHITREDLIVFFPLNADP 259
+E T+ + + S +S + L +FFP+N +P
Sbjct: 63 STELTVREFIKQMESLS--------YDVSDFLLSGRL-LFFPVNLEP 100
>gnl|CDD|238483 cd00983, recA, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange.
Length = 325
Score = 39.1 bits (92), Expect = 0.002
Identities = 27/77 (35%), Positives = 36/77 (46%), Gaps = 8/77 (10%)
Query: 145 EKRKQVFKITTGSTELDKILG-GGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRG 203
+ + V I TGS LD LG GG I E +G +GKT L L A+
Sbjct: 28 DAVQDVEVIPTGSLSLDIALGIGGYPKGRIIEIYGPESSGKTTL--ALHAIAEAQKL--- 82
Query: 204 YTGGKVIYVDSENTLYP 220
GG V ++D+E+ L P
Sbjct: 83 --GGTVAFIDAEHALDP 97
>gnl|CDD|215755 pfam00154, RecA, recA bacterial DNA recombination protein. RecA is
a DNA-dependent ATPase and functions in DNA repair
systems. RecA protein catalyzes an ATP-dependent DNA
strand-exchange reaction that is the central step in the
repair of dsDNA breaks by homologous recombination.
Length = 322
Score = 38.0 bits (89), Expect = 0.004
Identities = 29/96 (30%), Positives = 43/96 (44%), Gaps = 18/96 (18%)
Query: 126 KEACMKICDNSFLTAAQVVEKRKQVFKITTGSTELDKILG-GGIESMAITEAFGEFRTGK 184
K + M++ D + + V I+TGS LD LG GG+ I E +G +GK
Sbjct: 16 KGSIMRLGD----------KTVEDVEVISTGSLGLDIALGIGGLPKGRIIEIYGPESSGK 65
Query: 185 TQLSHTLSITAQLPDETRGYTGGKVIYVDSENTLYP 220
T L L A+ GG ++D+E+ L P
Sbjct: 66 TTL--ALHAIAEAQKA-----GGTAAFIDAEHALDP 94
>gnl|CDD|162659 TIGR02012, tigrfam_recA, protein RecA. This model describes
orthologs of the recA protein. RecA promotes
hybridization of homolgous regions of DNA. A segment of
ssDNA can be hybridized to another ssDNA region, or to a
dsDNA region. ATP is hydrolyzed in the process. Part of
the SOS respones, it is regulated by LexA via
autocatalytic cleavage [DNA metabolism, DNA replication,
recombination, and repair].
Length = 321
Score = 37.3 bits (87), Expect = 0.006
Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 8/69 (11%)
Query: 153 ITTGSTELDKILG-GGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKVIY 211
I+TGS LD LG GG+ I E +G +GKT L L A+ GG +
Sbjct: 36 ISTGSLSLDLALGVGGLPRGRIIEIYGPESSGKTTL--ALHAIAEAQKA-----GGTAAF 88
Query: 212 VDSENTLYP 220
+D+E+ L P
Sbjct: 89 IDAEHALDP 97
>gnl|CDD|236476 PRK09354, recA, recombinase A; Provisional.
Length = 349
Score = 35.5 bits (83), Expect = 0.029
Identities = 29/96 (30%), Positives = 43/96 (44%), Gaps = 18/96 (18%)
Query: 126 KEACMKICDNSFLTAAQVVEKRKQVFKITTGSTELDKILG-GGIESMAITEAFGEFRTGK 184
K + M++ D++ V I+TGS LD LG GG+ I E +G +GK
Sbjct: 24 KGSIMRLGDDA----------AMDVEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGK 73
Query: 185 TQLSHTLSITAQLPDETRGYTGGKVIYVDSENTLYP 220
T L L A+ GG ++D+E+ L P
Sbjct: 74 TTL--ALHAIAEAQKA-----GGTAAFIDAEHALDP 102
>gnl|CDD|180381 PRK06067, PRK06067, flagellar accessory protein FlaH; Validated.
Length = 234
Score = 34.9 bits (81), Expect = 0.031
Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 7/71 (9%)
Query: 153 ITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKVIYV 212
I+TG+ ELD+ LGGGI ++ G+ TGK+ LS A + KV +
Sbjct: 7 ISTGNEELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGK-------KVYVI 59
Query: 213 DSENTLYPLLN 223
+ENT L
Sbjct: 60 TTENTSKSYLK 70
>gnl|CDD|223993 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 34.5 bits (80), Expect = 0.067
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 8/64 (12%)
Query: 152 KITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKVIY 211
+I+TG ELD++LGGG+ ++ G+ GK+ L L + A+L GKV+Y
Sbjct: 74 RISTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTL--LLQVAARLAK------RGKVLY 125
Query: 212 VDSE 215
V E
Sbjct: 126 VSGE 129
>gnl|CDD|77219 PRK09519, recA, DNA recombination protein RecA; Reviewed.
Length = 790
Score = 34.7 bits (79), Expect = 0.071
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 8/77 (10%)
Query: 145 EKRKQVFKITTGSTELDKILG-GGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRG 203
E R+ + I TGS LD LG GG+ + E +G +GKT ++ AQ
Sbjct: 33 EARQPISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQA------ 86
Query: 204 YTGGKVIYVDSENTLYP 220
GG ++D+E+ L P
Sbjct: 87 -AGGVAAFIDAEHALDP 102
>gnl|CDD|163593 TIGR03881, KaiC_arch_4, KaiC domain protein, PAE1156 family.
Members of this protein family are archaeal
single-domain KaiC_related proteins, homologous to the
Cyanobacterial circadian clock cycle protein KaiC, an
autokinase/autophosphorylase that has two copies of the
domain.
Length = 229
Score = 33.2 bits (76), Expect = 0.11
Identities = 23/66 (34%), Positives = 29/66 (43%), Gaps = 7/66 (10%)
Query: 152 KITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKVIY 211
+++TG LDK+L GGI GE TGKT L D G VIY
Sbjct: 1 RLSTGVEGLDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHF-AYKGLRD------GDPVIY 53
Query: 212 VDSENT 217
V +E +
Sbjct: 54 VTTEES 59
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 33.2 bits (76), Expect = 0.14
Identities = 20/66 (30%), Positives = 31/66 (46%), Gaps = 7/66 (10%)
Query: 150 VFKITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKV 209
+ +I TG LD+ILGGG+ ++ G TGKT + + + G V
Sbjct: 2 MERIPTGIPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQF-LYEGARE------GEPV 54
Query: 210 IYVDSE 215
+YV +E
Sbjct: 55 LYVSTE 60
>gnl|CDD|181459 PRK08533, PRK08533, flagellar accessory protein FlaH; Reviewed.
Length = 230
Score = 32.7 bits (75), Expect = 0.16
Identities = 28/99 (28%), Positives = 43/99 (43%), Gaps = 29/99 (29%)
Query: 149 QVFKITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLS------------ITAQ 196
++ KI EL K LGGGI + ++ G+ TGK+ LS L+ ++ Q
Sbjct: 2 ELAKIELSRDELHKRLGGGIPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSTQ 61
Query: 197 LPD-------ETRGY------TGGKVIYVDSENTLYPLL 222
L + GY GK++Y+ +YPLL
Sbjct: 62 LTTTEFIKQMMSLGYDINKKLISGKLLYI----PVYPLL 96
>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 = 31.3 bits (71), Expect = 0.32
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 7/43 (16%)
Query: 173 ITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKVIYVDSE 215
+ FG +GKT L+ L++ GGKV+YVD E
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATK-------GGKVVYVDIE 36
>gnl|CDD|227624 COG5308, NUP170, Nuclear pore complex subunit [Intracellular
trafficking and secretion].
Length = 1263
Score = 32.6 bits (74), Expect = 0.35
Identities = 19/94 (20%), Positives = 36/94 (38%), Gaps = 14/94 (14%)
Query: 2 SQIMMQKKMSQIVDENNNNLSQMSLVQQQPSQGRASSQQ-------------SVHQARSS 48
+ Q K S+ EN L ++ ++++QP+ + +V++ S
Sbjct: 364 LMQLEQNKGSRDFYENLF-LDRLVMLKRQPNSSDMTETTEMSTIISPGIYFSAVNKRYDS 422
Query: 49 SQQSTGSVRTAAVEEEDEEDGEEFFQDVDILQNY 82
S + GS TA D+ D IL++
Sbjct: 423 SNTNKGSTVTAISLNVDQHKLWVSIPDYGILKSS 456
>gnl|CDD|238541 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein
is not related to archael radA any more than is to other
RecA-like NTPases. Sms has a role in recombination and
recombinational repair and is responsible for the
stabilization or processing of branched DNA molecules.
Length = 372
Score = 31.1 bits (71), Expect = 0.71
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 7/64 (10%)
Query: 152 KITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKVIY 211
+I TG ELD++LGGG+ ++ G+ GK+ L L + A+L GGKV+Y
Sbjct: 63 RIPTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTL--LLQVAARLAK-----RGGKVLY 115
Query: 212 VDSE 215
V E
Sbjct: 116 VSGE 119
>gnl|CDD|221001 pfam11146, DUF2905, Protein of unknown function (DUF2905). This is
a family of bacterial proteins conserved of unknown
function.
Length = 65
Score = 27.8 bits (63), Expect = 1.3
Identities = 9/38 (23%), Positives = 15/38 (39%), Gaps = 6/38 (15%)
Query: 224 IIAIASLVTLVGS------RLPMSFHITREDLIVFFPL 255
++ + L+ RLP I R + +FPL
Sbjct: 11 VLLVLGLLLPWLGKLLGLGRLPGDIRIRRGNFTFYFPL 48
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 30.1 bits (69), Expect = 1.4
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 152 KITTGSTELDKILGGGI 168
+I+TG ELD++LGGG+
Sbjct: 61 RISTGIGELDRVLGGGL 77
>gnl|CDD|226080 COG3550, HipA, Toxin module HipA, protein kinase of
phosphatidylinositol 3/4-kinase superfamily [General
function prediction only].
Length = 392
Score = 29.7 bits (67), Expect = 2.1
Identities = 18/72 (25%), Positives = 22/72 (30%), Gaps = 5/72 (6%)
Query: 245 TREDLIVFFPLNADPKKPVGGNIMAHASTTRISLRKGRGETRIAKIYDSPDMPEAEA--- 301
L+ D P I A + R T I K D+ PEA
Sbjct: 124 ALTALLRKASGIPDGITPTVHIIKAPDGLYAVKSNSDRISTSIDKELDALRYPEAAGLEV 183
Query: 302 --MFAITNGGIA 311
M A GG+A
Sbjct: 184 LCMEAARQGGVA 195
>gnl|CDD|221668 pfam12619, MCM2_N, Mini-chromosome maintenance protein 2. This
domain family is found in eukaryotes, and is typically
between 138 and 153 amino acids in length. The family
is found in association with pfam00493. Mini-chromosome
maintenance (MCM) proteins are essential for DNA
replication. These proteins use ATPase activity to
perform this function.
Length = 145
Score = 28.8 bits (65), Expect = 2.3
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 62 EEEDEEDGEEFFQD 75
E E+EEDGE+ F D
Sbjct: 20 EAEEEEDGEDLFGD 33
>gnl|CDD|185594 PTZ00395, PTZ00395, Sec24-related protein; Provisional.
Length = 1560
Score = 29.3 bits (65), Expect = 3.3
Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 4/65 (6%)
Query: 28 QQQPSQGRASSQQSVHQARSSSQQSTGSVRTAAVEEEDEEDGEEFFQDVDILQNYNINVA 87
+++ +++Q Q+ S +S+ S ++ E E + GEE + L IN
Sbjct: 548 KREDHPEGGTNRQKYEQSDEESVESSSSENSSENENEVTDKGEEIYS----LLKKTINRI 603
Query: 88 DIKKL 92
D+ K+
Sbjct: 604 DMNKI 608
>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 = 29.0 bits (65), Expect = 3.8
Identities = 22/67 (32%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 152 KITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLSHTLSITAQLPDETRGYTGGKVIY 211
+ ++G ELD++LGGGI ++ G+ GK+ L L + QL KV+Y
Sbjct: 75 RFSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTL--LLQVACQLAKNQM-----KVLY 127
Query: 212 VDSENTL 218
V E +L
Sbjct: 128 VSGEESL 134
>gnl|CDD|223971 COG1041, COG1041, Predicted DNA modification methylase [DNA
replication, recombination, and repair].
Length = 347
Score = 28.9 bits (65), Expect = 4.0
Identities = 17/91 (18%), Positives = 26/91 (28%), Gaps = 13/91 (14%)
Query: 107 TRRKMSQIKGFSEAKVDKIKEACMKICDNSFLTAAQVVEKRKQVFKITTGSTELDKILGG 166
R++ KG +A I V K + TE DK+ G
Sbjct: 108 RRKEQDVDKGLEKAIGGAIPSEG------------LRVSLSKPDEVVRVVVTE-DKVYLG 154
Query: 167 GIESMAITEAFGEFRTGKTQLSHTLSITAQL 197
+AF + K S+ +L
Sbjct: 155 LTVRERDRKAFEKRDPEKRPFFRPGSMDPRL 185
>gnl|CDD|163592 TIGR03880, KaiC_arch_3, KaiC domain protein, AF_0351 family. This
model represents a rather narrowly distributed archaeal
protein family in which members have a single copy of
the KaiC domain. This stands in contrast to the
circadian clock protein KaiC itself, with two copies of
the domain. Members are expected to have weak ATPase
activity, by homology to the
autokinase/autophosphorylase KaiC itself.
Length = 224
Score = 28.5 bits (64), Expect = 4.2
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 160 LDKILGGGIESMAITEAFGEFRTGKTQLS 188
LD++LGGG + GE+ TGKT S
Sbjct: 5 LDEMLGGGFPEGHVIVVIGEYGTGKTTFS 33
>gnl|CDD|165563 PHA03308, PHA03308, transcriptional regulator ICP4; Provisional.
Length = 1463
Score = 29.0 bits (64), Expect = 4.3
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 31 PSQGRASSQQSVHQARSSSQQSTGSVRTAAVEEEDEEDGEE 71
P + S ++H + SSS S S +++ EEDG+E
Sbjct: 1240 PCPDLSESSSTMHSSSSSSSSSCSSSSSSSDSSSSEEDGDE 1280
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 28.7 bits (65), Expect = 4.9
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 153 ITTGSTELDKILGGGIESMAITEAFGEFRTGKTQLS 188
I++G +LD++LGGG +I G TGKT L+
Sbjct: 255 ISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLLA 290
>gnl|CDD|131703 TIGR02655, circ_KaiC, circadian clock protein KaiC. Members of
this family are the circadian clock protein KaiC, part
of the kaiABC operon that controls circadian rhythm. It
may be universal in Cyanobacteria. Each member has two
copies of the KaiC domain (pfam06745), which is also
found in other proteins. KaiC performs
autophosphorylation and acts as its own transcriptional
repressor [Cellular processes, Other].
Length = 484
Score = 28.4 bits (63), Expect = 5.2
Identities = 18/53 (33%), Positives = 27/53 (50%)
Query: 135 NSFLTAAQVVEKRKQVFKITTGSTELDKILGGGIESMAITEAFGEFRTGKTQL 187
N F A + +R ++++G LD++ GGG +I A G TGKT L
Sbjct: 227 NIFPLGAMRLTQRSSNVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLL 279
>gnl|CDD|238429 cd00833, PKS, polyketide synthases (PKSs) polymerize simple fatty
acids into a large variety of different products, called
polyketides, by successive decarboxylating Claisen
condensations. PKSs can be divided into 2 groups,
modular type I PKSs consisting of one or more large
multifunctional proteins and iterative type II PKSs,
complexes of several monofunctional subunits.
Length = 421
Score = 28.3 bits (64), Expect = 5.6
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 9/38 (23%)
Query: 164 LGGGIESMAITEAFGEFRTG---------KTQLSHTLS 192
LG IE A+ + FG R+ K+ + H +
Sbjct: 311 LGDPIEVEALAKVFGGSRSADQPLLIGSVKSNIGHLEA 348
>gnl|CDD|219293 pfam07093, SGT1, SGT1 protein. This family consists of several
eukaryotic SGT1 proteins. Human SGT1 or hSGT1 is known
to suppress GCR2 and is highly expressed in the muscle
and heart. The function of this family is unknown
although it has been speculated that SGT1 may be
functionally analogous to the Gcr2p protein of
Saccharomyces cerevisiae which is known to be a
regulatory factor of glycolytic gene expression.
Length = 557
Score = 28.5 bits (64), Expect = 5.9
Identities = 12/70 (17%), Positives = 24/70 (34%), Gaps = 12/70 (17%)
Query: 15 DENNNNLSQMSLVQQQPSQGRASSQQSVHQA------RSSSQQSTGSVRTAAVEEEDEED 68
DE+++ S S + ++ S + + + ED++D
Sbjct: 493 DEDDDEDEDSS------SDSTLEELEEYMDQMDAELKQTDSSNNADISNSGSSGAEDDDD 546
Query: 69 GEEFFQDVDI 78
E + VDI
Sbjct: 547 DIEGVEPVDI 556
>gnl|CDD|235136 PRK03598, PRK03598, putative efflux pump membrane fusion protein;
Provisional.
Length = 331
Score = 27.6 bits (62), Expect = 8.1
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 28 QQQPSQGRASSQQSVHQARSSSQQSTGSVRTA 59
QQ + R S + ARSS Q+ ++++A
Sbjct: 133 QQGLWKSRTISANDLENARSSRDQAQATLKSA 164
>gnl|CDD|241386 cd13232, Ig-PH_SCAB1, Stomatal Closure Related Actin-Binding
Protein 1 Pleckstrin homology-like domain. SCAB1 is an
actin-binding protein that interacts with actin
filaments and regulates stomatal movement. SCAB1 is
composed of an actin-binding domain, two coiled-coil
(CC) domains, and a fused immunoglobulin (Ig) and PH
(Ig-PH) domain. SCAB1 homologs are widely present, often
in multiple copies (three in Arabidopsis), in plants
including eudicots, monocots, ferns and mosses, but are
not found in algae and non-plant species. The C-terminal
PH domain binds weakly with inositol phosphates via an
atypical basic surface patch. SCAB1 forms a dimeric
structure via its coiled-coil domains. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 119
Score = 26.7 bits (59), Expect = 8.9
Identities = 17/53 (32%), Positives = 21/53 (39%), Gaps = 12/53 (22%)
Query: 268 MAHASTTRISLRKGRGETRIAKIYDSPDM----------PEAEAMFAITNGGI 310
M H R+ LRKGR T AK S M A A+F + G+
Sbjct: 38 MFHIGKLRMKLRKGR--TTKAKEKYSSGMQLCGARGGGQAAARALFWLVKKGL 88
>gnl|CDD|234305 TIGR03672, rpl4p_arch, 50S ribosomal protein L4P. One of the
primary rRNA binding proteins, this protein initially
binds near the 5'-end of the 23S rRNA. It is important
during the early stages of 50S assembly. It makes
multiple contacts with different domains of the 23S rRNA
in the assembled 50S subunit and ribosome.
Length = 251
Score = 27.6 bits (62), Expect = 9.1
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 246 REDLI--VFFPLNADPKKPVGGNIMAHASTTRISLRKGRGETRIAKI 290
R DLI + +P G + A T+ S GRG R+ +I
Sbjct: 27 RPDLIKRAVLAAQTNRLQPYGADPYAGKRTSAESWGSGRGIARVPRI 73
>gnl|CDD|234084 TIGR03007, pepcterm_ChnLen, polysaccharide chain length determinant
protein, PEP-CTERM locus subfamily. Members of this
protein family belong to the family of polysaccharide
chain length determinant proteins (pfam02706). All are
found in species that encode the PEP-CTERM/exosortase
system predicted to act in protein sorting in a number
of Gram-negative bacteria, and are found near the epsH
homolog that is the putative exosortase gene [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 498
Score = 27.7 bits (62), Expect = 9.9
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 190 TLSITAQLPDETRGYTGGKVIYVDSENTLYPLLNIIAI 227
+ LPD Y +YVD+++ L PLL IA+
Sbjct: 28 GWGVVYFLPDR---YEASARVYVDTQSVLRPLLKGIAV 62
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
0.314 0.129 0.348
Gapped
Lambda K H
0.267 0.0626 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,392,679
Number of extensions: 1446425
Number of successful extensions: 1369
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1344
Number of HSP's successfully gapped: 74
Length of query: 315
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 218
Effective length of database: 6,635,264
Effective search space: 1446487552
Effective search space used: 1446487552
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: 42 (22.0 bits)
S2: 59 (26.7 bits)