RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780552|ref|YP_003064965.1| Holliday junction DNA helicase
RuvB [Candidatus Liberibacter asiaticus str. psy62]
(334 letters)
>gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 549 bits (1417), Expect = e-157
Identities = 201/322 (62%), Positives = 255/322 (79%), Gaps = 1/322 (0%)
Query: 9 SRNVSQEDADISL-LRPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGK 67
+ +E+ +I LRP++L+EF GQ + NLK+FIEAAK R EALDHVL GPPGLGK
Sbjct: 5 PETLEEEEDEIERSLRPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGK 64
Query: 68 TTLAQVVARELGVNFRSTSGPVIAKAGDLAALLTNLEDRDVLFIDEIHRLSIIVEEILYP 127
TTLA ++A E+GVN R TSGP + K GDLAA+LTNLE+ DVLFIDEIHRLS +VEEILYP
Sbjct: 65 TTLANIIANEMGVNIRITSGPALEKPGDLAAILTNLEEGDVLFIDEIHRLSPVVEEILYP 124
Query: 128 AMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLTNPLQDRFGIPIRLNFYEIED 187
AMEDF+LD+M+G+GP+ARS++++L FTLI ATTR GLLT+PL+DRFGI RL FY +E+
Sbjct: 125 AMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRAGLLTSPLRDRFGIVQRLEFYTVEE 184
Query: 188 LKTIVQRGAKLTGLAVTDEAACEIAMRSRGTPRIAGRLLRRVRDFAEVAHAKTITREIAD 247
L+ IV+R A++ G+ + +E A EIA RSRGTPRIA RLLRRVRDFA+V IT+EIAD
Sbjct: 185 LEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIAD 244
Query: 248 AALLRLAIDKMGFDQLDLRYLTMIARNFGGGPVGIETISAGLSEPRDAIEDLIEPYMIQQ 307
AL L +D++G D++D +YL I FGGGPVG++T++A L E RD IED+ EPY+IQQ
Sbjct: 245 KALDMLGVDELGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQ 304
Query: 308 GFIQRTPRGRLLMPIAWQHLGI 329
GFIQRTPRGR+ P A++HLG+
Sbjct: 305 GFIQRTPRGRVATPKAYEHLGL 326
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
RuvA specifically binds Holliday junctions as a sandwich
of two tetramers and maintains the configuration of the
junction. It forms a complex with two hexameric rings of
RuvB, the subunit that contains helicase activity. The
complex drives ATP-dependent branch migration of the
Holliday junction recombination intermediate. The
endonuclease RuvC resolves junctions.
Length = 305
Score = 427 bits (1099), Expect = e-120
Identities = 183/305 (60%), Positives = 236/305 (77%)
Query: 25 RTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNFRS 84
+ L EF GQ + L++FIEAAK R EALDH+L GPPGLGKTTLA ++A E+GVN +
Sbjct: 1 KLLAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNLKI 60
Query: 85 TSGPVIAKAGDLAALLTNLEDRDVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSA 144
TSGP + K GDLAA+LTNLE+ DVLFIDEIHRLS VEE+LYPAMEDF+LD+++G+GPSA
Sbjct: 61 TSGPALEKPGDLAAILTNLEEGDVLFIDEIHRLSPAVEELLYPAMEDFRLDIVIGKGPSA 120
Query: 145 RSVKINLSRFTLIAATTRVGLLTNPLQDRFGIPIRLNFYEIEDLKTIVQRGAKLTGLAVT 204
RSV+++L FTL+ ATTR G+LT+PL+DRFGI +RL FY +E+L IV R A L + +
Sbjct: 121 RSVRLDLPPFTLVGATTRAGMLTSPLRDRFGIILRLEFYTVEELAEIVSRSAGLLNVEIE 180
Query: 205 DEAACEIAMRSRGTPRIAGRLLRRVRDFAEVAHAKTITREIADAALLRLAIDKMGFDQLD 264
EAA EIA RSRGTPRIA RLLRRVRDFA+V K I R+IA AL L ID++G D++D
Sbjct: 181 PEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMIDELGLDEID 240
Query: 265 LRYLTMIARNFGGGPVGIETISAGLSEPRDAIEDLIEPYMIQQGFIQRTPRGRLLMPIAW 324
+ L+++ F GGPVG++T++A L E D IED+ EPY++Q GF+QRTPRGR+ +A+
Sbjct: 241 RKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRGRIATELAY 300
Query: 325 QHLGI 329
+HLG+
Sbjct: 301 EHLGL 305
>gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 92.5 bits (231), Expect = 1e-19
Identities = 76/262 (29%), Positives = 114/262 (43%), Gaps = 62/262 (23%)
Query: 21 LLRPRTLEEFTGQ---VEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARE 77
+RP+TL+E GQ + L+ IEA + L ++ GPPG GKTTLA+++A
Sbjct: 5 RMRPKTLDEVVGQEHLLGPGKPLRRMIEAGR-----LSSMILWGPPGTGKTTLARIIAGA 59
Query: 78 LGVNFRSTSGPVIAKAGDL------AALLTNLEDRDVLFIDEIHRLSIIVEEILYPAMED 131
F + S V + DL A + R +LFIDEIHR + ++ L P +ED
Sbjct: 60 TDAPFEALSA-VTSGVKDLREVIEEARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVED 118
Query: 132 FQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLTNPLQDRFGI--PI--RLNFYEI-- 185
G TLI ATT NP F + + R +E+
Sbjct: 119 -------G-------------TITLIGATTE-----NPS---FEVNPALLSRAQVFELKP 150
Query: 186 ---EDLKTIVQRGAKLTG---LAVTDEAACEIAMRSRGTPRIAGRLLRRVRDFAEVAHAK 239
ED++ +++R + + + DEA +A + G R A LL + A
Sbjct: 151 LSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLL----ELA-ALGVD 205
Query: 240 TITREIADAALLRLAI--DKMG 259
+IT E+ + AL + A DK G
Sbjct: 206 SITLELLEEALQKRAARYDKDG 227
>gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 64.7 bits (158), Expect = 3e-11
Identities = 61/195 (31%), Positives = 84/195 (43%), Gaps = 55/195 (28%)
Query: 20 SLLRPRTLEEFTGQVEACSNLKVFIEAAKA---RAEALDHV---LFVGPPGLGKTTLAQV 73
LRPRTLEEF GQ I RA D V + GPPG+GKTTLA++
Sbjct: 20 DRLRPRTLEEFVGQDH--------ILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARI 71
Query: 74 VARELGVNFRSTSGPVIAKAGDLAALLTNLED-------RDVLFIDEIHRLSIIVEEILY 126
+A +F S + V+A DL A + ++ R +LFIDE+HR + ++ L
Sbjct: 72 IANHTRAHFSSLNA-VLAGVKDLRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQDALL 130
Query: 127 PAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLTNP-------LQDRFGIPIR 179
P +E+ + TLI ATT NP L R + R
Sbjct: 131 PWVENGTI--------------------TLIGATTE-----NPYFEVNKALVSRSRL-FR 164
Query: 180 LNFYEIEDLKTIVQR 194
L EDL +++R
Sbjct: 165 LKSLSDEDLHQLLKR 179
>gnl|CDD|179026 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 56.0 bits (136), Expect = 1e-08
Identities = 27/56 (48%), Positives = 35/56 (62%), Gaps = 5/56 (8%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78
RPRTL+E GQ E LK +++ + + H+LF GPPG GKTT A +AREL
Sbjct: 12 RPRTLDEIVGQEEIVERLKSYVKE-----KNMPHLLFAGPPGTGKTTAALALAREL 62
>gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 51.5 bits (124), Expect = 3e-07
Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 9/61 (14%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEA----AKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78
RP+TL + G +A L+ +IE+ +A +L GPPG+GKT+LA +A +
Sbjct: 9 RPKTLSDVVGNEKAKEQLREWIESWLKGKPKKA-----LLLYGPPGVGKTSLAHALANDY 63
Query: 79 G 79
G
Sbjct: 64 G 64
>gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 139
Score = 49.6 bits (119), Expect = 1e-06
Identities = 36/139 (25%), Positives = 55/139 (39%), Gaps = 20/139 (14%)
Query: 56 HVLFVGPPGLGKTTLAQVVARELG-------VNFRSTS-----GPVIAKAGDLA----AL 99
VL VGPPG GK+ LA+ +A L R T+ G G + L
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIANGTTSWVDGPL 60
Query: 100 LTNLEDRDVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAA 159
+ + ++ +DEI+R + V L +++ +L L G + RF LIA
Sbjct: 61 VRAAREGEIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKVAPDDFAKRFRLIAT 120
Query: 160 TTRVGLLTN----PLQDRF 174
+ N L+ RF
Sbjct: 121 MNPLDRGLNELSPALRSRF 139
>gnl|CDD|163066 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC.
Length = 615
Score = 47.5 bits (113), Expect = 5e-06
Identities = 24/58 (41%), Positives = 30/58 (51%), Gaps = 5/58 (8%)
Query: 20 SLLRPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARE 77
SLLRPR E GQ A L AK + H++ GPPG+GKTT A++ E
Sbjct: 146 SLLRPRAFSEIVGQERAIKAL-----LAKVASPFPQHIILYGPPGVGKTTAARLALEE 198
>gnl|CDD|162267 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 = 45.7 bits (108), Expect = 2e-05
Identities = 37/115 (32%), Positives = 51/115 (44%), Gaps = 16/115 (13%)
Query: 26 TLEEFTGQVEACSNLKVFIEAAKARAEALDH--------VLFVGPPGLGKTTLAQVVARE 77
T E+ G EA ++ +E E +H VL GPPG GKT LA+ VA E
Sbjct: 176 TYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANE 235
Query: 78 LGVNFRSTSGPVIAKA------GDLAALLTNLEDR--DVLFIDEIHRLSIIVEEI 124
G F S +GP I L + E+ ++FIDEI ++ EE+
Sbjct: 236 AGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEV 290
Score = 42.2 bits (99), Expect = 2e-04
Identities = 20/34 (58%), Positives = 22/34 (64%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVI 90
VL GPPG GKT LA+ VA E G NF + GP I
Sbjct: 490 VLLFGPPGTGKTLLAKAVATESGANFIAVRGPEI 523
>gnl|CDD|128665 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 = 45.1 bits (106), Expect = 2e-05
Identities = 37/133 (27%), Positives = 51/133 (38%), Gaps = 27/133 (20%)
Query: 56 HVLFVGPPGLGKTTLAQVVARELG--------------------------VNFRSTSGPV 89
+L VGPPG GKTTLA+ +ARELG V + SG
Sbjct: 4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSG 63
Query: 90 IAKAGDLAALLTNLEDRDVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKI 149
+ AL DVL +DEI L +E L +E+ +L L++ + +
Sbjct: 64 ELRLRLALALA-RKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILT 122
Query: 150 NLSRFTLIAATTR 162
L A R
Sbjct: 123 TNDEKDLGPALLR 135
>gnl|CDD|183503 PRK12402, PRK12402, replication factor C small subunit 2;
Reviewed.
Length = 337
Score = 43.8 bits (104), Expect = 6e-05
Identities = 22/56 (39%), Positives = 29/56 (51%), Gaps = 5/56 (8%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78
RP LE+ GQ E L +++ L H+L GPPG GKT + +AREL
Sbjct: 10 RPALLEDILGQDEVVERLSRAVDSPN-----LPHLLVQGPPGSGKTAAVRALAREL 60
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 43.6 bits (103), Expect = 7e-05
Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 6/62 (9%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARE-LGVN 81
RP L++ G +A S L+V AR + +++ GPPG GKTT +A E LG N
Sbjct: 8 RPTKLDDIVGNEDAVSRLQVI-----ARDGNMPNLILSGPPGTGKTTSILALAHELLGPN 62
Query: 82 FR 83
++
Sbjct: 63 YK 64
>gnl|CDD|162266 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.
Length = 495
Score = 43.4 bits (103), Expect = 8e-05
Identities = 21/31 (67%), Positives = 22/31 (70%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSG 87
VL VGPPG GKT LA+ VA E GV F S SG
Sbjct: 91 VLLVGPPGTGKTLLAKAVAGEAGVPFFSISG 121
>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of
this protein family are the stage V sporulation protein
K (SpoVK), a close homolog of the Rubisco expression
protein CbbX (TIGR02880) and a members of the ATPase
family associated with various cellular activities
(pfam00004). Members are strictly limited to bacterial
endospore-forming species, but are not universal in this
group and are missing from the Clostridium group.
Length = 261
Score = 43.2 bits (102), Expect = 9e-05
Identities = 54/208 (25%), Positives = 87/208 (41%), Gaps = 44/208 (21%)
Query: 56 HVLFVGPPGLGKTTLAQVVAR---ELGVNFRSTSGPVI-AKAGDLAALL---TNLEDRD- 107
H++F G PG GKTT+A+++ + E+ V + G +I + DL T + R+
Sbjct: 44 HMIFKGNPGTGKTTVARILGKLFKEMNV---LSKGHLIEVERADLVGEYIGHTAQKTREV 100
Query: 108 -------VLFIDEIHRLSIIVE--------EILYPAMEDFQLDLMVGEGPSARSVKINLS 152
VLFIDE + L+ E + L MED + + ++ +
Sbjct: 101 IKKALGGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVL----ILAGYSDEMD 156
Query: 153 RFTLIAATTRVGLLTNP-LQDRFGIPIRLNFYEIEDLKTIVQRGAKLTGLAVTDEAACEI 211
F L NP L+ RF I I Y +E+L I +R K +T+EA ++
Sbjct: 157 YF----------LSLNPGLRSRFPISIDFPDYTVEELMEIAERMVKEREYKLTEEAKWKL 206
Query: 212 AMRSRGTPRIAGRLL---RRVRDFAEVA 236
+++ R R VR+ E A
Sbjct: 207 REHLYKVDQLSSREFSNARYVRNIIEKA 234
>gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 367
Score = 42.6 bits (100), Expect = 2e-04
Identities = 70/252 (27%), Positives = 100/252 (39%), Gaps = 65/252 (25%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNF 82
RP+T ++ GQ + L IE A+AL LF GP G+GKTT A+++AR+ +N
Sbjct: 12 RPQTFDDVVGQSHITNTLLNAIENNHL-AQAL---LFCGPRGVGKTTCARILARK--INQ 65
Query: 83 RSTSGPVIAKAGDLAAL----------LTNLEDR----------DVLFIDEIHRLSIIVE 122
P + ++ L + NL D+ + IDE+H LS
Sbjct: 66 PGYDDPNEDFSFNIFELDAASNNSVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLSSAA- 124
Query: 123 EILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLTNPLQDRFGIPIRLNF 182
F L E P A ++ I ATT + IP L+
Sbjct: 125 ---------FNAFLKTLEEPPAHAI--------FILATTEKHKI---------IPTILSR 158
Query: 183 YEIEDLKTIVQRGAK--LTGLAVT------DEAACEIAMRSRGTPRIAGRLLRRVRDFAE 234
+I D K I + K L G+AV D+A IA ++ G R A + RV F
Sbjct: 159 CQIFDFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSIFDRVVTFC- 217
Query: 235 VAHAKTITREIA 246
K ITR+
Sbjct: 218 ---GKNITRQAV 226
>gnl|CDD|179744 PRK04132, PRK04132, replication factor C small subunit;
Provisional.
Length = 846
Score = 42.5 bits (100), Expect = 2e-04
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 11/63 (17%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGK--TTLAQVVA----R 76
RP+ L++ GQ LK +++ ++ H+LF GPPG+GK T +V+A
Sbjct: 14 RPQRLDDIVGQEHIVKRLKHYVKTG-----SMPHLLFAGPPGVGKCLTGDTKVIANGELF 68
Query: 77 ELG 79
E+G
Sbjct: 69 EIG 71
>gnl|CDD|184926 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 42.1 bits (99), Expect = 2e-04
Identities = 66/256 (25%), Positives = 99/256 (38%), Gaps = 53/256 (20%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNF 82
RP+T E GQ K+ I A K + + ++ F GP G GKTT+A+++A+ L
Sbjct: 9 RPKTFSEVVGQDHV---KKLIINALKKNSISHAYI-FAGPRGTGKTTVARILAKSLNCEN 64
Query: 83 RSTSGPV----IAKAGDLAALLTNLE-----DRDVLFIDEIHRLS--------------I 119
R P ++ D + +E +R IDEI ++
Sbjct: 65 RKGVEPCNECRACRSIDEGTFMDVIELDAASNRG---IDEIRKIRDAVGYRPMEGKYKVY 121
Query: 120 IVEEILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLTNPLQDRFGIPIR 179
I++E+ E F L E P + V + AT TN + I R
Sbjct: 122 IIDEVHMLTKEAFNALLKTLEEPPSHVV--------FVLAT------TNLEKVPPTIISR 167
Query: 180 LNFYE-----IEDLKTIVQRGAKLTGLAVTDEAACEIAMRSRGTPRIAGRLLRRVRDFAE 234
E E + +Q A+ G+ + EA IA R+ G R A +L +V F+E
Sbjct: 168 CQVIEFRNISDELIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTMLEQVWKFSE 227
Query: 235 VAHAKTITREIADAAL 250
IT E AL
Sbjct: 228 ----GKITLETVHEAL 239
>gnl|CDD|161849 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction.
Length = 413
Score = 42.1 bits (99), Expect = 2e-04
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 14/76 (18%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAKAG----DLAALLTNL--------- 103
+L +GP G GKT LAQ +AR L V F + +AG D+ +L L
Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVE 178
Query: 104 -EDRDVLFIDEIHRLS 118
+ +++IDEI ++S
Sbjct: 179 KAQKGIIYIDEIDKIS 194
>gnl|CDD|180644 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau;
Validated.
Length = 563
Score = 41.3 bits (97), Expect = 3e-04
Identities = 37/112 (33%), Positives = 51/112 (45%), Gaps = 15/112 (13%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNF 82
RPR GQ LK IE+ K A A +F GP G+GKT+ A+ AR L
Sbjct: 11 RPRDFNSLEGQDFVVETLKHSIESNKI-ANAY---IFSGPRGVGKTSSARAFARCLNC-- 64
Query: 83 RSTSGPVIAKAGDLAAL--LTNLEDRDVLFIDEIHRLSI-----IVEEILYP 127
+GP G+ ++ + N DV+ ID S+ I EEI++P
Sbjct: 65 --VNGPTPMPCGECSSCKSIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFP 114
>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 = 40.4 bits (95), Expect = 6e-04
Identities = 26/69 (37%), Positives = 32/69 (46%), Gaps = 3/69 (4%)
Query: 22 LRPRTLEE-FTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELG- 79
R + E GQ +A V +E K A VL GPPG GKT LA +++ELG
Sbjct: 17 GEARYVSEGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGE 76
Query: 80 -VNFRSTSG 87
F SG
Sbjct: 77 DTPFCPISG 85
Score = 29.6 bits (67), Expect = 1.2
Identities = 31/112 (27%), Positives = 46/112 (41%), Gaps = 32/112 (28%)
Query: 108 VLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLT 167
VLFIDE+H L I L A+E L+ +I AT R G+ T
Sbjct: 278 VLFIDEVHMLDIECFSFLNRALES------------------ELAP-IVILATNR-GICT 317
Query: 168 ---NPLQDRFGIP---------IRLNFYEIEDLKTIVQRGAKLTGLAVTDEA 207
+ GIP I Y E++K I++ A+ G+ +++EA
Sbjct: 318 IRGTDIISPHGIPLDLLDRLLIITTEPYTREEIKQILEIRAQEEGVEISEEA 369
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 40.2 bits (95), Expect = 8e-04
Identities = 17/28 (60%), Positives = 21/28 (75%)
Query: 56 HVLFVGPPGLGKTTLAQVVARELGVNFR 83
HVL G PGL KT LA+ +AR LG++FR
Sbjct: 1 HVLLEGVPGLAKTLLARTLARSLGLDFR 28
>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.
Length = 531
Score = 39.4 bits (92), Expect = 0.001
Identities = 59/251 (23%), Positives = 86/251 (34%), Gaps = 71/251 (28%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEAL-----DHVLFVGPPGLGKTTLAQVVARE 77
RP++ +E GQ E I+A KA AL HV+ GPPG+GKT A++V E
Sbjct: 60 RPKSFDEIIGQEEG-------IKALKA---ALCGPNPQHVIIYGPPGVGKTAAARLVLEE 109
Query: 78 LGVNFRSTSGPVIAKAGDLAALLTNLEDR------------------------------- 106
N S A ++ A ++R
Sbjct: 110 AKKNPASPFKEG-AAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKP 168
Query: 107 --------DVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKINL------- 151
VLFIDEI L + L +ED ++ L + S N+
Sbjct: 169 GAVTRAHGGVLFIDEIGELHPVQMNKLLKVLEDRKVFL---DSAYYNSENPNIPSHIHDI 225
Query: 152 ------SRFTLIAATTRVGLLTNPLQDRFGIPIRLNFYEIEDLKTIVQRGAKLTGLAVTD 205
+ F LI ATTR P + I E++K I + A+ G+ +
Sbjct: 226 FQNGLPADFRLIGATTRNPEEIPPALRSRCVEIFFRPLLDEEIKEIAKNAAEKIGINLEK 285
Query: 206 EAACEIAMRSR 216
A I +
Sbjct: 286 HALELIVKYAS 296
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University).
Length = 637
Score = 38.4 bits (89), Expect = 0.003
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 43 FIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAK 92
+E A R +L GP G GK+T +++++ELG+ + S P +
Sbjct: 104 VLENAPKRI-----LLITGPSGCGKSTTIKILSKELGIQVQEWSNPTLPD 148
>gnl|CDD|162028 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock.
Length = 775
Score = 38.0 bits (89), Expect = 0.004
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 59 FVGPPGLGKTTLAQVVARELGVNF 82
VGPPG+GKT+L + +A+ L F
Sbjct: 352 LVGPPGVGKTSLGKSIAKALNRKF 375
>gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA.
Length = 731
Score = 38.1 bits (89), Expect = 0.004
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 58 LFVGPPGLGKTTLAQVVARELGVNF 82
LF GP G+GKT LA+ +A LGV+
Sbjct: 488 LFTGPTGVGKTELAKQLAEALGVHL 512
Score = 31.6 bits (72), Expect = 0.33
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 20/78 (25%)
Query: 58 LFVGPPGLGKTTLAQVVARELGVN-----------FRSTSGPVIAKA---GD----LAAL 99
L VG PG+GKT +A+ +A + + G ++A GD L A+
Sbjct: 207 LLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDMGSLLAGTKYRGDFEERLKAV 266
Query: 100 LTNLEDRD--VLFIDEIH 115
++ +E +LFIDEIH
Sbjct: 267 VSEIEKEPNAILFIDEIH 284
>gnl|CDD|116338 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 37.2 bits (87), Expect = 0.007
Identities = 27/96 (28%), Positives = 39/96 (40%), Gaps = 21/96 (21%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFR--------------STSGPVIAKAGDLAA---- 98
LF+GP G+GKT LA+ +A L + R S S + A G +
Sbjct: 6 FLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVGYEEGG 65
Query: 99 LLTNLEDRD---VLFIDEIHRLSIIVEEILYPAMED 131
LT R ++ IDEI + V+ L +E
Sbjct: 66 QLTEAVRRKPYSIVLIDEIEKAHPGVQNDLLQILEG 101
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 36.7 bits (86), Expect = 0.008
Identities = 26/66 (39%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAKA--GDLAALLTNLED--RD----V 108
VL GPPG GKT LA+ VA E F G + + G+ A L+ L + R+ +
Sbjct: 168 VLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSI 227
Query: 109 LFIDEI 114
+FIDEI
Sbjct: 228 IFIDEI 233
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 36.6 bits (84), Expect = 0.009
Identities = 18/31 (58%), Positives = 21/31 (67%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSG 87
VL VGPPG GKT LA+ +A E V F + SG
Sbjct: 188 VLMVGPPGTGKTLLAKAIAGEAKVPFFTISG 218
>gnl|CDD|184917 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 36.7 bits (85), Expect = 0.009
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVAREL 78
RP+ +E GQ LK ++ + + H +F GP G GKTT+A+++A+ L
Sbjct: 11 RPKFFKEVIGQEIVVRILKNAVKLQR-----VSHAYIFAGPRGTGKTTIARILAKVL 62
>gnl|CDD|184924 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 36.2 bits (83), Expect = 0.011
Identities = 40/127 (31%), Positives = 52/127 (40%), Gaps = 36/127 (28%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVARELGVN 81
RPR E GQ L +E + L H LF G G+GKTT+A+++A+ L
Sbjct: 10 RPRNFNELVGQNHVSRALSSALERGR-----LHHAYLFTGTRGVGKTTIARILAKCLNCE 64
Query: 82 FRSTSGPVIAKAG----------DL----AALLTNLED-RDVL---------------FI 111
TS P A DL AA T +ED R++L I
Sbjct: 65 TGVTSTPCEVCATCKAVNEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLI 124
Query: 112 DEIHRLS 118
DE+H LS
Sbjct: 125 DEVHMLS 131
>gnl|CDD|184935 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 36.3 bits (84), Expect = 0.012
Identities = 23/54 (42%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAR 76
RP T E GQ + LK I K A A LF GP G+GKTT A++ A+
Sbjct: 12 RPSTFESVVGQEALTTTLKNAIATNKL-AHAY---LFCGPRGVGKTTCARIFAK 61
>gnl|CDD|180719 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 36.0 bits (84), Expect = 0.014
Identities = 17/41 (41%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 38 SNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78
K FIE E L LF G G GKT L+ +A+EL
Sbjct: 170 EKCKNFIENFDKNNENL---LFYGNTGTGKTFLSNCIAKEL 207
>gnl|CDD|180856 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 35.9 bits (83), Expect = 0.015
Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 6/57 (10%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVAREL 78
RP+T ++ GQ LK I++ K + H LF GP G GKT++A++ A L
Sbjct: 13 RPKTFDDIVGQDHIVQTLKNIIKSNK-----ISHAYLFSGPRGTGKTSVAKIFANAL 64
>gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF.
Length = 282
Score = 35.8 bits (83), Expect = 0.015
Identities = 32/142 (22%), Positives = 46/142 (32%), Gaps = 41/142 (28%)
Query: 7 LLSRNVSQEDADISLLRPRTLEEFTGQVEAC-SNLKVFIEAAKARAEALDH---VLFVGP 62
LL VS E A L + + L+ + E L+ + VGP
Sbjct: 143 LLRAGVSPELARELLEKLPERADAEDAWRWLREALEKMLPVKPEEDEILEQGGVIALVGP 202
Query: 63 PGLGKTT----LA----------------------------QVVARELGVNFRSTSGPVI 90
G+GKTT LA + A+ LGV + V
Sbjct: 203 TGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILGVPVK-----VA 257
Query: 91 AKAGDLAALLTNLEDRDVLFID 112
+L L L D+D++ ID
Sbjct: 258 RDPKELRKALDRLRDKDLILID 279
>gnl|CDD|178887 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 35.9 bits (84), Expect = 0.016
Identities = 10/30 (33%), Positives = 21/30 (70%)
Query: 56 HVLFVGPPGLGKTTLAQVVARELGVNFRST 85
+++ +G G GK+T+ +++A+ LG +F T
Sbjct: 6 NIVLIGFMGAGKSTIGRLLAKRLGYDFIDT 35
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 35.5 bits (82), Expect = 0.018
Identities = 27/66 (40%), Positives = 34/66 (51%), Gaps = 8/66 (12%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNF-RSTSGPVIAK-AGDLAALLTNL----EDR--DV 108
V+ GPPG GKT LA+ VA E F R +I K GD L+ L E+ +
Sbjct: 220 VILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSI 279
Query: 109 LFIDEI 114
+FIDEI
Sbjct: 280 VFIDEI 285
>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 546
Score = 35.4 bits (81), Expect = 0.019
Identities = 31/105 (29%), Positives = 48/105 (45%), Gaps = 7/105 (6%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNF 82
RP++ E GQ A ++L +E K LF G G+GKTTL +++A+ L
Sbjct: 11 RPQSFAEVAGQQHALNSLVHALETQKVHHA----YLFTGTRGVGKTTLGRLLAKCLNCKT 66
Query: 83 RSTSGPVIAKAGDLAALLTNLEDRDVLFIDEIHRLSI-IVEEILY 126
T+ P +A + N D++ ID R + +EIL
Sbjct: 67 GVTAEPCNKCENCVA--INNNSFIDLIEIDAASRTGVEETKEILD 109
>gnl|CDD|184916 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 584
Score = 35.6 bits (82), Expect = 0.019
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVARELGVN 81
RP T E GQ L ++A + ++H LF GP G GKT+ A+++AR L
Sbjct: 8 RPATFAEVVGQEHVTEPLSSALDAGR-----INHAYLFSGPRGCGKTSSARILARSLNCA 62
Query: 82 FRSTSGP 88
T+ P
Sbjct: 63 QGPTATP 69
>gnl|CDD|180029 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 35.1 bits (82), Expect = 0.023
Identities = 29/78 (37%), Positives = 37/78 (47%), Gaps = 26/78 (33%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIA------KAG----DLAALLTNL--- 103
+L +GP G GKT LAQ +AR L V F IA +AG D+ +L L
Sbjct: 111 ILLIGPTGSGKTLLAQTLARILDVPF------AIADATTLTEAGYVGEDVENILLKLLQA 164
Query: 104 EDRDV-------LFIDEI 114
D DV ++IDEI
Sbjct: 165 ADYDVEKAQRGIVYIDEI 182
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 35.1 bits (81), Expect = 0.026
Identities = 24/59 (40%), Positives = 29/59 (49%), Gaps = 10/59 (16%)
Query: 23 RPRTLEEFTGQVEACSNLK---VFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78
RP+T E GQ + LK F AA A LF G G GKTTLA++ A+ L
Sbjct: 12 RPQTFSEILGQDAVVAVLKNALRFNRAAHA-------YLFSGIRGTGKTTLARIFAKAL 63
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 34.7 bits (79), Expect = 0.036
Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 4/66 (6%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNF 82
RP+T E GQ +K + A LF G G+GKTT+A++ A+ L
Sbjct: 11 RPQTFAEVAGQ----ETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCET 66
Query: 83 RSTSGP 88
T P
Sbjct: 67 APTGEP 72
>gnl|CDD|184933 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 527
Score = 34.3 bits (79), Expect = 0.045
Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 12/60 (20%)
Query: 23 RPRTLEEFTGQ---VEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVAREL 78
RP++ E GQ V A +N + L H LF G G+GKTTLA+++A+ L
Sbjct: 11 RPKSFSELVGQEHVVRALTN--------ALEQQRLHHAYLFTGTRGVGKTTLARILAKSL 62
>gnl|CDD|162029 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
Members of this family from Pyrococcus horikoshii and
Pyrococcus abyssi each contain a predicted intein.
Length = 608
Score = 34.4 bits (79), Expect = 0.045
Identities = 22/71 (30%), Positives = 34/71 (47%), Gaps = 8/71 (11%)
Query: 25 RTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNFRS 84
R +++ GQ EA +E K A+ +VL +G PG+GK+ LA+ +A EL +
Sbjct: 15 RLIDQVIGQEEA-------VEIIKKAAKQKRNVLLIGEPGVGKSMLAKAMA-ELLPDEEL 66
Query: 85 TSGPVIAKAGD 95
V D
Sbjct: 67 EDILVYPNPED 77
Score = 28.3 bits (63), Expect = 3.1
Identities = 40/170 (23%), Positives = 67/170 (39%), Gaps = 36/170 (21%)
Query: 106 RDVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGP--SARSVKINL--SRFTLIAATT 161
+ VL+IDEI + + V++ L A++D + + G+ S V+ F L+A+
Sbjct: 218 KGVLYIDEIKTMPLEVQQYLLTALQDKKFPI-TGQSENSSGAMVRTEPVPCDFILVASGN 276
Query: 162 RVGL--LTNPLQDRFGIPIRLNFYEI--------------EDLKTIVQRGAKLTGLA-VT 204
L + L+ R IR YE+ + ++ + Q K + T
Sbjct: 277 LDDLEGMHPALRSR----IRGYGYEVYMKDTMPDTPENRDKLVQFVAQEVKKDGRIPHFT 332
Query: 205 DEAACEI---AMRSRGTP-------RIAGRLLRRVRDFAEVAHAKTITRE 244
+A EI A R G R G L+R D A+ + +T E
Sbjct: 333 RDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAE 382
>gnl|CDD|185633 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 34.0 bits (78), Expect = 0.055
Identities = 14/26 (53%), Positives = 15/26 (57%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNF 82
VL GPPG GKT LA+ VA F
Sbjct: 182 VLLYGPPGTGKTMLAKAVAHHTTATF 207
>gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 33.8 bits (78), Expect = 0.055
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 7/55 (12%)
Query: 24 PRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78
R +++ GQ A ++V +AAK R HV+ +G PG GK+ LA+ +A L
Sbjct: 27 ERLIDQVIGQEHA---VEVIKKAAKQRR----HVMMIGSPGTGKSMLAKAMAELL 74
Score = 26.5 bits (59), Expect = 9.6
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 108 VLFIDEIHRLSIIVEEILYPAMED 131
VLFIDEI+ L + ++ L AM++
Sbjct: 229 VLFIDEINTLDLESQQSLLTAMQE 252
>gnl|CDD|184929 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 33.9 bits (78), Expect = 0.060
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78
RP+T + TGQ L+ I+ + A A LF G G+GKT+ A+++A+ L
Sbjct: 11 RPQTFSDLTGQEHVSRTLQNAIDTGRV-AHAF---LFTGARGVGKTSTARILAKAL 62
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 34.0 bits (78), Expect = 0.063
Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAKA--GDLAALLTNL------EDRDV 108
VL GPPG GKT LA+ VA E F G + + G+ A L+ + + +
Sbjct: 159 VLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSI 218
Query: 109 LFIDEI 114
+FIDEI
Sbjct: 219 IFIDEI 224
>gnl|CDD|178078 PLN02459, PLN02459, probable adenylate kinase.
Length = 261
Score = 33.7 bits (77), Expect = 0.067
Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 9/77 (11%)
Query: 56 HVLFVGPPGLGKTTLAQVVARELGVNFRSTSGPV---IAKAGDLAALLTNLEDRDVLFID 112
+ +F+G PG+GK T A +++ LGV +T V I +G L A L + ++ L D
Sbjct: 31 NWVFLGCPGVGKGTYASRLSKLLGVPHIATGDLVREEIKSSGPLGAQLKEIVNQGKLVPD 90
Query: 113 EI------HRLSIIVEE 123
EI RL EE
Sbjct: 91 EIIFSLLSKRLEAGEEE 107
>gnl|CDD|177379 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 33.4 bits (77), Expect = 0.074
Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 7/83 (8%)
Query: 58 LFVGPPGLGKTTLAQVVARELGVNFRSTSGP------VIAKAGDLAALLTNLEDRDVLFI 111
L PG GKTT+A+ + E+G +G V + A+ ++ V+ I
Sbjct: 47 LHSPSPGTGKTTVAKALCNEVGAEVLFVNGSDCRIDFVRNRLTRFASTVSLTGGGKVIII 106
Query: 112 DEIHRLSI-IVEEILYPAMEDFQ 133
DE RL + + L ME +
Sbjct: 107 DEFDRLGLADAQRHLRSFMEAYS 129
>gnl|CDD|162839 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau
subunit. A translational frameshift leads to early
termination and a truncated protein subunit gamma,
about 1/3 shorter than tau and present in roughly equal
amounts. This frameshift mechanism is not necessarily
universal for species with DNA polymerase III but
appears conserved in the exterme thermophile Thermus
thermophilis.
Length = 355
Score = 33.3 bits (77), Expect = 0.087
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 12/60 (20%)
Query: 23 RPRTLEEFTGQ---VEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVAREL 78
RP+T E+ GQ V+ N I+ + + H LF GP G GKT++A++ A+ L
Sbjct: 9 RPQTFEDVIGQEHIVQTLKNA---IKNGR-----IAHAYLFSGPRGTGKTSIARIFAKAL 60
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 32.9 bits (76), Expect = 0.11
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 57 VLFVGPPGLGKTTLAQVVAR 76
+L G PG GK+T AQ +A
Sbjct: 260 ILIAGAPGAGKSTFAQALAE 279
>gnl|CDD|184914 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 32.9 bits (75), Expect = 0.12
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAR 76
R +T E GQ L+ I + A A LF GP G+GKT+ A+++A+
Sbjct: 11 RSQTFAELVGQEHVVQTLRNAIAEGRV-AHAY---LFTGPRGVGKTSTARILAK 60
>gnl|CDD|184726 PRK14527, PRK14527, adenylate kinase; Provisional.
Length = 191
Score = 32.8 bits (75), Expect = 0.13
Identities = 16/29 (55%), Positives = 22/29 (75%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRST 85
V+F+GPPG GK T A+ +A+ELG+ ST
Sbjct: 9 VIFLGPPGAGKGTQAERLAQELGLKKLST 37
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 32.6 bits (74), Expect = 0.16
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 59 FVGPPGLGKTTLAQVVARELG 79
VGPPG+GKT+L Q +A+ G
Sbjct: 354 LVGPPGVGKTSLGQSIAKATG 374
>gnl|CDD|162744 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins
in this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 32.4 bits (74), Expect = 0.16
Identities = 12/24 (50%), Positives = 18/24 (75%)
Query: 61 GPPGLGKTTLAQVVARELGVNFRS 84
GPPG GKTT+A+++A +L + S
Sbjct: 7 GPPGSGKTTVAKILAEKLSLKLIS 30
>gnl|CDD|180750 PRK06921, PRK06921, hypothetical protein; Provisional.
Length = 266
Score = 32.4 bits (74), Expect = 0.18
Identities = 23/68 (33%), Positives = 29/68 (42%), Gaps = 15/68 (22%)
Query: 59 FVGPPGLGKTTLAQVVARELGVNFRSTSGPVI-----AKAGDLAALLTNLEDR------- 106
+G PG GKT L A EL R PV+ GDL LE +
Sbjct: 122 LLGQPGSGKTHLLTAAANEL---MRKKGVPVLYFPFVEGFGDLKDDFDLLEAKLNRMKKV 178
Query: 107 DVLFIDEI 114
+VLFID++
Sbjct: 179 EVLFIDDL 186
>gnl|CDD|162313 TIGR01351, adk, adenylate kinases. Adenylate kinase (EC 2.7.4.3)
converts ATP + AMP to ADP + ADP, that is, uses ATP as a
phosphate donor for AMP. Most members of this family
are known or believed to be adenylate kinase. However,
some members accept other nucleotide triphosphates as
donors, may be unable to use ATP, and may fail to
complement adenylate kinase mutants. An example of a
nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10)
is a GTP:AMP phosphotransferase. This family is
designated subfamily rather than equivalog for this
reason.
Length = 210
Score = 32.2 bits (74), Expect = 0.20
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGV 80
++ +GPPG GK T A+ +A + G+
Sbjct: 2 LVLLGPPGSGKGTQAKRIAEKYGL 25
>gnl|CDD|179771 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 32.1 bits (74), Expect = 0.24
Identities = 13/24 (54%), Positives = 19/24 (79%)
Query: 61 GPPGLGKTTLAQVVARELGVNFRS 84
GPPG GKTT+A+++A +LG+ S
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHVS 30
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 31.8 bits (72), Expect = 0.25
Identities = 11/21 (52%), Positives = 18/21 (85%)
Query: 58 LFVGPPGLGKTTLAQVVAREL 78
+F GP G+GKTT+A+++A+ L
Sbjct: 44 IFFGPRGVGKTTIARILAKRL 64
>gnl|CDD|179433 PRK02496, adk, adenylate kinase; Provisional.
Length = 184
Score = 31.6 bits (72), Expect = 0.26
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRST 85
++F+GPPG GK T A V+A L + ST
Sbjct: 4 LIFLGPPGAGKGTQAVVLAEHLHIPHIST 32
>gnl|CDD|181180 PRK07952, PRK07952, DNA replication protein DnaC; Validated.
Length = 244
Score = 31.7 bits (72), Expect = 0.27
Identities = 27/101 (26%), Positives = 41/101 (40%), Gaps = 23/101 (22%)
Query: 33 QVEACSNLKVFIEAAKARAEALDH----VLFVGPPGLGKTTLAQVVARELGVNFRSTSGP 88
+VE + + A+ E D +F G PG GK LA + EL + +S
Sbjct: 75 RVECEGQMNA-LSKARQYVEEFDGNIASFIFSGKPGTGKNHLAAAICNELLLRGKSV--- 130
Query: 89 VIAKAGDLAA---------------LLTNLEDRDVLFIDEI 114
+I D+ + LL +L + D+L IDEI
Sbjct: 131 LIITVADIMSAMKDTFSNSETSEEQLLNDLSNVDLLVIDEI 171
>gnl|CDD|183438 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 31.4 bits (71), Expect = 0.31
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 6/71 (8%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVARELGVN 81
RPR GQ L +E + L H LF G G+GKTTL++++A+ L
Sbjct: 11 RPRDFTTLVGQEHVVRALTHALEQQR-----LHHAYLFTGTRGVGKTTLSRILAKSLNCT 65
Query: 82 FRSTSGPVIAK 92
G + A+
Sbjct: 66 GADGEGGITAQ 76
>gnl|CDD|184915 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 31.6 bits (72), Expect = 0.31
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 12/60 (20%)
Query: 23 RPRTLEEFTGQ---VEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVAREL 78
RPR+ E GQ V+A +N + L H LF G G+GKTT+++++A+ L
Sbjct: 11 RPRSFSEMVGQEHVVQALTNALT--------QQRLHHAYLFTGTRGVGKTTVSRILAKSL 62
>gnl|CDD|150510 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 31.4 bits (72), Expect = 0.33
Identities = 25/90 (27%), Positives = 33/90 (36%), Gaps = 28/90 (31%)
Query: 56 HVLFV-GPPGLGKTTLA-------QVVARELGVNFRSTSGPVIAK-----AGDL------ 96
V V G PG GKT +A F S + P++ AGDL
Sbjct: 2 AVFLVTGGPGTGKTVVALNLFAELSDSDLGRTAVFLSGNHPLVLVLYEALAGDLKVRKKK 61
Query: 97 -----AALLTNLEDR----DVLFIDEIHRL 117
+ + NL DV+ +DE HRL
Sbjct: 62 LFRKPTSFINNLHKAPPHEDVVIVDEAHRL 91
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728).
Length = 262
Score = 31.3 bits (71), Expect = 0.33
Identities = 17/39 (43%), Positives = 19/39 (48%), Gaps = 7/39 (17%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAKAGD 95
V GP G GKTTLA VAR+ PV+ GD
Sbjct: 24 VHLRGPAGTGKTTLAMHVARKRD-------RPVMLINGD 55
>gnl|CDD|181191 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 31.4 bits (72), Expect = 0.34
Identities = 42/140 (30%), Positives = 57/140 (40%), Gaps = 62/140 (44%)
Query: 23 RPRTLEEFTGQ---VEACSNLKVFIEAAKARAEALDH------VLFVGPPGLGKTTLAQV 73
RP+T E GQ + A +N ALD LF G G+GKTT+A++
Sbjct: 11 RPQTFAEVVGQEHVLTALAN-------------ALDLGRLHHAYLFSGTRGVGKTTIARL 57
Query: 74 VAR----ELGVNFRSTSGPV--------IAKAG---DL----AALLTNLED-RDVL---- 109
+A+ E G+ T+ P I G DL AA T +ED R++L
Sbjct: 58 LAKGLNCETGI----TATPCGECDNCREIE-QGRFVDLIEIDAASRTKVEDTRELLDNVQ 112
Query: 110 -----------FIDEIHRLS 118
IDE+H LS
Sbjct: 113 YAPARGRFKVYLIDEVHMLS 132
>gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 31.4 bits (72), Expect = 0.35
Identities = 13/21 (61%), Positives = 16/21 (76%), Gaps = 1/21 (4%)
Query: 57 VLFVGPPGLGKTT-LAQVVAR 76
V VGP G+GKTT LA++ AR
Sbjct: 224 VALVGPTGVGKTTTLAKLAAR 244
>gnl|CDD|139997 PRK13938, PRK13938, phosphoheptose isomerase; Provisional.
Length = 196
Score = 31.2 bits (70), Expect = 0.42
Identities = 28/91 (30%), Positives = 39/91 (42%), Gaps = 6/91 (6%)
Query: 42 VFIEAAKARAEALDHVLFVGPPGLGKTTL-AQVVARELGVNFRSTSGPVIAKAGDLAALL 100
VF A + A D + + G + L A ARELGV + +G + + A L
Sbjct: 102 VFARALEGSARPGDTLFAISTSGNSMSVLRAAKTARELGVTVVAMTGESGGQLAEFADFL 161
Query: 101 TNLEDRDVLFIDE-----IHRLSIIVEEILY 126
N+ RD I E IH +S VE L+
Sbjct: 162 INVPSRDTGRIQESHIVFIHAISEHVEHALF 192
>gnl|CDD|184928 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 491
Score = 30.9 bits (70), Expect = 0.42
Identities = 56/216 (25%), Positives = 75/216 (34%), Gaps = 81/216 (37%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTSGP-----------------VIAKAGDLAAL 99
+L VG G+GKTT A++++ L + TS P VI AA
Sbjct: 38 ILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEID---AAS 94
Query: 100 LTNLEDRDVLF----------------IDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPS 143
T+++D V+ IDE+H LS F L E P
Sbjct: 95 NTSVDDIKVILENSCYLPISSKFKVYIIDEVHMLSN----------SAFNALLKTLEEP- 143
Query: 144 ARSVKINLSRFTLIAATTRVGLLTNPLQDRFGIPI-------RLNFYEI------EDLKT 190
A VK I ATT V IP+ R + +I E L
Sbjct: 144 APHVK-------FILATTEVK----------KIPVTIISRCQRFDLQKIPTDKLVEHLVD 186
Query: 191 IVQRGAKLTGLAVTDEAACEIAMRSRGTPRIAGRLL 226
I AK + +E+ IA S G+ R A LL
Sbjct: 187 I----AKKENIEHDEESLKLIAENSSGSMRNALFLL 218
>gnl|CDD|161840 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
DnaA is involved in DNA biosynthesis; initiation of
chromosome replication and can also be transcription
regulator. The C-terminal of the family hits the pfam
bacterial DnaA (bac_dnaA) domain family. For a review,
see Kaguni (2006).
Length = 405
Score = 31.0 bits (71), Expect = 0.43
Identities = 35/127 (27%), Positives = 50/127 (39%), Gaps = 21/127 (16%)
Query: 9 SRNVSQEDADISLLRPR-TLEEFTGQVEACSNLKVFIEAAKARAEALDHV---LFV-GPP 63
S E + S L P+ T + F V SN ++ AA A AE LF+ G
Sbjct: 90 PPEASAEPTNNSPLNPKYTFDNF---VVGKSN-RLAHAAALAVAENPGKAYNPLFIYGGV 145
Query: 64 GLGKTTLAQVVARELGVNFRS-----------TSGPVIA-KAGDLAALLTNLEDRDVLFI 111
GLGKT L + E+ N + T+ V A + + D+L I
Sbjct: 146 GLGKTHLLHAIGNEILENNPNAKVVYVSSEKFTNDFVNALRNNKMEEFKEKYRSVDLLLI 205
Query: 112 DEIHRLS 118
D+I L+
Sbjct: 206 DDIQFLA 212
>gnl|CDD|184251 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 31.0 bits (71), Expect = 0.47
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 61 GPPGLGKTTLAQVVAREL 78
GPPG+GKTTL +A L
Sbjct: 7 GPPGVGKTTLVLKIAELL 24
>gnl|CDD|161993 TIGR00678, holB, DNA polymerase III, delta' subunit. At position
126-127 of the seed alignment, this family lacks the HM
motif of gamma/tau; at 132 it has a near-invariant A
vs. an invariant F in gamma/tau.
Length = 188
Score = 30.7 bits (70), Expect = 0.51
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 58 LFVGPPGLGKTTLAQVVAREL 78
LF GP G+GK LA +A+ L
Sbjct: 18 LFAGPEGVGKELLALALAKAL 38
>gnl|CDD|181233 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 30.8 bits (70), Expect = 0.53
Identities = 13/35 (37%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 58 LFVGPPGLGKTTLAQVVAREL-----GVNFRSTSG 87
L G G GKT LA +A EL V F +
Sbjct: 118 LLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQ 152
>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 509
Score = 30.5 bits (68), Expect = 0.58
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVARELGVN 81
RPR +E GQ L ++ + L H LF G G+GKTT+++++A+ L
Sbjct: 11 RPRCFQEVIGQAPVVRALSNALDQ-----QYLHHAYLFTGTRGVGKTTISRILAKCLNCE 65
Query: 82 FRSTSGP 88
++ P
Sbjct: 66 KGVSANP 72
>gnl|CDD|179010 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 30.6 bits (70), Expect = 0.59
Identities = 13/22 (59%), Positives = 14/22 (63%)
Query: 57 VLFVGPPGLGKTTLAQVVAREL 78
VL GPPG GKTT + V EL
Sbjct: 58 VLIYGPPGTGKTTTVKKVFEEL 79
>gnl|CDD|172992 PRK14526, PRK14526, adenylate kinase; Provisional.
Length = 211
Score = 30.6 bits (69), Expect = 0.59
Identities = 13/29 (44%), Positives = 21/29 (72%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRST 85
++F+GPPG GK T+A++++ EL ST
Sbjct: 3 LVFLGPPGSGKGTIAKILSNELNYYHIST 31
>gnl|CDD|178957 PRK00279, adk, adenylate kinase; Reviewed.
Length = 215
Score = 30.5 bits (70), Expect = 0.62
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRST 85
++ +GPPG GK T A+ +A + G+ ST
Sbjct: 3 LILLGPPGAGKGTQAKFIAEKYGIPHIST 31
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 30.6 bits (69), Expect = 0.63
Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVA 75
RP T +E GQ ++K + AA + LF GP G+GKTT A+++A
Sbjct: 9 RPITFDEVVGQ----EHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIA 57
>gnl|CDD|163254 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
Members of this protein family are Hda (Homologous to
DnaA). These proteins are about half the length of DnaA
and homologous over length of Hda. In the model species
Escherichia coli, the initiation of DNA replication
requires DnaA bound to ATP rather than ADP; Hda helps
facilitate the conversion of DnaA-ATP to DnaA-ADP.
Length = 226
Score = 30.6 bits (70), Expect = 0.64
Identities = 22/104 (21%), Positives = 39/104 (37%), Gaps = 8/104 (7%)
Query: 18 DISLLRPRTLEEF--TGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVA 75
D+ L T + F G E L + A + + + G G GK+ L Q
Sbjct: 5 DVGLPDDPTFDNFYAGGNAEL---LAALRQLAAGKGD--RFLYLWGESGSGKSHLLQAAC 59
Query: 76 RELGVNFRSTS-GPVIAKAGDLAALLTNLEDRDVLFIDEIHRLS 118
+S P+ A +L LE D++ +D++ ++
Sbjct: 60 AAAEERGKSAIYLPLAELAQADPEVLEGLEQADLVCLDDVEAIA 103
>gnl|CDD|163401 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity.
Length = 512
Score = 30.5 bits (69), Expect = 0.70
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 57 VLFVGPPGLGKTTLAQVVAREL 78
VL GPPG GKT +A+ VA L
Sbjct: 219 VLLYGPPGCGKTLIAKAVANSL 240
>gnl|CDD|180131 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 30.2 bits (69), Expect = 0.78
Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAK-ARAEALDHVLFVGPPGLGKTTLAQVVAREL 78
RP+T E+ GQ LK I+ K + A LF GP G GKT+ A++ A+ +
Sbjct: 11 RPQTFEDVVGQEHITKTLKNAIKQGKISHA-----YLFSGPRGTGKTSAAKIFAKAV 62
>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 363
Score = 30.2 bits (68), Expect = 0.85
Identities = 38/129 (29%), Positives = 51/129 (39%), Gaps = 40/129 (31%)
Query: 23 RPRTLEEFTGQ---VEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELG 79
RP+ + GQ V A SN A L G G+GKTT+A+++A+ L
Sbjct: 11 RPQYFRDIIGQKHIVTAISNGLSLGRIHHA-------WLLSGTRGVGKTTIARLLAKSLN 63
Query: 80 VNFRSTSGPV--------IAKAG--DL----AALLTNLED-RDVL--------------- 109
TS P I K DL AA T +E+ R++L
Sbjct: 64 CQNGITSNPCRKCIICKEIEKGLCLDLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVY 123
Query: 110 FIDEIHRLS 118
IDE+H LS
Sbjct: 124 LIDEVHMLS 132
>gnl|CDD|184313 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 30.2 bits (69), Expect = 0.86
Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 12/55 (21%)
Query: 21 LLRPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVA 75
L++P T+E Q L AA A + L V P GLGKT +A +V
Sbjct: 8 LIKPNTIEARLYQQ----LL-----AATALK---KNTLVVLPTGLGKTAIALLVI 50
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 30.1 bits (68), Expect = 0.95
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 17/57 (29%)
Query: 24 PRTLEEF-----TG----QVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLA 71
+T EE+ TG Q+++ +L FIE R E +++ +GP G+GKT LA
Sbjct: 71 VKTFEEYDFTFATGAPQKQLQSLRSLS-FIE----RNE---NIVLLGPSGVGKTHLA 119
>gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional.
Length = 169
Score = 29.7 bits (67), Expect = 1.1
Identities = 14/26 (53%), Positives = 19/26 (73%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNF 82
+ VG G GKTTL + +ARELG++F
Sbjct: 4 IFLVGYMGAGKTTLGKALARELGLSF 29
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 29.5 bits (66), Expect = 1.3
Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 10/70 (14%)
Query: 55 DHVLFVGPPGLGKTTLA---QVVARELG--VNFRSTSGPV-----IAKAGDLAALLTNLE 104
++V+F+GPPG GKT LA + A + G V F + + V AG L A L L
Sbjct: 99 ENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWVARLAAAHHAGRLQAELVKLG 158
Query: 105 DRDVLFIDEI 114
+L +DE+
Sbjct: 159 RYPLLIVDEV 168
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain.
Length = 499
Score = 29.4 bits (66), Expect = 1.5
Identities = 39/163 (23%), Positives = 57/163 (34%), Gaps = 42/163 (25%)
Query: 57 VLFVGPPGLGKTTLAQ----------------------VVARELGVN------FR----S 84
+L GPPG GKT LA +V + + FR S
Sbjct: 214 LLLFGPPGSGKTMLASRLQGILPPLTNEEAIETARIWSLVGKLIDRKQIKQRPFRSPHHS 273
Query: 85 TSGPVIAKAGDLAAL-LTNLEDRDVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPS 143
S P + G + +L VLF+DE+ V + L +ED + + S
Sbjct: 274 ASKPALVGGGPIPLPGEISLAHNGVLFLDELPEFKRSVLDALREPIEDGSISI------S 327
Query: 144 ARSVKINL-SRFTLIAAT--TRVGLLTNPLQDRFGIPIRLNFY 183
S KI +RF L+AA G P +++ Y
Sbjct: 328 RASAKIFYPARFQLVAAMNPCPCGHYGGKNTHCRCSPQQISRY 370
>gnl|CDD|169554 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 29.3 bits (65), Expect = 1.5
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 6/67 (8%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQVVARELGVN 81
RP+T + GQ L+ ++ + L H L G G+GKTT+A+++A+ L
Sbjct: 11 RPKTFADLVGQEHVVKALQNALDEGR-----LHHAYLLTGTRGVGKTTIARILAKSLNCE 65
Query: 82 FRSTSGP 88
P
Sbjct: 66 NAQHGEP 72
>gnl|CDD|169667 PRK09112, PRK09112, DNA polymerase III subunit delta'; Validated.
Length = 351
Score = 29.2 bits (66), Expect = 1.5
Identities = 14/27 (51%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 46 AAKARAEALDH-VLFVGPPGLGKTTLA 71
A R L H +LF GP G+GK TLA
Sbjct: 36 AQAYREGKLHHALLFEGPEGIGKATLA 62
>gnl|CDD|182893 PRK11000, PRK11000, maltose/maltodextrin transporter ATP-binding
protein; Provisional.
Length = 369
Score = 29.2 bits (66), Expect = 1.5
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 57 VLFVGPPGLGKTTLAQVVA 75
V+FVGP G GK+TL +++A
Sbjct: 32 VVFVGPSGCGKSTLLRMIA 50
>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 29.1 bits (65), Expect = 1.6
Identities = 50/198 (25%), Positives = 81/198 (40%), Gaps = 31/198 (15%)
Query: 108 VLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLT 167
V IDE+H LS F L E P ++ I ATT + +
Sbjct: 130 VYIIDEVHMLSTAA----------FNAFLKTLEEPPPHAI--------FIFATTELHKIP 171
Query: 168 NPLQDRFGIPIRLNFYEI--EDLKTIVQRGAKLTGLAVTDEAACEIAMRSRGTPRIAGRL 225
+ R R NF I +++++ +Q + G+ + +A IA +++G+ R A +
Sbjct: 172 ATIASRCQ---RFNFKRIPLDEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDAQSI 228
Query: 226 LRRVRDFAEVAHAKTITREIADAALLRLAIDKMGFDQLDLRYLTMIARNFGGGPVGIE-- 283
L +V F+ + A+ + A LL D+ FD D IA N + +
Sbjct: 229 LDQVIAFSVGSEAEKVIAYQGVAELLNYIDDEQFFDVTD-----AIAENDAVKMLEVARF 283
Query: 284 TISAGLSEPRDAIEDLIE 301
I G E +D +E LIE
Sbjct: 284 VIDNGYDE-QDFLEKLIE 300
>gnl|CDD|184912 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 29.2 bits (66), Expect = 1.8
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 10/70 (14%)
Query: 23 RPRTLEEFTGQVEACS-NLKVFIEAAK-ARAEALDHVLFVGPPGLGKTTLAQVVARELGV 80
RP+ +E GQ EA + LK + + + A A LF GP G GKT+ A+++A+ L
Sbjct: 11 RPQRFDELVGQ-EAIATTLKNALISNRIAPA-----YLFTGPRGTGKTSSARILAKSL-- 62
Query: 81 NFRSTSGPVI 90
N ++ P
Sbjct: 63 NCLNSDKPTP 72
>gnl|CDD|179660 PRK03839, PRK03839, putative kinase; Provisional.
Length = 180
Score = 28.9 bits (65), Expect = 1.9
Identities = 10/22 (45%), Positives = 18/22 (81%)
Query: 61 GPPGLGKTTLAQVVARELGVNF 82
G PG+GKTT+++++A +LG +
Sbjct: 7 GTPGVGKTTVSKLLAEKLGYEY 28
>gnl|CDD|181541 PRK08727, PRK08727, hypothetical protein; Validated.
Length = 233
Score = 28.7 bits (64), Expect = 2.0
Identities = 46/167 (27%), Positives = 75/167 (44%), Gaps = 15/167 (8%)
Query: 47 AKARAEALDHVLFVGPPGLGKTTLA-QVVARELGVNFRSTSGPVIAKAGDLAALLTNLED 105
A A ++ D + GP G GKT LA + A S P+ A AG L L LE
Sbjct: 34 ALAAGQSSDWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQAAAGRLRDALEALEG 93
Query: 106 RDVLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGL 165
R ++ +D + ++ E+ + A+ DF AR+ I L +T + L
Sbjct: 94 RSLVALDGLESIAGQREDEV--ALFDFH--------NRARAAGITL-LYTARQMPDGLAL 142
Query: 166 LTNPLQDRFGIPIRLNFYEIEDL--KTIVQRGAKLTGLAVTDEAACE 210
+ L+ R IR+ ++D+ +++ A+ GLA+ DEAA +
Sbjct: 143 VLPDLRSRLAQCIRIGLPVLDDVARAAVLRERAQRRGLAL-DEAAID 188
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme ethanolamine
ammonia lyase. The function of this gene is unknown,
although the presence of an N-terminal GxxGxGK motif
implies a GTP-binding site.
Length = 142
Score = 28.9 bits (65), Expect = 2.1
Identities = 21/84 (25%), Positives = 30/84 (35%), Gaps = 15/84 (17%)
Query: 57 VLFVGPPGLGKTTLAQVV-----------ARELGVNFRSTSGPVIAKAGDLAALLTNLED 105
++F+G G GKTTL Q + A E T G + +AL+ D
Sbjct: 3 IMFIGSVGCGKTTLTQALQGEEILYKKTQAVEYNDGAIDTPGEYVENRRLYSALIVTAAD 62
Query: 106 RDVLFIDEIHRLSIIVEEILYPAM 129
DV+ S E +P
Sbjct: 63 ADVI----ALVQSATDPESRFPPG 82
>gnl|CDD|180308 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 28.7 bits (64), Expect = 2.2
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78
RP ++ GQ +K + A + +F GP G+GKT++A++ A+ +
Sbjct: 11 RPHNFKQIIGQ----ELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAI 62
>gnl|CDD|180615 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 28.6 bits (64), Expect = 2.2
Identities = 14/41 (34%), Positives = 16/41 (39%), Gaps = 4/41 (9%)
Query: 44 IEAAKARAEALDH----VLFVGPPGLGKTTLAQVVARELGV 80
+ A A VL G G GKTTLA +A G
Sbjct: 1 MLVALIAARLCGGGMITVLIDGRSGSGKTTLAGALAARTGF 41
>gnl|CDD|180989 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated.
Length = 365
Score = 28.5 bits (64), Expect = 2.3
Identities = 20/64 (31%), Positives = 26/64 (40%), Gaps = 6/64 (9%)
Query: 14 QEDADISLLRPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHV-LFVGPPGLGKTTLAQ 72
+ D + PR G A + L R+ L H L GP G+GK TLA
Sbjct: 5 EADREEGAPHPRETTALFGHAAAEAAL-----LDAYRSGRLHHAWLIGGPQGIGKATLAY 59
Query: 73 VVAR 76
+AR
Sbjct: 60 RMAR 63
>gnl|CDD|129128 TIGR00017, cmk, cytidylate kinase. This family consists of
cytidylate kinase, which catalyzes the phosphorylation
of cytidine 5-monophosphate (dCMP) to cytidine 5
-diphosphate (dCDP) in the presence of ATP or GTP. UMP
and dCMP can also act as acceptors.
Length = 217
Score = 28.5 bits (64), Expect = 2.4
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 61 GPPGLGKTTLAQVVARELGVNFRSTSGPVIAKAGDLAALL--TNLEDRDVL 109
GP G GK+T+A+ VA +LG + + + +A LAAL +L D L
Sbjct: 9 GPSGAGKSTVAKAVAEKLGYAYLDSGA--MYRAIALAALQNRVDLTSEDAL 57
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 28.7 bits (65), Expect = 2.4
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 57 VLFVGPPGLGKTTLAQVVARE 77
++ +G G GKTTL Q + E
Sbjct: 4 IMLIGRSGCGKTTLTQALNGE 24
>gnl|CDD|184582 PRK14236, PRK14236, phosphate transporter ATP-binding protein;
Provisional.
Length = 272
Score = 28.5 bits (64), Expect = 2.5
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 10/70 (14%)
Query: 1 MMDREGLLSRNVSQEDADISLLRPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFV 60
+M L N+S E + + R L F G +A ++ + I K R A F+
Sbjct: 8 LMALPLLDVLNLSDEQTALEV---RNLNLFYGDKQALFDISMRI--PKNRVTA-----FI 57
Query: 61 GPPGLGKTTL 70
GP G GK+TL
Sbjct: 58 GPSGCGKSTL 67
>gnl|CDD|184913 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 944
Score = 28.6 bits (64), Expect = 2.6
Identities = 30/95 (31%), Positives = 39/95 (41%), Gaps = 38/95 (40%)
Query: 58 LFVGPPGLGKTTLAQVVAR----ELGVNFRSTSGPV--------IA-------------- 91
LF G G+GKT+LA++ A+ E GV T+ P IA
Sbjct: 42 LFTGTRGVGKTSLARLFAKGLNCEQGV----TATPCGVCSSCVEIAQGRFVDLIEVDAAS 97
Query: 92 --KAGDLAALLTNLEDR------DVLFIDEIHRLS 118
K D LL N++ R V IDE+H LS
Sbjct: 98 RTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLS 132
>gnl|CDD|184728 PRK14530, PRK14530, adenylate kinase; Provisional.
Length = 215
Score = 28.6 bits (64), Expect = 2.6
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 56 HVLFVGPPGLGKTTLAQVVARELGVNFRST 85
+L +G PG GK T + +A E GV +T
Sbjct: 5 RILLLGAPGAGKGTQSSNLAEEFGVEHVTT 34
>gnl|CDD|180790 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 28.3 bits (63), Expect = 2.7
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 58 LFVGPPGLGKTTLAQVVARELGVNFRSTSGP 88
LF G G+GKTTL+++ A+ L TS P
Sbjct: 42 LFTGTRGVGKTTLSRIFAKALNCETGVTSQP 72
>gnl|CDD|178902 PRK00149, dnaA, chromosomal replication initiation protein;
Reviewed.
Length = 450
Score = 28.2 bits (64), Expect = 2.7
Identities = 14/37 (37%), Positives = 17/37 (45%), Gaps = 4/37 (10%)
Query: 46 AAKARAEALDHV---LFV-GPPGLGKTTLAQVVAREL 78
AA A AE LF+ G GLGKT L + +
Sbjct: 136 AALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNYI 172
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 28.2 bits (64), Expect = 2.8
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 60 VGPPGLGKTTLAQVVAREL 78
VGP G+GKTT A+++A L
Sbjct: 371 VGPNGIGKTTFAKLLAGVL 389
>gnl|CDD|181743 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 28.4 bits (64), Expect = 2.8
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 57 VLFVGPPGLGKTTLAQVVARELG 79
V GPPG GK+TLA+ + L
Sbjct: 36 VGIAGPPGAGKSTLAEFLEALLQ 58
>gnl|CDD|181106 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 28.4 bits (64), Expect = 2.9
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 58 LFVGPPGLGKTTLAQVVAREL 78
LF GP G GKT+ A+++AR L
Sbjct: 41 LFSGPRGCGKTSSARILARSL 61
>gnl|CDD|179638 PRK03731, aroL, shikimate kinase II; Reviewed.
Length = 171
Score = 28.4 bits (64), Expect = 3.1
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 60 VGPPGLGKTTLAQVVARELGVNFRST 85
VG G GKTT+ +A+ LG F T
Sbjct: 8 VGARGCGKTTVGMALAQALGYRFVDT 33
>gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal.
Members of this protein are L-seryl-tRNA(Sec) kinase.
This enzyme is part of a two-step pathway in Eukaryota
and Archaea for performing selenocysteine biosynthesis
by changing serine misacylated on selenocysteine-tRNA
to selenocysteine. This enzyme performs the first step,
phosphorylation of the OH group of the serine side
chain. This family represents archaeal proteins with
this activity.
Length = 249
Score = 28.2 bits (63), Expect = 3.2
Identities = 8/22 (36%), Positives = 17/22 (77%)
Query: 57 VLFVGPPGLGKTTLAQVVAREL 78
++ G PG+GK+T ++ +A++L
Sbjct: 2 IILTGLPGVGKSTFSKELAKKL 23
>gnl|CDD|178622 PLN03073, PLN03073, ABC transporter F family; Provisional.
Length = 718
Score = 27.9 bits (62), Expect = 3.5
Identities = 13/29 (44%), Positives = 20/29 (68%), Gaps = 4/29 (13%)
Query: 60 VGPPGLGKTTLAQVVAREL----GVNFRS 84
VGP G+GK+T+ ++++ EL G FRS
Sbjct: 541 VGPNGIGKSTILKLISGELQPSSGTVFRS 569
>gnl|CDD|147939 pfam06048, DUF927, Domain of unknown function (DUF927). Family of
bacterial proteins of unknown function.
Length = 284
Score = 28.0 bits (63), Expect = 3.5
Identities = 22/75 (29%), Positives = 29/75 (38%), Gaps = 15/75 (20%)
Query: 59 FVGPPGLGKTTLAQVVA------RELGVNFRSTSGPVIAKAGDLAALLTNLEDRDVLFID 112
FVG GKTT ++ A L ++RST A L A + D L +D
Sbjct: 196 FVGDSSTGKTTALKLAASVWGNPDTLIRSWRST-------ANGLEATASEHNDT-PLILD 247
Query: 113 EIHRLS-IIVEEILY 126
EI V +Y
Sbjct: 248 EISEADPREVGGAVY 262
>gnl|CDD|183622 PRK12608, PRK12608, transcription termination factor Rho;
Provisional.
Length = 380
Score = 28.1 bits (63), Expect = 3.6
Identities = 24/97 (24%), Positives = 32/97 (32%), Gaps = 36/97 (37%)
Query: 58 LFVGPPGLGKTTLAQVVARELGVNF---------------------RSTSGPVIAKAGD- 95
L V PP GKT L Q +A + N RS G V A D
Sbjct: 137 LIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDR 196
Query: 96 -------LAALLTNLEDRD-------VLFIDEIHRLS 118
+A L+ R V+ +D + RL+
Sbjct: 197 PPDEHIRVAELVLERAKRLVEQGKDVVILLDSLTRLA 233
>gnl|CDD|149480 pfam08433, KTI12, Chromatin associated protein KTI12. This is a
family of chromatin associated proteins which interact
with the Elongator complex, a component of the
elongating form of RNA polymerase II. The Elongator
complex has histone acetyltransferase activity.
Length = 266
Score = 28.0 bits (63), Expect = 3.6
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 57 VLFVGPPGLGKTTLAQVVAREL 78
++ G P GK+T A+ +A+ L
Sbjct: 2 IILTGLPSSGKSTRAKELAKYL 23
>gnl|CDD|181675 PRK09162, PRK09162, hypoxanthine-guanine phosphoribosyltransferase;
Provisional.
Length = 181
Score = 27.9 bits (63), Expect = 3.7
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 101 TNLEDRDVLFIDEI----HRLSIIVEEIL 125
+L+ R VL +D+I H L+ I + L
Sbjct: 93 ESLKGRTVLVVDDILDEGHTLAAIRDRCL 121
>gnl|CDD|178433 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 27.9 bits (62), Expect = 3.8
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 5/73 (6%)
Query: 46 AAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAKAGDLAALLTNLED 105
A+K + E + ++ GP G GK+ LA +A+ L S + + D+ + +L +
Sbjct: 15 ASKTKKEKV--IVISGPTGAGKSRLALELAKRLNGEIISADSVQVYRGLDVGSAKPSLSE 72
Query: 106 RDVL---FIDEIH 115
R + ID +H
Sbjct: 73 RKEVPHHLIDILH 85
>gnl|CDD|177370 PHA02530, pseT, polynucleotide kinase; Provisional.
Length = 300
Score = 27.7 bits (62), Expect = 3.9
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 58 LFVGPPGLGKTTLAQVVARELG 79
L VG PG GK+T A+ A +
Sbjct: 6 LTVGVPGSGKSTWAREFAAKNP 27
>gnl|CDD|130679 TIGR01618, phage_P_loop, phage nucleotide-binding protein. This
model represents an uncharacterized family of proteins
from a number of phage of Gram-positive bacteria. This
protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near
its amino end. The function of this protein is unknown.
Length = 220
Score = 27.8 bits (62), Expect = 4.4
Identities = 22/100 (22%), Positives = 42/100 (42%), Gaps = 14/100 (14%)
Query: 57 VLFVGPPGLGKTTLA-QVVARELGVNFRSTSGPVIAKAGDLAALLTNLEDRDVLFIDEIH 115
L G PG GKT+ + + L ++F +S +L E+ D+ D++
Sbjct: 15 YLIYGKPGTGKTSTIKYLPGKTLVLSFDMSS-----------KVLIGDENVDIADHDDMP 63
Query: 116 RLSIIVEEILYPAMEDFQLDLMVGEGPSA--RSVKINLSR 153
+ +VE + ++ + D +V + SA N+ R
Sbjct: 64 PIQAMVEFYVMQNIQAVKYDNIVIDNISALQNLWLENIGR 103
>gnl|CDD|181578 PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.
Length = 227
Score = 27.6 bits (62), Expect = 4.5
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 9/61 (14%)
Query: 61 GPPGLGKTTLAQVV---ARELGVNFRSTSGPVIAKAGDLAALLTNLEDRDVLFIDEIHRL 117
G G G++ L Q + A G N R + A L A + E ++ +D++ RL
Sbjct: 49 GEAGSGRSHLLQALVADASYGGRNAR-----YLDAASPLLAFDFDPEA-ELYAVDDVERL 102
Query: 118 S 118
Sbjct: 103 D 103
>gnl|CDD|131926 TIGR02880, cbbX_cfxQ, probable Rubsico expression protein CbbX.
Proteins in this family are now designated CbbX. Some
previously were CfxQ (carbon fixation Q). Its gene is
often found immmediately downstream of the Rubisco
large and small chain genes, and it is suggested to be
necessary for Rubisco expression. CbbX has been shown
to be necessary for photoautotrophic growth. This
protein belongs to the larger family of pfam00004,
ATPase family Associated with various cellular
Activities. Within that larger family, members of this
family are most closely related to the stage V
sporulation protein K, or SpoVK, in endospore-forming
bacteria such as Bacillus subtilis.
Length = 284
Score = 27.5 bits (61), Expect = 4.6
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 56 HVLFVGPPGLGKTTLAQVVAREL 78
H+ F G PG GKTT+A +A+ L
Sbjct: 60 HMSFTGNPGTGKTTVALRMAQIL 82
>gnl|CDD|172994 PRK14528, PRK14528, adenylate kinase; Provisional.
Length = 186
Score = 27.7 bits (61), Expect = 4.7
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 54 LDHVLFVGPPGLGKTTLAQVVARELGVNFRST 85
+ +++F+GPPG GK T A+++ L + ST
Sbjct: 1 MKNIIFMGPPGAGKGTQAKILCERLSIPQIST 32
>gnl|CDD|184919 PRK14955, PRK14955, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 397
Score = 27.5 bits (61), Expect = 4.8
Identities = 36/144 (25%), Positives = 61/144 (42%), Gaps = 25/144 (17%)
Query: 108 VLFIDEIHRLSIIVEEILYPAMEDFQLDLMVGEGPSARSVKINLSRFTLIAATTRVGLLT 167
V IDE+H LSI F L E P ++ I ATT + +
Sbjct: 130 VYIIDEVHMLSIAA----------FNAFLKTLEEPPPHAI--------FIFATTELHKIP 171
Query: 168 NPLQDRFGIPIRLNFYEI--EDLKTIVQRGAKLTGLAVTDEAACEIAMRSRGTPRIAGRL 225
+ R R NF I E+++ +Q + G++V +A I +++G+ R A +
Sbjct: 172 ATIASRCQ---RFNFKRIPLEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDAQSI 228
Query: 226 LRRVRDFA-EVAHAKTIT-REIAD 247
L +V F+ E +I ++A+
Sbjct: 229 LDQVIAFSVESEGEGSIRYDKVAE 252
>gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein;
Provisional.
Length = 445
Score = 27.5 bits (61), Expect = 4.9
Identities = 23/68 (33%), Positives = 30/68 (44%), Gaps = 10/68 (14%)
Query: 61 GPPGLGKTTLAQVVA---RELGVN---FRS---TSGPVIA-KAGDLAALLTNLEDRDVLF 110
GP G GKT L Q RE G RS T V A ++G++ + D LF
Sbjct: 148 GPEGSGKTHLMQAAVHALRESGGKILYVRSELFTEHLVSAIRSGEMQRFRQFYRNVDALF 207
Query: 111 IDEIHRLS 118
I++I S
Sbjct: 208 IEDIEVFS 215
>gnl|CDD|182917 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 27.5 bits (61), Expect = 5.0
Identities = 28/84 (33%), Positives = 36/84 (42%), Gaps = 32/84 (38%)
Query: 58 LFVGPPGLGKTTLAQVVARELGVNFRSTSGPV---IAKA-----------------GDL- 96
L VG G+GKT +A+ G+ +R G V +A GD
Sbjct: 211 LLVGESGVGKTAIAE------GLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFE 264
Query: 97 ---AALLTNLE-DRD-VLFIDEIH 115
ALL LE D + +LFIDEIH
Sbjct: 265 KRFKALLKQLEQDTNSILFIDEIH 288
>gnl|CDD|162636 TIGR01978, sufC, FeS assembly ATPase SufC. SufC is part of the SUF
system, shown in E. coli to consist of six proteins and
believed to act in Fe-S cluster formation during
oxidative stress. SufC forms a complex with SufB and
SufD. SufC belongs to the ATP-binding cassette
transporter family (pfam00005) but is no longer thought
to be part of a transporter. The complex is reported as
cytosolic (PubMed:12554644) or associated with the
membrane (PubMed:11943156). The SUF system also includes
a cysteine desulfurase (SufS, enhanced by SufE) and a
probable iron-sulfur cluster assembly scaffold protein,
SufA.
Length = 243
Score = 27.2 bits (61), Expect = 5.4
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 56 HVLFVGPPGLGKTTLAQVVA-RELGVNFRSTSGPVIAKAGDLAALLTNLEDRDVLFI 111
H + +GP G GK+TL++ +A ++ TSG ++ K DL L + R LF+
Sbjct: 29 HAI-MGPNGSGKSTLSKTIAGHP---SYEVTSGTILFKGQDLLELEPDERARAGLFL 81
>gnl|CDD|178749 PLN03210, PLN03210, Resistant to P. syringae 6; Provisional.
Length = 1153
Score = 27.5 bits (61), Expect = 5.6
Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 3/67 (4%)
Query: 19 ISLLRPRTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAREL 78
++L E+F G + + + + +E + V G G+GKTT+A+ + L
Sbjct: 175 LNLTPSNDFEDFVGIEDHIAKMSSLLHLE---SEEVRMVGIWGSSGIGKTTIARALFSRL 231
Query: 79 GVNFRST 85
F+S+
Sbjct: 232 SRQFQSS 238
>gnl|CDD|182331 PRK10247, PRK10247, putative ABC transporter ATP-binding protein
YbbL; Provisional.
Length = 225
Score = 27.4 bits (61), Expect = 6.2
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 4/42 (9%)
Query: 58 LFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAKAGDLAAL 99
L GP G GK+TL ++VA + TSG ++ + D++ L
Sbjct: 37 LITGPSGCGKSTLLKIVASLIS----PTSGTLLFEGEDISTL 74
>gnl|CDD|129002 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 27.3 bits (61), Expect = 6.3
Identities = 12/44 (27%), Positives = 21/44 (47%)
Query: 46 AAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNFRSTSGPV 89
AA+ E + +GP G GK++L + + R L ++ G
Sbjct: 70 AAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEEYSKTPEGRR 113
>gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 27.1 bits (60), Expect = 6.5
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 45 EAAKARAEALDHVLFVGPPGLGKTTLAQVVARELG 79
EA +A L V+ P G GKT A + A E
Sbjct: 15 EAIEALLSGLRDVILAAPTGSGKTLAALLPALEAL 49
>gnl|CDD|179724 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 27.2 bits (61), Expect = 6.7
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 13/68 (19%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRSTS-GPV---IAKAGDLAALLTNLEDRDVLF-- 110
V+ G PG+GKTT+ +L +++ + G V +AK L E RD +
Sbjct: 5 VVVTGVPGVGKTTVLNKALEKLKEDYKIVNFGDVMLEVAKEEGLV------EHRDEMRKL 58
Query: 111 -IDEIHRL 117
+E L
Sbjct: 59 PPEEQKEL 66
>gnl|CDD|172997 PRK14531, PRK14531, adenylate kinase; Provisional.
Length = 183
Score = 27.1 bits (60), Expect = 6.8
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVNFRST 85
+LF+GPPG GK T A + G+ ST
Sbjct: 5 LLFLGPPGAGKGTQAARLCAAHGLRHLST 33
>gnl|CDD|180357 PRK06031, PRK06031, phosphoribosyltransferase; Provisional.
Length = 233
Score = 27.0 bits (60), Expect = 7.1
Identities = 19/34 (55%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 46 AAKARAEALDHVLFVGPPGLGKTTLAQVVARELG 79
A KARA D V G P LG TLA VAR+LG
Sbjct: 77 AEKARAFDPDVV--AGLPTLG-LTLAAAVARKLG 107
>gnl|CDD|181430 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau;
Validated.
Length = 535
Score = 26.9 bits (60), Expect = 7.1
Identities = 22/62 (35%), Positives = 30/62 (48%), Gaps = 16/62 (25%)
Query: 23 RPRTLEEFTGQVEACSNLKVFIEAAKARAEALDH------VLFVGPPGLGKTTLAQVVAR 76
RP+ +E GQ E+ S K + ALD+ LF G G GKT+ A++ AR
Sbjct: 9 RPKHFDELIGQ-ESVS---------KTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFAR 58
Query: 77 EL 78
L
Sbjct: 59 AL 60
>gnl|CDD|171510 PRK12452, PRK12452, cardiolipin synthetase; Reviewed.
Length = 509
Score = 26.8 bits (59), Expect = 7.4
Identities = 11/41 (26%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 267 YLTMIARNFGGGPVGIETISAGLSEPRDAIEDLIEPYMIQQ 307
+LT + + FGGGP T + L+ ++++ I+Q
Sbjct: 123 HLTEVVQKFGGGPAADRTTTKLLTNGDQTFSEILQ--AIEQ 161
>gnl|CDD|163051 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 529
Score = 27.0 bits (60), Expect = 7.6
Identities = 11/58 (18%), Positives = 20/58 (34%), Gaps = 5/58 (8%)
Query: 56 HVLFVGPPGLGKTTLAQVVARELGVNFRSTSGPVIAKAGDLAALLTNLEDRDVLFIDE 113
V +GP G GK+TL ++ + G + L + R + +
Sbjct: 363 RVAILGPSGSGKSTLLMLLTG-----LLDPLQGEVTLDGVSVSSLQDELRRRISVFAQ 415
>gnl|CDD|183342 PRK11860, PRK11860, bifunctional 3-phosphoshikimate
1-carboxyvinyltransferase/cytidine monophosphate kinase;
Provisional.
Length = 661
Score = 26.9 bits (60), Expect = 7.8
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 43 FIEAAKARAEALDHVLFVGPPGLGKTTLAQVVARELGVNF 82
A+A A+ + + GP GK T+A VA LG ++
Sbjct: 431 LFSVAQADADRVPVICIDGPTASGKGTVAARVAEALGYHY 470
>gnl|CDD|181538 PRK08699, PRK08699, DNA polymerase III subunit delta'; Validated.
Length = 325
Score = 26.8 bits (59), Expect = 8.1
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 58 LFVGPPGLGKTTLAQVVAREL 78
LF G G+GKT A+ A+ L
Sbjct: 25 LFAGKKGIGKTAFARFAAQAL 45
>gnl|CDD|163223 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins.
Length = 852
Score = 26.8 bits (60), Expect = 8.3
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 58 LFVGPPGLGKTTLAQVVAREL 78
LF+GP G+GKT LA+ +A L
Sbjct: 599 LFLGPTGVGKTELAKALAEFL 619
>gnl|CDD|184411 PRK13946, PRK13946, shikimate kinase; Provisional.
Length = 184
Score = 26.8 bits (60), Expect = 8.3
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 47 AKARAEALDH--VLFVGPPGLGKTTLAQVVARELGVNFR 83
+ AL V+ VG G GK+T+ + +A LG+ F
Sbjct: 1 EERARAALGKRTVVLVGLMGAGKSTVGRRLATMLGLPFL 39
>gnl|CDD|129254 TIGR00150, HI0065_YjeE, ATPase, YjeE family. Members of this
family have a conserved nucleotide-binding motif
GXXGXGKT and a nucleotide-binding fold. Member protein
YjeE of Haemophilus influenzae (HI0065) was shown to
have ATPase activity.
Length = 133
Score = 26.6 bits (59), Expect = 8.4
Identities = 20/50 (40%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 40 LKVFIEAAKARAEALDH---VLFVGPPGLGKTTLAQVVARELGVNFRSTS 86
K + KA A+ LD VL G G GKTTL Q + + LG+ TS
Sbjct: 5 EKAMDKFGKAFAKPLDFGTVVLLKGDLGAGKTTLVQGLLQGLGIQGNVTS 54
>gnl|CDD|181965 PRK09580, sufC, cysteine desulfurase ATPase component; Reviewed.
Length = 248
Score = 26.7 bits (59), Expect = 8.4
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 60 VGPPGLGKTTLAQVVA-RELGVNFRSTSGPVIAKAGDLAAL 99
+GP G GK+TL+ +A RE ++ T G V K DL L
Sbjct: 33 MGPNGSGKSTLSATLAGRE---DYEVTGGTVEFKGKDLLEL 70
>gnl|CDD|182623 PRK10657, PRK10657, isoaspartyl dipeptidase; Provisional.
Length = 388
Score = 26.7 bits (60), Expect = 8.5
Identities = 14/29 (48%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 139 GE-GPSARSVKINLSRFTLIAATTRVGLL 166
GE G S R+ ++ LS T TT VGLL
Sbjct: 70 GEGGFSTRTPEVQLSDLTEAGITTVVGLL 98
>gnl|CDD|182692 PRK10744, pstB, phosphate transporter ATP-binding protein;
Provisional.
Length = 260
Score = 26.5 bits (59), Expect = 9.0
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 7/52 (13%)
Query: 25 RTLEEFTGQVEACSNLKVFIEAAKARAEALDHVLFVGPPGLGKTTLAQVVAR 76
R L + G+ A N+ + I + A F+GP G GK+TL + R
Sbjct: 17 RNLNFYYGKFHALKNINLDIAKNQVTA-------FIGPSGCGKSTLLRTFNR 61
>gnl|CDD|178800 PRK00023, cmk, cytidylate kinase; Provisional.
Length = 225
Score = 26.6 bits (60), Expect = 9.2
Identities = 10/19 (52%), Positives = 16/19 (84%)
Query: 61 GPPGLGKTTLAQVVARELG 79
GP G GK T+A+++A++LG
Sbjct: 11 GPAGSGKGTVAKILAKKLG 29
>gnl|CDD|105560 PRK12339, PRK12339, 2-phosphoglycerate kinase; Provisional.
Length = 197
Score = 26.7 bits (59), Expect = 9.2
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 57 VLFVGPPGLGKTTLAQVVARELGVN 81
G PG+GKT+++ +AR ++
Sbjct: 6 HFIGGIPGVGKTSISGYIARHRAID 30
>gnl|CDD|131030 TIGR01975, isoAsp_dipep, isoaspartyl dipeptidase IadA. The
L-isoaspartyl derivative of Asp arises non-enzymatically
over time as a form of protein damage. In this
isomerization, the connectivity of the polypeptide
changes to pass through the beta-carboxyl of the side
chain. Much but not all of this damage can be repaired
by protein-L-isoaspartate (D-aspartate)
O-methyltransferase. This model describes the
isoaspartyl dipeptidase IadA, apparently one of two such
enzymes in E. coli, an enzyme that degrades isoaspartyl
dipeptides and may unblock degradation of proteins that
cannot be repaired. This model also describes closely
related proteins from other species (e.g. Clostridium
perfringens, Thermoanaerobacter tengcongensis) that we
assume to be equivalent in function. This family shows
homology to dihydroorotases.
Length = 389
Score = 26.7 bits (59), Expect = 9.3
Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 139 GE-GPSARSVKINLSRFTLIAATTRVGLL 166
GE GP+ R+ ++ LS T TT VGLL
Sbjct: 70 GEGGPTTRTPELTLSDITKGGVTTVVGLL 98
>gnl|CDD|173382 PTZ00088, PTZ00088, adenylate kinase 1; Provisional.
Length = 229
Score = 26.7 bits (59), Expect = 9.3
Identities = 7/21 (33%), Positives = 16/21 (76%)
Query: 57 VLFVGPPGLGKTTLAQVVARE 77
++ G PG+GK T A++++++
Sbjct: 9 IVLFGAPGVGKGTFAEILSKK 29
>gnl|CDD|163375 TIGR03649, ergot_EASG, ergot alkaloid biosynthesis protein,
AFUA_2G17970 family. This family consists of fungal
proteins of unknown function associated with secondary
metabolite biosynthesis, such as of the ergot alkaloids
such as ergovaline. Nomenclature differs because gene
order differs - this is EasG in Neotyphodium lolii but
is designated ergot alkaloid biosynthetic protein A in
several other fungi.
Length = 285
Score = 26.5 bits (59), Expect = 9.4
Identities = 26/93 (27%), Positives = 33/93 (35%), Gaps = 18/93 (19%)
Query: 57 VLFVGPPGLGKTTLAQV---VARELGVN-FRSTSGPVIAKAGD----LAALLTNLEDRD- 107
V V PP AR GV F S +I K G + A L +L +
Sbjct: 71 VYLVAPPIPDLAPPMIKFIDFARSKGVRRFVLLSASIIEKGGPAMGQVHAHLDSLGGVEY 130
Query: 108 -VL--------FIDEIHRLSIIVEEILYPAMED 131
VL F +E H +I E +Y A D
Sbjct: 131 TVLRPTWFMENFSEEFHVEAIRKENKIYSATGD 163
>gnl|CDD|184719 PRK14511, PRK14511, maltooligosyl trehalose synthase; Provisional.
Length = 879
Score = 26.5 bits (59), Expect = 9.6
Identities = 12/57 (21%), Positives = 20/57 (35%), Gaps = 7/57 (12%)
Query: 44 IEAAKARAEALDHVLF------VGPPGLGKTTLAQVVAR-ELGVNFRSTSGPVIAKA 93
A+ R D + + + + R E V F+ +GPV+AK
Sbjct: 462 AARARRRLPEADWPVLDFLEDVLLGRAARELPRGRRKLRLEFAVRFQQLTGPVMAKG 518
>gnl|CDD|165405 PHA03133, PHA03133, thymidine kinase; Provisional.
Length = 368
Score = 26.4 bits (58), Expect = 10.0
Identities = 15/32 (46%), Positives = 19/32 (59%)
Query: 48 KARAEALDHVLFVGPPGLGKTTLAQVVARELG 79
+ +A AL + GP GLGKTT A +A LG
Sbjct: 34 QQKASALLRIYVDGPHGLGKTTTAAALAAALG 65
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.323 0.140 0.396
Gapped
Lambda K H
0.267 0.0636 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,730,176
Number of extensions: 396975
Number of successful extensions: 1434
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1403
Number of HSP's successfully gapped: 233
Length of query: 334
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 240
Effective length of database: 3,963,321
Effective search space: 951197040
Effective search space used: 951197040
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (25.9 bits)